Human papillomavirus (HPV) virus-like particle (VLP) vaccines were recently licensed. Although neutralizing Ab titers are thought to be the main effectors of protection against infection, early predictors of long-term efficacy are not yet defined and a comprehensive understanding of innate and adaptive immune responses to vaccination is still lacking. Here, microarrays were used to compare the gene expression signature in HPV-16 L1 VLP-stimulated PBMCs from 17 vaccine and 4 placebo recipients before vaccination and 1 mo after receiving the second immunization. Vaccination with a monovalent HPV-16 L1 VLP vaccine was associated with modulation of genes involved in the inflammatory/defense response, cytokine, IFN, and cell cycle pathways in VLP-stimulated PBMCs. Additionally, there was up-regulation of probesets associated with cytotoxic (GZMB, TNFSF10) and regulatory (INDO, CTLA4) activities. The strongest correlations with neutralizing Ab titers were found for cyclin D2 (CCND2) and galectin (LGALS2). Twenty-two differentially expressed probesets were selected for confirmation by RT-PCR in an independent sample set. Agreement with microarray data was seen for more than two-thirds of these probesets. Up-regulation of immune/defense response genes by HPV-16 L1 VLP, in particular, IFN-induced genes, was observed in PBMCs collected before vaccination, with many of these genes being further induced following vaccination. In conclusion, we identified important innate and adaptive response-related genes induced by vaccination with HPV-16 L1 VLP. Further studies are needed to identify gene expression signatures of immunogenicity and long-term protection with potential utility in prediction of long-term HPV vaccination outcomes in clinical trials.

Cervical cancer is the second most common cancer among women worldwide (1, 2). The recent development of prophylactic human papillomavirus (HPV)4 vaccines provides an important new avenue for the prevention of this cancer and others linked to HPV infection.

The current HPV prophylactic vaccines consist of noninfectious, L1 recombinant HPV-like particles (VLP) (3, 4). Vaccine clinical trials have shown nearly complete protection against cervical intraepithelial neoplasia 2 or greater lesions (5, 6, 7). Neutralizing Abs are thought to be the main effectors of protection. A robust humoral response has been observed after vaccination (8, 9, 10), and Ab levels against HPV-16 remain relatively high in the first few years after vaccination (11, 12, 13). However, length of protection afforded by vaccination is not currently known.

Studies by our group and others have shown that in addition to Ab responses, strong cell-mediated immune responses are observed after vaccination (14, 15, 16, 17). It is known that cell-mediated immune responses are required for Ab production and for maintenance of Ab levels over time. Thus, it could be postulated that the patterns of innate and acquired cellular immune responses following initial vaccination might influence Ab responses and duration of protection afforded by vaccination (18, 19). A better understanding of these early responses to vaccination might help elucidate mechanisms of vaccine protection via neutralizing Abs, and assist in the identification of early markers of long-lasting vaccine responses.

Microarray analysis has been applied to determine gene expression patterns in studies of disease pathogenesis (20, 21, 22, 23), immune response to infection (24, 25, 26, 27, 28, 29, 30), and immune response after immunization (31, 32). However, few studies have looked at vaccine-induced responses in humans (33, 34, 35).

To characterize the immune response to HPV-16 L1 VLP vaccination, we used microarray chips that cover 8638 verified sequences to investigate the gene profile associated with a recall response to the vaccine in leukocytes from vaccine recipients. We identified probesets that were differentially expressed in PBMCs from vaccine recipients after in vitro stimulation with HPV-16 L1 VLP compared with pre-vaccination samples. We also analyzed the “primary” response to HPV-16 L1 VLP, independent of vaccination, by comparing the gene expression pattern of cells incubated with HPV-16 L1 VLP and unstimulated cells, using prevaccination samples.

Additionally, the correlation of gene expression to neutralizing Ab titers developed after vaccination was examined to evaluate potential determinants of strong Ab responses. Key results were confirmed by RT-PCR in an independent set of vaccinated individuals.

This is the first study that evaluates the immune response to an HPV VLP vaccine using microarray technology. Our results contribute to a broader understanding of the effects of vaccination with a monovalent HPV-16 L1 VLP vaccine. The approach used herein and the gene expression profile defined in this study may prove to be useful for future prediction of long-term HPV vaccination outcomes in ongoing clinical trials.

Participants were selected from a double-blind, randomized, placebo-controlled phase II trial of a monovalent HPV-16 L1 VLP vaccine without adjuvant, which was conducted in a sample of 220 healthy, HIV-seronegative adult female volunteers 18–25 years of age, as described previously (17). Briefly, subjects were enrolled at The Johns Hopkins University Center for Immunization Research (Baltimore, MD). Prevaccination HPV-16 Ab or DNA status was not a criterion for eligibility into the trial. Subjects were determined by history to be at low risk for HPV-16 exposure. Individuals were not eligible to participate if they had a history of more than four lifetime sexual partners or more than two sexual partners within the preceding 6 mo. Additional exclusion criteria included history of abnormal cervical cytology, immunodeficiency, anaphylaxis to medicines or vaccines, receipt of blood products within 3 mo of enrollment, current pregnancy or lactation, and any other condition that might interfere with the study objectives. Women were randomly assigned to receive three i.m. doses of either 50 μg of HPV-16 L1 VLP vaccine without adjuvant, or placebo (0.5 ml saline). Blood specimens were collected before the initial dose (month 0) and 1 mo after each of the subsequent vaccinations (months 2 and 7). The Johns Hopkins University Institutional Review Board approved the protocol for this study. Blood specimens were shipped to the HPV Immunology Laboratory (Frederick, MD), where PBMCs were cryopreserved.

Twenty-seven subjects (20 vaccine and 7 placebo recipients) were randomly selected for microarray measurements. Only month 0 and month 2 samples were selected for this study because earlier findings indicated that the largest increases in cytokine responses were typically observed at month 2 (17). Month 0 and 2 samples from 10 additional vaccine recipients were selected for a second, confirmatory phase of our study by RT-PCR.

HPV-16 L1 VLPs were expressed in baculovirus-infected Sf9 insect cells (Novavax). Production of clinical lots of recombinant HPV-16 L1 VLP vaccines was performed in accordance with Good Manufacturing Practices guidelines as previously reported (36). The VLPs used in vitro to stimulate PBMCs were similar to the ones used to vaccinate the subjects included in this study. VLPs were provided at 1 mg/ml, stored at −80°C, and thawed immediately preceding in vitro stimulation, as previously described (16).

Cryopreserved PBMCs were thawed and cultured (2.0 × 106 cells/ml) as previously described (17). PBMCs (10 × 106) were plated in each well of a 6-well plate (Costar) in RPMI 1640 medium supplemented with penicillin-streptomycin (100 μg/ml-100 U/ml; Invitrogen), l-glutamine (2 mM), HEPES buffer (10 mM), and 10% heat-inactivated FCS (HyClone). Cells were cultured for 72 h at 37°C with media, HPV-16 L1 VLP (2.5 μg/ml), or Sf9/baculovirus insect cell lysate (0.1 μg/ml; Novavax), all diluted in cell culture media. Media was used as a background measurement for untreated cells. The Sf9/baculovirus insect cell lysate was used as a control Ag for the L1 VLP production system.

A total of eight incubations were set up on the same day for each subject. Incubations for two subjects were set up on the same day. The order of sample preparation was randomly defined from the list of selected subjects.

When harvesting, cultures were centrifuged and cell-free supernatants were aliquoted and frozen at −80°C. Total RNA extracts were performed using an RNeasy Total RNA isolation kit (Qiagen). RLT lysis buffer was quickly added to the culture well and then to the cell pellet to include both adherent and suspension cells. RNA purity and integrity were tested by microcapillary electrophoresis using the Agilent 2100 bioanalyzer (Agilent Technologies).

Microarray gene expression analysis was performed using the human genome focus array from the Affymetrix GeneChip system (Affymetrix) that contains ∼8700 probesets to 8638 characterized human genes. Total RNA preparation and labeled cRNA synthesis and hybridization were performed according to the manufacturer’s recommended protocol (Affymetrix). In short, 10 μg of total RNA was used for double-stranded cDNA (ds-cDNA) synthesis with the SuperScript II reverse transcriptase kit (Invitrogen) and an oligo(dT) primer containing a T7 RNA polymerase promoter to prime the first-strand synthesis. Biotin-labeled cRNA was obtained by in vitro transcription after addition of T7 RNA polymerase and biotinylated nucleotides (Enzo Biochem) to the ds-cDNA. Labeled cRNA was fragmented and hybridized to the GeneChips, which were then washed and stained with streptavidin-conjugated PE by using the Affymetrix GeneChip fluid station 400. To assess the quality of hybridization, the following quality control filters were used: scaling factor, background, percentage of present calls, noise, housekeeping genes (3′/5′ ratios and intensity for GAPDH and actin), RNA degradation slope, and presence or absence of internal spike controls.

Gene expression levels were determined by laser scanning of the GeneChip at 570 nm and were log2-transformed following MAS5 probeset summarization. All results from a donor were excluded if one of the conditions (media and VLP cultures for the pre- and postvaccination specimens) did not fulfill one of the previously mentioned quality control filters used to ensure that all chips were of comparable quality. These quality control procedures resulted in exclusion of two of the vaccine recipients and one placebo. One additional vaccine recipient was excluded due to a high degree of granulocyte contamination (61% vs 0.2–13.6% granulocytes for remaining samples), possibly due to poor PBMC Ficoll isolation, and because neutralizing Abs against HPV-16 were detectable before vaccination. Two additional placebos were excluded because they had detectable Abs in the course of our study. After all exclusions, 17 vaccine and 4 placebo recipients were used in subsequent analysis.

Data from probesets that were not reliably detected with a mean intensity more than log2 of 5 in at least one experimental condition (media and VLP cultures for the pre- and postvaccination specimens) were excluded before further analysis. A total of 7145 probesets remained after applying this criterion.

The data discussed in this publication have been deposited in the National Center for Biotechnology Information’s Gene Expression Omnibus (GEO) (37) and are accessible through GEO series accession no. GSE13587 (www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc).

Major lymphocyte subsets for all samples were determined by flow cytometry (FC-500, Beckman Coulter), as previously described (38). Flow cytometric analysis of main lymphocyte subsets indicated that overall levels of major lymphocyte subsets did not change considerably after vaccination (mean + SD pre- vs postvaccination were: CD3+ cells, 78 ± 7 vs 77 ± 9; CD19+ cells, 10 ± 6 vs 10 + 5; CD16+/56+ cells, 11 ± 6 vs 11 ± 6). Additionally, placebo recipients had also similar overall levels of leukocyte subsets (mean ± SD month 0 vs month 2 were: CD3 cells, 77 ± 4 vs 79 ± 5; CD19 cells, 11 ± 3 vs 11 ± 6; CD16+/CD56+ cells 9 ± 1 vs 8 ± 3).

HPV-16-neutralizing Ab titers were determined using a pseudovirus-based neutralization assay performed as previously described (39). Serum neutralization titers were defined as the reciprocal of the highest dilution that caused at least 50% reduction in secreted alkaline phosphatase activity. A negative control using the bovine papillomavirus pseudovirus was performed for all samples. Undetectable Ab levels were considered as 0. All individuals selected for the microarray analysis had no detectable Abs before vaccination. After vaccination, all individuals developed Ab titers against HPV-16 (month 2 mean titer, 843 ± 748, range, 78–2602; month 7 mean titer, 5209 ± 7383, range, 111–25,571; month 12 mean titer, 2366 ± 4184, range, 148–15,317).

Real-time PCR measurements were performed with samples from 10 independent vaccine recipients collected at month 0 and month 2 postvaccination within this same clinical trial. These individuals were selected randomly based on availability of cryopreserved PBMCs at both time points and were not tested by microarray. One subject was excluded from analysis because anti-HPV-16-neutralizing Abs were detectable before vaccination. All remaining nine donors had no detectable neutralizing Ab titers before vaccination and thus a similar prevaccination Ab status as the individuals used for the microarray experiments. Additionally, an induction in anti-HPV-16 titers was observed at month 2 after the first dose (mean titer at month 2, 2675 ± 2644, neutralizing titer range, 333-8508).

A total of 22 probesets (see Table V) were selected for confirmation. All selected probesets had an average fold induction of 2.0 or higher by microarray (range, 2.0–5.0), which was observed in at least 50% of subjects (range, 50–83%). Ten selected probesets had statistically significant differences before and after vaccination with significance levels of p ≤ 0.001. These included GZMB, IFNG, HSD11B1, INDO, GGTLA1, KIF20A, GOLPH2, IL6, IL3, and AICDA. The remaining 12 probesets were selected either because their expression levels correlated with Ab titers at month 7 or 12 (r > 0.52; five probesets: CYP27B1, INHBA, MMP12, CD1B, and CCL7) or they were cytokines/chemokines of potential interest (seven probesets: CSF2, IL2, IL5, CXCL13, LTA, LIF, and CCL13).

PBMC incubation and total RNA extraction were performed as described above. One microgram of total RNA extract was reverse-transcribed with random hexamer primers, using SuperScript reverse transcriptase (Invitrogen). One-twentieth of the first-strand cDNA synthesis reaction was used as template. Predesigned primer and probe kits (TaqMan gene expression assays; Applied Biosystems) and the TaqMan universal PCR master mix (Applied Biosystems) were used according to manufacturers’ recommendations. Briefly, stock reaction solutions were prepared by mixing 10 μl of PCR master mix (2×), 1 μl of primer kit (20×), and 7.1 μl of diethyl pyrocarbonate-treated water per reaction. Stock solution (18.1 μl) was dispensed to each well, and 1.9 μl of cDNA was then added (total volume per reaction of 20 μl). The following temperature program was used for all genes: 2 min at 52°C, 10 min at 95°C, and 50 cycles of 15 s at 95°C and 1 min at 60°C. Fluorescence intensity was measured in real time during the extension step using the iCycler IQ multicolor real-time PCR detection system (Bio-Rad). The following formula was used to determine fold induction for each gene:

here CtXVpost indicates threshold cycle of the analyzed gene in month 2 cells treated with VLP; CtRVpost, threshold cycle of RPLPO (acidic ribosomal phosphoprotein P0 subunit) in month 2 cells treated with VLP; CtXMpost, threshold cycle of the analyzed gene in month 2 cells treated with media; CtRMpost, threshold cycle of RPLPO in month 2 cells treated with media; CtXVpre, threshold cycle of the analyzed gene in month 0 cells treated with VLP; CtRVpre, threshold cycle of RPLPO in month 0 cells treated with VLP; CtXMpre, threshold cycle of the analyzed gene in month 0 cells treated with media; and CtRMpre, threshold cycle of RPLPO in month 0 cells treated with media.

To determine the cutoff value for PCR results, the fold change for RPLPO was calculated as follows:

This was used to determine variability of RPLPO for all subjects and to define the lowest fold change to consider a gene as up-regulated. Based on this, only genes with a fold change higher than the average plus two SDs of the value obtained for RPLPO were considered positive (i.e., 2.14-fold change).

To determine vaccination-induced changes, gene expression levels (presented as log2 of intensity) for each probeset were compared before and after vaccination. Media-incubated expression levels were subtracted from VLP-incubated samples to adjust for background noise. Paired t tests comparing the mean before and after vaccination were used to determine statistical significance. To account for the evaluation of the large number of genes, p values of <0.001 were considered significant. Furthermore, only probesets with log2 expression change (n-fold) ≤1.3 (down-regulated) or >1.3 (up-regulated) were considered. For the a priori analysis, changes in gene expression for a predefined set of probesets within preselected pathways (defense, inflammation, cytokine, IFN, cell cycle, signal transduction) were evaluated. The selection of probesets was based on the list of gene ontology pathways obtained for the probesets present in the human genome focus array. A p value of <0.001 (and fold change >1.3) was used to define a significantly differentially expressed probeset. The probesets were then mapped to our a priori list of probesets in pathways of interest. The rates of differential expression in these pathways were compared with the rates of differential expression among nonpathway probesets. Gene set analysis, a permutation-based approach, was used to compute p values for the predefined gene sets (25).

We compared the direction and magnitude of expression values from the vaccine recipients to that from four placebos to ensure that effects seen in vaccinated women were specific and not observed among placebo controls. Since the number of placebo recipients was small, we relied on the magnitude of effect rather than statistical significance to determine the specificity of findings among vaccinated women.

For the exploratory analyses, functional annotation and biological term enrichment analysis of regulated probesets were performed by using the DAVID knowledge base (40). This approach assumes independence under the null hypothesis.

Expression values for PBMCs incubated in culture media were evaluated before and after vaccination for background measurements. Gene expression values of VLP-treated cells were corrected for background by subtracting results from unstimulated cells. Paired t tests were conducted to compare expression levels for each probeset before and after vaccination. All probesets that were differentially expressed at a significance level of p < 0.05 (and fold change >1.3) were considered, including the 113 probesets that were significant at p < 0.001 (and fold change >1.3). Since the purpose of this post hoc evaluation was of an exploratory nature, we used a high p value threshold to define probesets of interest and did not adjust for multiple comparisons. Functional annotation of the differentially expressed probesets was performed using DAVID version 2.0 (41).

To determine whether there is an association between gene expression and Ab levels for differentially expressed probesets, we calculated the Spearman correlation of the difference in expression levels post- and prevaccination (corrected for background, as summarized above) with neutralizing Ab titers at months 2, 7, and 12.

The main aim of our study was to determine changes in gene expression that are associated with HPV vaccination. To this end, we compared gene expression levels in PBMCs from vaccine recipients obtained before vaccination and 1 mo after the second vaccine dose (month 2). After filtering, we observed that overall 128 of 7145 probesets (1.8%) were found to be significantly differentially expressed after vaccination (p < 0.001). Among these, 113 probesets met the fold-change criteria (fold-change >1.3). Of these, 63 (56%) were up-regulated and 50 (44%) were down-regulated. None of these probesets were significantly differentially expressed in baculovirus-treated cultures following vaccination, when compared with levels in baculovirus-treated prevaccination samples (all p values were >0.001, data not shown). Also, with the exception of probeset PLA2G4B, none of these probesets demonstrated evidence of differential expression of comparable magnitude among the placebo subjects evaluated (data not shown).

Forty-eight of the 113 significantly differentiated probesets mapped within the 2345 probesets identified within the six pathways targeted for our a priori analysis (cell cycle, cytokines, defense, inflammation, IFN response, and cell signaling). As shown in Table I, the percentage of differentially expressed probesets was significantly increased in the cell cycle (1.7 fold, p < 0.001), cytokine (2.3-fold, p = 0.002), defense (2.7-fold, p = 0.002), inflammation (3.0-fold, p = 0.004), and IFN (4.6-fold, p = 0.037) pathways when compared with rates of differential expression among the 4800 probesets that did not map to probesets within a priori pathways (1.4%). The lists of significantly differentially expressed probesets (p < 0.001) within these a priori pathways are presented in Table II. The most significant up-regulated probesets were RRM2 (cell cycle pathway), CTSC (defense pathway), IFNG (cytokine and defense pathways), RFC3 (cell cycle pathway), and INDO (defense and IFN pathways), and the most significant down-regulated probesets were TSC1 (cell cycle pathway), CD14 (defense and inflammation pathways), ADORA2B and DPP4 (defense pathway), as well as GRN (cytokine pathway).

Table I.

Frequency of differentially expressed (DE) probesets within a priori-defined biological pathways and enrichment ratio compared to probesets not within a priori-defined pathways

A Priori PathwayPercentage of DE Probesets in Pathway (no. of DE probesets/no. total probesets in pathway)DE Enrichment Ratio (a priori pathway/not in a priori pathways)apbNo. of Up-/Down-Regulated Probesets
Complete arraya 1.35 (65/4800)   34/30 
Cell cycle 2.29 (12/525) 1.69 <0.001 8/4 
Cytokine 3.11 (9/289) 2.30 0.002 7/2 
Defense 3.63 (22/606) 2.68 0.002 15/7 
Inflammation 4.00 (6/150) 2.95 0.004 3/3 
Interferon 6.25 (2/32) 4.62 0.037 2/0 
Signal transduction 1.78 (28/1577) 1.31 0.920 11/17 
A Priori PathwayPercentage of DE Probesets in Pathway (no. of DE probesets/no. total probesets in pathway)DE Enrichment Ratio (a priori pathway/not in a priori pathways)apbNo. of Up-/Down-Regulated Probesets
Complete arraya 1.35 (65/4800)   34/30 
Cell cycle 2.29 (12/525) 1.69 <0.001 8/4 
Cytokine 3.11 (9/289) 2.30 0.002 7/2 
Defense 3.63 (22/606) 2.68 0.002 15/7 
Inflammation 4.00 (6/150) 2.95 0.004 3/3 
Interferon 6.25 (2/32) 4.62 0.037 2/0 
Signal transduction 1.78 (28/1577) 1.31 0.920 11/17 
a

Excluding probesets mapping to a priori pathways listed in the table. Note: there is an overlap of probesets across pathways.

b

Multiple comparison p value computed using a bootstrap method as described in Materials and Methods; p < 0.05 is considered significant.

A similar list for the pathway that did not have significant evidence for enrichment in our a priori evaluation (cell signaling) is presented in supplemental Table I.5 The list of significantly differentially expressed probesets not within one of our a priori pathways is shown in supplemental Table II. A summary of overall gene expression profiles induced by vaccination (p < 0.001) is summarized in Fig. 1. Biological term enrichment analysis was performed using DAVID. In addition to the above a priori pathways, the following were found to have evidence for enrichment: up-regulated pathways-receptor binding (nine probesets), catabolism (nine probesets), hemopoietic or lymphoid cell development (four probesets), cell death (eight probesets), and peptidase activity (eight probesets); down-regulated pathways-programmed cell death (seven probesets), phosphoric ester hydrolase (four probesets), and alcohol metabolism (four probesets).

FIGURE 1.

Expression of profiles of probesets significantly modulated by VLP in PBMCs from vaccine recipients before and after vaccination with HPV-16 L1 VLP. PBMC from vaccine recipients were incubated with HPV-16 L1 VLP or media as indicated in Materials and Methods. Functional annotation of probesets differentially expressed (p < 0.001) was done using DAVID. Up-regulated genes are shown in red and down-regulated genes in green. Each row represents a probeset and each column represents an individual.

FIGURE 1.

Expression of profiles of probesets significantly modulated by VLP in PBMCs from vaccine recipients before and after vaccination with HPV-16 L1 VLP. PBMC from vaccine recipients were incubated with HPV-16 L1 VLP or media as indicated in Materials and Methods. Functional annotation of probesets differentially expressed (p < 0.001) was done using DAVID. Up-regulated genes are shown in red and down-regulated genes in green. Each row represents a probeset and each column represents an individual.

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For our exploratory analysis, we expanded the evaluation to probesets differentially expressed at a p < 0.05 cutoff level, and 624 of 7145 probesets (8.7%) were found to be differentially expressed (330 up-regulated, and 294 down-regulated; Table III).

Durability of protection after vaccination has not been established, but it is possible that individuals developing higher neutralizing titers upon immunization will have longer lasting protection against HPV infection. If so, understanding the immunological profile of individuals who develop higher neutralizing titers upon immunization might help elucidate the molecular mechanisms of long-term protection. With this in mind, we compared probeset expression levels induced by vaccination against neutralizing titers at 1 mo after second vaccination (month 2) and 1 or 6 mo after the third vaccination (month 7 or 12, respectively). Only individuals negative for neutralizing Abs before vaccination were included. For this analysis, we considered the subset of 624 probesets that were differentially expressed at a p < 0.05.

Correlations were typically lower when vaccination-induced changes in probeset expression levels (measured at month 2) were compared against neutralizing Ab levels at month 2 (98% of correlations were between −0.50 and +0.50 at month 2, compared with 87% when month 7 and 84% when month 12 neutralizing Ab levels were used). Table IV summarizes results for the subset of 22 probesets observed to have a correlation with neutralizing Abs of >0.60 or <−0.60 at both month 7 and month 12 after vaccination. A complete list of results is provided in supplemental Table III. The highest positive correlations at both month 7 and month 12 after vaccination correlation (>0.70 at both time points) was observed for the following probesets: CCND2 (month 7, r = 0.88; month 12, r = 0.82), LGALS2 (month 7, r = 0.86; month 12, r = 0.74), and IL1RN (month 7, r = 0.75; month 12, r = 0.73).

Table IV.

Spearman correlation of gene expression with neutralizing Ab levelsa

Affymetrix IDGene SymbolGene NameFold Changebp MicroarraySpearman’s rc
Month 2Month 7**cMonth 12**
200953_s_at CCND2 Cyclin D2 1.42 0.000378 ** 0.88 0.82 
208450_at LGALS2 lectin, galactoside-binding, soluble, 2 (galectin 2) 3.03 0.004025 ** 0.86 0.74 
212657_s_at IL1RN IL-1R antagonist 1.61 0.035551 ** 0.75 0.73 
206749_at CD1B CD1B Ag 2.91 0.004909 ** 0.68 0.73 
203564_at FANCG Fanconi anemia, complementation group G 1.52 0.006110 ** 0.68 0.65 
221287_at RNASEL Ribonuclease l (2′,5′-oligoisoadenylate synthetase-dependent) −1.84 0.015826 ** 0.64 0.84 
206181_at SLAMF1 Signaling lymphocytic activation molecule family member 1 1.42 0.0004684 ** 0.64 0.60 
205638_at BAI3 Brain-specific angiogenesis inhibitor 3 −1.71 0.037898 ** 0.63 0.71 
205633_s_at ALAS1 Aminolevulinate, δ-, synthase 1 1.60 0.000591 ** 0.61 0.70 
204092_s_at AURKA Aurora kinase A 1.49 0.037044 ** 0.61 0.63 
204504_s_at HIRIP3 HIRA-interacting protein 3 1.55 0.031187 ** 0.60 0.81 
206206_at CD180 CD180 Ag −1.39 0.035730 ** −0.61 −0.66 
203126_at IMPA2 Inositol(myo)-1(or 4)-monophosphatase 2 −1.34 0.013930 ** −0.62 −0.62 
34187_at RBMS2 RNA binding motif, single-stranded interacting protein 2 1.89 0.031861 ** −0.62 −0.65 
202838_at FUCA1 Fucosidase, α-L-1, tissue −2.05 0.010039 ** −0.64 −0.76 
201753_s_at ADD3 Adducin 3 (γ) −1.35 0.026385 ** −0.64 −0.64 
209774_x_at CXCL2 Chemokine (C-X-C motif) ligand 2 −1.76 0.002054 ** −0.69 −0.61 
219697_at HS3ST2 Heparan sulfate (glucosamine) 3-O-sulfotransferase 2 −2.64 0.000260 ** −0.69 −0.62 
204394_at SLC43A1 Solute carrier family 43, member 1 −1.37 0.004684 ** −0.69 −0.64 
221558_s_at LEF1 Lymphoid enhancer-binding factor 1 −1.36 0.000026 ** −0.76 −0.69 
212552_at HPCAL1 Hippocalcin-like 1 −1.32 0.002917 ** −0.76 −0.75 
201820_at KRT5 Keratin 4 −2.00 0.012345 ** −0.90 −0.73 
Affymetrix IDGene SymbolGene NameFold Changebp MicroarraySpearman’s rc
Month 2Month 7**cMonth 12**
200953_s_at CCND2 Cyclin D2 1.42 0.000378 ** 0.88 0.82 
208450_at LGALS2 lectin, galactoside-binding, soluble, 2 (galectin 2) 3.03 0.004025 ** 0.86 0.74 
212657_s_at IL1RN IL-1R antagonist 1.61 0.035551 ** 0.75 0.73 
206749_at CD1B CD1B Ag 2.91 0.004909 ** 0.68 0.73 
203564_at FANCG Fanconi anemia, complementation group G 1.52 0.006110 ** 0.68 0.65 
221287_at RNASEL Ribonuclease l (2′,5′-oligoisoadenylate synthetase-dependent) −1.84 0.015826 ** 0.64 0.84 
206181_at SLAMF1 Signaling lymphocytic activation molecule family member 1 1.42 0.0004684 ** 0.64 0.60 
205638_at BAI3 Brain-specific angiogenesis inhibitor 3 −1.71 0.037898 ** 0.63 0.71 
205633_s_at ALAS1 Aminolevulinate, δ-, synthase 1 1.60 0.000591 ** 0.61 0.70 
204092_s_at AURKA Aurora kinase A 1.49 0.037044 ** 0.61 0.63 
204504_s_at HIRIP3 HIRA-interacting protein 3 1.55 0.031187 ** 0.60 0.81 
206206_at CD180 CD180 Ag −1.39 0.035730 ** −0.61 −0.66 
203126_at IMPA2 Inositol(myo)-1(or 4)-monophosphatase 2 −1.34 0.013930 ** −0.62 −0.62 
34187_at RBMS2 RNA binding motif, single-stranded interacting protein 2 1.89 0.031861 ** −0.62 −0.65 
202838_at FUCA1 Fucosidase, α-L-1, tissue −2.05 0.010039 ** −0.64 −0.76 
201753_s_at ADD3 Adducin 3 (γ) −1.35 0.026385 ** −0.64 −0.64 
209774_x_at CXCL2 Chemokine (C-X-C motif) ligand 2 −1.76 0.002054 ** −0.69 −0.61 
219697_at HS3ST2 Heparan sulfate (glucosamine) 3-O-sulfotransferase 2 −2.64 0.000260 ** −0.69 −0.62 
204394_at SLC43A1 Solute carrier family 43, member 1 −1.37 0.004684 ** −0.69 −0.64 
221558_s_at LEF1 Lymphoid enhancer-binding factor 1 −1.36 0.000026 ** −0.76 −0.69 
212552_at HPCAL1 Hippocalcin-like 1 −1.32 0.002917 ** −0.76 −0.75 
201820_at KRT5 Keratin 4 −2.00 0.012345 ** −0.90 −0.73 
a

Neutralizing Ab titers were as described in Materials and Methods.

b

(VLP-media) expression levels as defined in Materials and Methods.

c

Double asterisks (**) indicate that only probe sets with correlation coefficient values of r > 0.60 or r < −0.60 at at both month 7 and month 12 are shown (p ≤ 0.05 in all cases).

To confirm the microarray results, a subset of 22 differentially expressed genes (defined in Materials and Methods) was selected for confirmation by PCR using samples from an independent group of vaccine recipients (n = 9). As shown in Table V, the expression pattern of the selected genes concurred with the microarray data for 15 of 22 of the analyzed probesets (GZMB, IFNG, HSD11B1, INDO, IL6, IL3, CSF2, CYP27B1, IL2, IL5, INHBA, MMP12, CD1B, CCL7, and LIF). For a smaller group of six probesets, the frequency of up-regulated probesets was lower using PCR than was observed with microarray (GGTLA1, KIF20A, AICDA, CXCL13, LTA, and CCL13). Finally, no up-regulation (mean fold change, 1.4) was detected by PCR for one of the selected probesets (GOLPH2), while 61% of samples showed an up-regulation by microarray analysis.

Table V.

Confirmation of microarray results with real-time PCR in an independent sample (n = 9)

GeneGene NameFrequency (>2-Fold)Mean Fold ChangeMean Fold Change-Only Respondersp Microarray
Microarray (%)RT-PCR (%)MicroarrayRT-PCRMicroarrayRT-PCR
GZMB Granzyme b 12/18 (67) 7/9 (78) 2.3 3.0 3.0 3.6 0.00002 
IFNG IFN-γ 12/18 (67) 5/8 (62) 2.6 5.0 4.0 7.0 0.00002 
HSD11B1 Hydroxysteroid (11-β) dehydrogenase 1 15/18 (83) 7/8 (88) 3.5 4.0 4.8 4.4 0.00005 
INDO Indoleamine-pyrrole 2,3-dioxygenase 11/18 (61) 5/9 (56) 2.5 2.4 3.5 3.5 0.00006 
IL6 IL-6 9/18 (50) 6/8 (75) 2.2 4.5 3.5 5.7 0.00030 
IL3 IL-3 (CSF, multiple) 11/18 (61) 5/9 (56) 4.0 2.9 9.3 4.2 0.00030 
CSF2 CSF2 (granulocyte-macrophage) 12/18 (67) 5/8 (62) 3.3 3.5 6.6 4.7 0.00125 
CYP27B1 Cytochrome p450, family 27, subfamily B, polypeptide 1 13/18 (72) 7/9 (78) 2.4 3.2 3.8 3.8 0.00133 
IL2 IL-2 11/18 (61) 4/8 (50) 3.9 3.7 9.0 6.4 0.00187 
IL5 IL-5 (CSF, eosinophil) 11/18 (61) 7/8 (88) 4.1 67.5 10.8 77.0 0.00399 
INHBA Inhibin, β A (activin A, activin AB α polypeptide) 15/18 (83) 7/9 (78) 5.0 9.2 9.0 11.5 0.00418 
MMP12 Matrix metallopeptidase 12 (macrophage elastase) 12/18 (67) 5/8 (62) 2.7 39.7 6.5 62.8 0.00476 
CD1B CD1B Ag 11/18 (61) 6/8 (75) 2.9 5.7 5.7 7.3 0.00491 
CCL7 Chemokine (C-C motif) ligand 7 10/18 (56) 7/9 (78) 2.4 49.2 5.9 63.1 0.00807 
LIF Leukemia inhibitory factor 10/18 (56) 5/9 (56) 2.0 2.6 4.0 3.4 0.00901 
GGTLA1 γ- Glutamyltransferase-like activity 1 13/18 (72) 3/8 (38) 3.9 5.0 6.3 12.0 0.00006 
KIF20A Kinesin family member 20A 13/18 (72) 3/9 (33) 4.6 1.7 7.8 2.9 0.00015 
AICDA Activation-induced cytidine deaminase 10/18 (56) 4/9 (44) 2.9 2.2 5.3 3.6 0.00033 
CXCL13 Chemokine (C-X-C motif) ligand 13 (B cell chemoattractant) 10/18 (56) 3/9 (33) 3.4 2.3 9.4 3.9 0.00454 
LTA Lymphotoxin α (TNF superfamily, member 1) 12/18 (67) 4/9 (44) 4.0 2.4 11.7 3.4 0.00685 
CCL13 Chemokine (C-C motif) ligand 13 13/18 (72) 3/8 (38) 2.2 10.0 4.1 24.8 0.02919 
GOLPH2 Golgi phosphoprotein 2 11/18 (61) 0/8 (0) 3.1 1.4 5.5 N/A 0.00020 
GeneGene NameFrequency (>2-Fold)Mean Fold ChangeMean Fold Change-Only Respondersp Microarray
Microarray (%)RT-PCR (%)MicroarrayRT-PCRMicroarrayRT-PCR
GZMB Granzyme b 12/18 (67) 7/9 (78) 2.3 3.0 3.0 3.6 0.00002 
IFNG IFN-γ 12/18 (67) 5/8 (62) 2.6 5.0 4.0 7.0 0.00002 
HSD11B1 Hydroxysteroid (11-β) dehydrogenase 1 15/18 (83) 7/8 (88) 3.5 4.0 4.8 4.4 0.00005 
INDO Indoleamine-pyrrole 2,3-dioxygenase 11/18 (61) 5/9 (56) 2.5 2.4 3.5 3.5 0.00006 
IL6 IL-6 9/18 (50) 6/8 (75) 2.2 4.5 3.5 5.7 0.00030 
IL3 IL-3 (CSF, multiple) 11/18 (61) 5/9 (56) 4.0 2.9 9.3 4.2 0.00030 
CSF2 CSF2 (granulocyte-macrophage) 12/18 (67) 5/8 (62) 3.3 3.5 6.6 4.7 0.00125 
CYP27B1 Cytochrome p450, family 27, subfamily B, polypeptide 1 13/18 (72) 7/9 (78) 2.4 3.2 3.8 3.8 0.00133 
IL2 IL-2 11/18 (61) 4/8 (50) 3.9 3.7 9.0 6.4 0.00187 
IL5 IL-5 (CSF, eosinophil) 11/18 (61) 7/8 (88) 4.1 67.5 10.8 77.0 0.00399 
INHBA Inhibin, β A (activin A, activin AB α polypeptide) 15/18 (83) 7/9 (78) 5.0 9.2 9.0 11.5 0.00418 
MMP12 Matrix metallopeptidase 12 (macrophage elastase) 12/18 (67) 5/8 (62) 2.7 39.7 6.5 62.8 0.00476 
CD1B CD1B Ag 11/18 (61) 6/8 (75) 2.9 5.7 5.7 7.3 0.00491 
CCL7 Chemokine (C-C motif) ligand 7 10/18 (56) 7/9 (78) 2.4 49.2 5.9 63.1 0.00807 
LIF Leukemia inhibitory factor 10/18 (56) 5/9 (56) 2.0 2.6 4.0 3.4 0.00901 
GGTLA1 γ- Glutamyltransferase-like activity 1 13/18 (72) 3/8 (38) 3.9 5.0 6.3 12.0 0.00006 
KIF20A Kinesin family member 20A 13/18 (72) 3/9 (33) 4.6 1.7 7.8 2.9 0.00015 
AICDA Activation-induced cytidine deaminase 10/18 (56) 4/9 (44) 2.9 2.2 5.3 3.6 0.00033 
CXCL13 Chemokine (C-X-C motif) ligand 13 (B cell chemoattractant) 10/18 (56) 3/9 (33) 3.4 2.3 9.4 3.9 0.00454 
LTA Lymphotoxin α (TNF superfamily, member 1) 12/18 (67) 4/9 (44) 4.0 2.4 11.7 3.4 0.00685 
CCL13 Chemokine (C-C motif) ligand 13 13/18 (72) 3/8 (38) 2.2 10.0 4.1 24.8 0.02919 
GOLPH2 Golgi phosphoprotein 2 11/18 (61) 0/8 (0) 3.1 1.4 5.5 N/A 0.00020 

Finally, we evaluated the direct effect of HPV-16 L1VLP on gene expression of PBMC obtained before vaccination by comparing levels of gene expression in PBMC incubated with HPV-16 L1 VLP against media-treated cells. This comparison allowed us to analyze the primary, vaccine-independent response to HPV-16 L1 VLP.

One-hundred thirty-nine probesets were differentially expressed at a significance level of p < 0.001 (106 up-regulated, 33 down-regulated) in prevaccination PBMCs incubated with HPV-16 L1 VLP (supplemental Table IV). An additional 258 probesets were differentially expressed at the 0.001< p < 0.05 level (154 up-regulated, 104 down-regulated). Pathway enrichment evaluation was suggestive of enrichment for probesets mapping to genes from inflammatory, immune response, chemotaxis, signal transduction, and cell proliferation pathways, as summarized in Fig. 2. Interestingly, at least 26 of the 260 up-regulated probesets are IFN-induced genes or play a role in IFN signaling. There was an overlap between the probesets directly induced by HPV-16 L1 VLP before vaccination and those differentially expressed in postvaccination samples (n = 91 or 9 up-regulated probesets and 45 or 7 down-regulated probesets when using p < 0.05 or p < 0.001, respectively; Fig. 3). The overlapped probesets belong to the most enriched pathways observed in HPV-16 L1 VLP-treated PBMCs (for example, IFN-γ, IL-6, granzyme B, INDO, and several chemokines). The up-regulated, overlapping probesets significant at p < 0.001 were INDO, LAMP3, TYMS, ALAS1, RRM2, CD38, IL6, IFNG, and AKAP2. Down-regulated overlapping probesets significant at p < 0.001 included CD9, HS3ST2, SORL1, ADFP, DFNA5, EPAS1, and ALDH3A2. A complete list of overlapping differentially expressed probesets is shown in supplemental Table IV.

FIGURE 2.

Expression profiles of probesets significantly modulated following incubation of prevaccination PBMCs with HPV-16 L1 VLP when compared to media-treated PBMCs. PBMC from prevaccination samples were incubated with HPV-16 L1 VLP as indicated in Materials and Methods. Functional annotation of probesets differentially expressed was done using DAVID. Up-regulated genes are shown in red and down-regulated genes in green.

FIGURE 2.

Expression profiles of probesets significantly modulated following incubation of prevaccination PBMCs with HPV-16 L1 VLP when compared to media-treated PBMCs. PBMC from prevaccination samples were incubated with HPV-16 L1 VLP as indicated in Materials and Methods. Functional annotation of probesets differentially expressed was done using DAVID. Up-regulated genes are shown in red and down-regulated genes in green.

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FIGURE 3.

Number of probesets with increased or decreased expression in HPV-16 L1 VLP-treated PBMC from vaccine recipients induced by vaccination (vaccination-specific effect) or independent of vaccination (direct effect). Number of probesets overlapping the lists of vaccination-specific probesets and the ones modulated by a direct HPV-16 L1VLP effect are also shown.

FIGURE 3.

Number of probesets with increased or decreased expression in HPV-16 L1 VLP-treated PBMC from vaccine recipients induced by vaccination (vaccination-specific effect) or independent of vaccination (direct effect). Number of probesets overlapping the lists of vaccination-specific probesets and the ones modulated by a direct HPV-16 L1VLP effect are also shown.

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In this study, we characterized the gene expression pattern of recall immune responses to the HPV-16 L1 VLP by comparing pre- and postvaccination gene expression patterns of PBMCs incubated with HPV-16 L1 VLP Ag to better characterize the cellular and innate immune responses in vaccination against HPV. Although the effector mechanism of protection for this vaccine is thought to be neutralizing Abs, our results show that multiple pathways within the cellular and innate arms of the immune system are targeted upon vaccination. The exact role of these pathways in protection or duration of protection is still unknown, but based on the results presented herein it deserves further investigation. The analysis of correlation between differentially expressed genes and neutralizing Ab levels allowed us to identify genes (in particular CCND2, LGALS2, and IL-1RN) that may be predictors of prolonged Ab responses. New studies are necessary to better determine which pre- and postvaccination clinical, immunological, and expression profiles are most associated with long-term protection against HPV.

We took two different approaches to data analysis: a conservative approach that takes into account the potential high false discovery rate that may accompany the high number of statistical comparisons performed, and an exploratory approach to define additional biological pathways and probesets altered in a recall immune response to the vaccine. Using the conservative approach, we preselected pathways based on overall knowledge of microbial immune responses. This reduced the number of comparisons made and focused our analysis on the strongest a priori pathways expected to be involved in immune responses to vaccination. Our results suggest that the response to HPV-16 L1 VLP in vaccine recipients involves modulation of genes within the cell cycle, cytokine, defense, inflammation, and IFN pathways. This finding is consistent with the induction of various arms of the immune response (42, 43) and with our previous data that a recall response to HPV-16 L1 VLP involves a broad and complex pattern of cytokines and chemokines (16, 17).

No significant enrichment was observed for the signal transduction pathway in our conservative analysis despite differential expression in genes that belonged to this pathway. A possible explanation for this observation might be that the definition of this pathway is broad (1577 probesets), and that the differentially expressed probesets within the pathway represent a small subset of the total number. In our exploratory analysis, the signal transduction pathway was found to be overrepresented. This information may be used for hypothesis generation in future studies.

Within the pathways evaluated, we identified up-regulation of genes involved in cytotoxic (CTSC, GZMA, GZMB, TNFSF10, FASLG) and important immunoregulatory functions (INDO, HSD11B1, CTLA4, SOCS1). These results suggest that the immune response to HPV-16 L1 VLP induces a complex modulation of various components of the cell-mediated immune response, including cytokine secretion, cytotoxic response, and activation of feedback mechanisms involving immunoregulatory genes. These results raise the need for future studies determining the contributing roles of these pathways in immunogenicity induced by VLPs. A better understanding of these pathways may be also useful in the design of improved vaccine strategies. Additionally, a substantial fraction of the differentially expressed probesets was down-regulated after vaccination, including genes that fell into cell death, immune response, signaling, and metabolism pathways. Because we used PBMCs, the transcriptional change is representative of the changes from various cell types comprising the PBMC population and the cross-talk of extracellular signals, such as cytokines induced directly or indirectly by the VLPs. Interestingly, expression of a number of these down-regulated genes and corresponding proteins, such as CD9, CD14, ly86, LEF-1, and CD26, have been shown to be down-modulated in the context of cell activation and/or inflammatory signals (44, 45, 46, 47). Such changes may relate to the shutting down of specific elements to better mount a protective immune response to HPV vaccine and avoid excessive inflammatory signals or limit feedback signaling. However, the underlying mechanisms and impact of these transcriptional changes in the development of an immune response to vaccination are not known.

When we examined the correlation of probeset expression levels with neutralizing Ab titers, more probesets correlated to Ab levels at months 7 and 12 postvaccination than at month 2. The highest correlations at month 7 and month 12 were obtained for cyclin D2 (CCND2), which plays an essential role controlling the cell cycle at the G1/S transition (48); galectin 2 (LGALS2), a galactoside-binding lectin that has been shown to promote apoptosis in activated T cells and to shift immune responses to a Th2 profile (49); and IL-1 receptor antagonist (IL-1RN), a regulator of IL-1 induced inflammatory response. In fact, cyclin D2 and AICDA are components of signaling cascades needed for B cell proliferation and Ab production (50, 51). However, the potential role of galectin-2 and IL-1 receptor antagonist in B cell responses is unclear and could be of an indirect nature since these are immune regulatory molecules. Confirmation of the role of the products of these genes in B cell memory responses to the vaccine would be informative in the future.

To confirm the microarray results, we selected PBMCs from an independent group of vaccine recipients and measured RNA expression for a subset of 22 probesets representing various biological pathways targeted by vaccination. We observed a comparable frequency of responders for 68% of analyzed genes (15 of 22). For an additional 27% (6 of 22) of analyzed genes, differential expression was similar to that observed by microarray testing, but at a lower frequency. We were unable to observe evidence of differential expression as noted by microarray for 1 of the 22 selected genes. These results validate our microarray findings and suggest that the HPV-16 L1 VLP-specific response after vaccination involves activation of a complex cell-mediated immune response.

Our results demonstrate that the immune response to vaccination is heterogeneous among vaccine recipients at the gene expression level. For all the probesets analyzed, only a fraction of the participants were considered responders when looking at one gene at a time. The highest frequency was observed for HSD11B1 (15 of 18 donors in microarray, and 7 of 8 with RT-PCR). However, when “responders” are defined by the global expression profile of multiple genes at one time, the response rate is high (data not shown). Whether this heterogeneity of response will have an impact on long-term memory and quality of the immune responses over time needs to be addressed in further studies. It is possible that heterogeneity of response may be associated with previous exposures to HPV. Studies of comparison of expression profiles induced by vaccination in naturally infected vs naive individuals are warranted. Additionally, identification of gene signatures associated with infection or vaccination will also be important.

In addition to the evaluation of vaccine-specific immune responses, we characterized the vaccination-independent responses to VLP by comparing HPV-16 L1 VLP-incubated cells with media controls in prevaccination samples. Our analysis revealed that incubation with HPV-16 L1 VLP before vaccination induces up-regulation of the defense response, cytokine/inflammation, signal transduction, and cell proliferation pathways. If the responses elicited by HPV-16 L1 VLP in the post- and prevaccination responses are compared, ∼30% of the probesets modulated by VLP (136 out of 397; p < 0.05) before vaccination overlap with the HPV-16 L1 VLP-specific responses induced by vaccination. Interestingly, for most of the overlapping probesets, responses observed after incubation with HPV-16 L1 VLP are stronger than before vaccination. This probably reflects an increase in the number of responding cells after vaccination. In contrast to the vaccination-specific responses, a strong induction of an IFN response was observed in the vaccination-independent responses. These findings are important considering the current potential applications of VLP as vectors for Ag delivery and as vaccines for various pathogens and tumors (52).

PBMCs are a valuable tool to study immune responses to various diseases (29, 30, 53). Use of PBMCs, however, has some limitations that need to be taken into account. PBMCs are heterogeneous in their cell composition. For this reason, an enhanced or reduced gene expression might be restricted to particular cell populations. Additionally, the response to stimulation with HPV-16 L1 VLP in an ex vivo system might differ from responses that occur in disease-relevant tissues. Also, since the number of memory cells in PBMCs is low, a recall response could be diluted by the response from other cell populations. Thus, it is conceivable that large alterations in the expression of a unique gene from an underrepresented cell type may be overlooked upon examination of the PBMC population. Despite these considerations, we confirmed a group of genes using RT-PCR analysis, and a good correlation for a number of genes with neutralizing Ab levels was observed. Moreover, we found no correlation between levels of gene expression and the percentage of leukocyte subpopulations, suggesting that differences seen were not likely to be due to changes in cell populations. In fact, flow cytometric analysis of main lymphocyte subsets revealed no major cell subset differences between baseline (month 0) and month 2 samples.

An additional potential limitation of our study is the fact that results observed may not be directly extrapolated to patterns that will be obtained after vaccination with the commercially available HPV L1 VLP vaccines, because participants in our study were immunized with HPV-16 L1VLP without an adjuvant. Additionally, the HPV-16 L1 VLP vaccine used in our study is monovalent and produced in a recombinant baculovirus system. However, our results provide interesting and unique information on HPV-16 L1 VLP-specific changes, independent of adjuvant effects.

In conclusion, we used gene expression profiling to identify important adaptive and innate immune responses induced by vaccination with HPV-16 L1 VLP vaccine. We also identified differentially expressed genes predictive of neutralizing Ab titers. Interestingly, the host transcriptional response to HPV-16 L1 VLPs following vaccination varies considerably among donors, raising the need for further studies to better understand the potential impact of those differences in APC function, T cell and B cell responses, and how these gene signatures predict immunogenicity and long-term outcome.

Douglas R. Lowy is a named inventor on U.S. government-owned HPV vaccine patents that are licensed to Merck and GlaxoSmithKline and is entitled to limited royalties as specified by federal law.

Table II.

Genes demonstrating significant differential expressiona

Gene SymbolGene NameAffymetrix IDFold Changep
Within the cell cycle pathway     
 Up-regulated genes (expression higher postvaccination than prevaccination)     
  RRM2 Ribonucleotide reductase M2 polypeptide 209773_s_at 2.06 0.000002 
  RFC3 Replication factor C (activator 1) 3, 38 kDa 204127_at 1.78 0.000022 
  PMS2 ///PMS2CL PMS2 postmeiotic segregation increased 2 (Saccharomyces cerevisiae) 209805_at 1.93 0.000257 
  PRC1 Protein regulator of cytokinesis 1 218009_s_at 1.92 0.000321 
  CCNB2 Cyclin B2 202705_at 1.66 0.000377 
  CCND2 Cyclin D2 200953_s_at 1.42 0.000378 
  GINS2 DNA replication complex GINS protein PSF2 221521_s_at 3.50 0.000599 
  BUB1 BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast) 209642_at 2.16 0.000754 
 Down-regulated genes (expression lower postvaccination than prevaccination)     
  TSC1 Tuberous sclerosis 1 209390_at −1.36 0.000023 
  LCK Lymphocyte-specific protein tyrosine kinase 204891_s_at −1.31 0.000244 
  CDC25B Cell division cycle 25B 201853_s_at −1.36 0.000428 
  ARHGEF1 Rho guanine nucleotide exchange factor (GEF) 1 203055_s_at −1.36 0.000724 
Within the cytokine pathway     
 Up-regulated genes (expression higher postvaccination than prevaccination)     
  IFNG IFN-γ 210354_at 2.57 0.000022 
  CXCL11 Chemokine (C-X-C motif) ligand 11 210163_at 2.39 0.000086 
  IL6 IL-6 (IFN-β2) 205207_at 2.18 0.000295 
  IL3 IL-3 (CSF, multiple) 207906_at 4.03 0.000303 
  CXCL9 Chemokine (C-X-C motif) ligand 9 203915_at 1.91 0.000507 
  TNF TNF (TNF superfamily, member 2) 207113_s_at 1.81 0.000638 
  IL15 IL-15 205992_s_at 1.32 0.000979 
 Down-regulated genes (expression lower postvaccination than prevaccination)     
  GRN Granulin 211284_s_at −1.52 0.000082 
  CSF3R CSF3R (granulocyte) 203591_s_at −1.44 0.000355 
Within the defense pathway     
 Up-regulated genes (expression higher postvaccination than prevaccination)     
  CTSC Cathepsin C 201487_at 1.52 0.000006 
  IFNG IFN-γ 210354_at 2.57 0.000022 
  INDO Indoleamine-pyrrole 2,3-dioxygenase 210029_at 2.47 0.000058 
  CXCL11 Chemokine (C-X-C motif) ligand 11 210163_at 2.39 0.000086 
  KIR2DS5 Killer cell Ig-like receptor, two domains, short cytoplasmic tail, 5 208203_x_at 2.11 0.000110 
  ADAR Adenosine deaminase, RNA-specific 201786_s_at 1.37 0.000249 
  IL6 IL-6 (IFN-β2) 205207_at 2.18 0.000295 
  IL3 IL-3 (CSF, multiple) 207906_at 4.03 0.000303 
  AICDA Activation-induced cytidine deaminase 219841_at 2.91 0.000333 
  SLAMF1 Signaling lymphocytic activation molecule family member 1 206181_at 1.42 0.000468 
  CXCL9 Chemokine (C-X-C motif) ligand 9 203915_at 1.91 0.000507 
  TNF TNF (TNF superfamily, member 2) 207113_s_at 1.81 0.000638 
  GZMA Granzyme A (granzyme 1, CTL-associated serine esterase 3) 205488_at 1.59 0.000755 
  C1QB Complement component 1, q subcomponent, β polypeptide 202953_at 1.59 0.000775 
  IL15 IL-15 205992_s_at 1.32 0.000979 
 Down-regulated genes (expression lower postvaccination than prevaccination)     
  CD14 CD14 Ag 201743_at −2.46 0.000031 
  ADORA2B Adenosine A2b receptor 205891_at −1.69 0.000077 
  DPP4 Dipeptidylpeptidase 4 (CD26, adenosine deaminase complexing protein 2) 203717_at −1.35 0.000241 
  LY86 Lymphocyte Ag 86 205859_at −1.45 0.000340 
  CSF3R CSF3R (granulocyte) 203591_s_at −1.44 0.000355 
  PLA2G4B Phospholipase A2, group IVB (cytosolic) 60528_at −1.34 0.000546 
  FCGRT Fc fragment of IgG, receptor, transporter, α 218831_s_at −1.68 0.000678 
Within the inflammation pathway     
 Up-regulated genes (expression higher postvaccination than prevaccination)     
  CXCL11 Chemokine (C-X-C motif) ligand 11 210163_at 2.39 0.000086 
  CXCL9 Chemokine (C-X-C motif) ligand 9 203915_at 1.91 0.000507 
  TNF TNF (TNF superfamily, member 2) 207113_s_at 1.81 0.000638 
(Table continues
Gene SymbolGene NameAffymetrix IDFold Changep
Within the cell cycle pathway     
 Up-regulated genes (expression higher postvaccination than prevaccination)     
  RRM2 Ribonucleotide reductase M2 polypeptide 209773_s_at 2.06 0.000002 
  RFC3 Replication factor C (activator 1) 3, 38 kDa 204127_at 1.78 0.000022 
  PMS2 ///PMS2CL PMS2 postmeiotic segregation increased 2 (Saccharomyces cerevisiae) 209805_at 1.93 0.000257 
  PRC1 Protein regulator of cytokinesis 1 218009_s_at 1.92 0.000321 
  CCNB2 Cyclin B2 202705_at 1.66 0.000377 
  CCND2 Cyclin D2 200953_s_at 1.42 0.000378 
  GINS2 DNA replication complex GINS protein PSF2 221521_s_at 3.50 0.000599 
  BUB1 BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast) 209642_at 2.16 0.000754 
 Down-regulated genes (expression lower postvaccination than prevaccination)     
  TSC1 Tuberous sclerosis 1 209390_at −1.36 0.000023 
  LCK Lymphocyte-specific protein tyrosine kinase 204891_s_at −1.31 0.000244 
  CDC25B Cell division cycle 25B 201853_s_at −1.36 0.000428 
  ARHGEF1 Rho guanine nucleotide exchange factor (GEF) 1 203055_s_at −1.36 0.000724 
Within the cytokine pathway     
 Up-regulated genes (expression higher postvaccination than prevaccination)     
  IFNG IFN-γ 210354_at 2.57 0.000022 
  CXCL11 Chemokine (C-X-C motif) ligand 11 210163_at 2.39 0.000086 
  IL6 IL-6 (IFN-β2) 205207_at 2.18 0.000295 
  IL3 IL-3 (CSF, multiple) 207906_at 4.03 0.000303 
  CXCL9 Chemokine (C-X-C motif) ligand 9 203915_at 1.91 0.000507 
  TNF TNF (TNF superfamily, member 2) 207113_s_at 1.81 0.000638 
  IL15 IL-15 205992_s_at 1.32 0.000979 
 Down-regulated genes (expression lower postvaccination than prevaccination)     
  GRN Granulin 211284_s_at −1.52 0.000082 
  CSF3R CSF3R (granulocyte) 203591_s_at −1.44 0.000355 
Within the defense pathway     
 Up-regulated genes (expression higher postvaccination than prevaccination)     
  CTSC Cathepsin C 201487_at 1.52 0.000006 
  IFNG IFN-γ 210354_at 2.57 0.000022 
  INDO Indoleamine-pyrrole 2,3-dioxygenase 210029_at 2.47 0.000058 
  CXCL11 Chemokine (C-X-C motif) ligand 11 210163_at 2.39 0.000086 
  KIR2DS5 Killer cell Ig-like receptor, two domains, short cytoplasmic tail, 5 208203_x_at 2.11 0.000110 
  ADAR Adenosine deaminase, RNA-specific 201786_s_at 1.37 0.000249 
  IL6 IL-6 (IFN-β2) 205207_at 2.18 0.000295 
  IL3 IL-3 (CSF, multiple) 207906_at 4.03 0.000303 
  AICDA Activation-induced cytidine deaminase 219841_at 2.91 0.000333 
  SLAMF1 Signaling lymphocytic activation molecule family member 1 206181_at 1.42 0.000468 
  CXCL9 Chemokine (C-X-C motif) ligand 9 203915_at 1.91 0.000507 
  TNF TNF (TNF superfamily, member 2) 207113_s_at 1.81 0.000638 
  GZMA Granzyme A (granzyme 1, CTL-associated serine esterase 3) 205488_at 1.59 0.000755 
  C1QB Complement component 1, q subcomponent, β polypeptide 202953_at 1.59 0.000775 
  IL15 IL-15 205992_s_at 1.32 0.000979 
 Down-regulated genes (expression lower postvaccination than prevaccination)     
  CD14 CD14 Ag 201743_at −2.46 0.000031 
  ADORA2B Adenosine A2b receptor 205891_at −1.69 0.000077 
  DPP4 Dipeptidylpeptidase 4 (CD26, adenosine deaminase complexing protein 2) 203717_at −1.35 0.000241 
  LY86 Lymphocyte Ag 86 205859_at −1.45 0.000340 
  CSF3R CSF3R (granulocyte) 203591_s_at −1.44 0.000355 
  PLA2G4B Phospholipase A2, group IVB (cytosolic) 60528_at −1.34 0.000546 
  FCGRT Fc fragment of IgG, receptor, transporter, α 218831_s_at −1.68 0.000678 
Within the inflammation pathway     
 Up-regulated genes (expression higher postvaccination than prevaccination)     
  CXCL11 Chemokine (C-X-C motif) ligand 11 210163_at 2.39 0.000086 
  CXCL9 Chemokine (C-X-C motif) ligand 9 203915_at 1.91 0.000507 
  TNF TNF (TNF superfamily, member 2) 207113_s_at 1.81 0.000638 
(Table continues
Table IIA.

(Continued)

Gene SymbolGene NameAffymetrix IDFold Changep
 Down-regulated genes (expression lower postvaccination than prevaccination)     
  CD14 CD14 Ag 201743_at −2.46 0.000031 
  LY86 Lymphocyte Ag 86 205859_at −1.45 0.000340 
  PLA2G4B Phospholipase A2, group IVB (cytosolic) 60528_at −1.34 0.000546 
Within the IFN pathway     
 Up-regulated genes (expression higher postvaccination than prevaccination)     
  INDO Indoleamine-pyrrole 2,3-dioxygenase 210029_at 2.47 0.000058 
  CXCL9 Chemokine (C-X-C motif) ligand 9 203915_at 1.91 0.000507 
Gene SymbolGene NameAffymetrix IDFold Changep
 Down-regulated genes (expression lower postvaccination than prevaccination)     
  CD14 CD14 Ag 201743_at −2.46 0.000031 
  LY86 Lymphocyte Ag 86 205859_at −1.45 0.000340 
  PLA2G4B Phospholipase A2, group IVB (cytosolic) 60528_at −1.34 0.000546 
Within the IFN pathway     
 Up-regulated genes (expression higher postvaccination than prevaccination)     
  INDO Indoleamine-pyrrole 2,3-dioxygenase 210029_at 2.47 0.000058 
  CXCL9 Chemokine (C-X-C motif) ligand 9 203915_at 1.91 0.000507 
a

VLP-media expression levels are as defined in Materials and Methods.

Table III.

Differentially expressed genes after vaccination using p < 0.05 as the cutoff

Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
UP-REGULATED GENES     DOWN-REGULATED GENES     
209773_s_at 2.06 0.000002 RRM2 Ribonucleotide reductase M2 polypeptide 201005_at −1.82 0.00000007 CD9 CD9 Ag (p24) 
208921_s_at 1.48 0.000004 SRI Sorcin 201029_s_at −1.30 0.000002 CD99 CD99 Ag 
201487_at 1.52 0.000006 CTSC Cathepsin C 205695_at −2.51 0.000009 SDS Serine dehydratase 
200039_s_at 1.34 0.000010 PSMB2 Proteasome (prosome, macropain) subunit, β type, 2 203509_at −1.71 0.000012 SORL1 sortilin-related receptor, L(DLR class) A repeats-containing 
210164_at 2.33 0.000015 GZMB Granzyme B (granzyme 2, cytotoxic T lymphocyte-associated serine esterase 1) 201591_s_at −1.51 0.000020 NISCH Nischarin 
210354_at 2.57 0.000022 IFNG IFN-γ 209390_at −1.36 0.000023 TSC1 Tuberous sclerosis 1 
204127_at 1.78 0.000022 RFC3 Replication factor C (activator 1) 3, 38 kDa 221558_s_at −1.36 0.000026 LEF1 Lymphoid enhancer-binding factor 1 
204777_s_at 1.65 0.000030 MAL Mal, T cell differentiation protein 201743_at −2.46 0.000031 CD14 CD14 Ag 
217848_s_at 1.86 0.000048 PPA1 Pyrophosphatase (inorganic) 1 203979_at −2.14 0.000032 CYP27A1 Cytochrome p450, family 27, subfamily A, polypeptide 1 
201274_at 1.39 0.000049 PSMA5 Proteasome (prosome, macropain) subunit, α type, 5 204647_at −1.99 0.000056 HOMER3 Homer homolog 3 (Drosophila
205404_at 3.49 0.000052 HSD11B1 Hydroxysteroid (11-β) dehydrogenase 1 205891_at −1.69 0.000077 ADORA2B Adenosine A2b receptor 
210029_at 2.47 0.000058 INDO Indoleamine-pyrrole 2,3-dioxygenase 205960_at −2.80 0.000082 PDK4 Pyruvate dehydrogenase kinase, isozyme 4 
219210_s_at 1.40 0.000063 RAB8B Rab8b, member ras oncogene family 211284_s_at −1.52 0.000082 GRN Granulin 
205582_s_at 3.90 0.000065 GGTLA1 γ-Glutamyltransferase-like activity 1 203695_s_at −1.82 0.000089 DFNA5 Deafness, autosomal dominant 5 
216268_s_at 1.51 0.000077 JAG1 Jagged 1 (Alagille syndrome) 214198_s_at −1.34 0.000101 DGCR2 KIAA0163 gene product 
202760_s_at 1.58 0.000082 AKAP2 ///PALM2-AKAP2 A kinase (PRKA) anchor protein 2 204134_at −2.87 0.000153 PDE2A Phosphodiesterase 2A, cGMP-stimulated 
210163_at 2.39 0.000086 CXCL11 Chemokine (C-X-C motif) ligand 11 222240_s_at −1.36 0.000158 ISYNA1 Myo-inositol 1-phosphate synthase A1 
203471_s_at 1.40 0.000087 PLEK Pleckstrin 203382_s_at −2.95 0.000183 APOE Apolipoprotein E 
202941_at 1.34 0.000092 NDUFV2 NADH dehydrogenase (ubiquinone) flavoprotein 2, 24 kDa 204906_at −1.36 0.000190 RPS6KA2 Ribosomal protein S6 kinase, 90 kDa, polypeptide 2 
209765_at 1.77 0.000096 ADAM19 ADAM metallopeptidase domain 19 (meltrin β) 52940_at −1.52 0.000204 SIGIRR Single Ig and Toll-IL-1R (TIR) domain 
208203_x_at 2.11 0.000110 KIR2DS5 Killer cell Ig-like receptor, two domains, long cytoplasmic tail, 2 219889_at −1.41 0.000207 FRAT1 Rrequently rearranged in advanced T cell lymphomas 
212581_x_at 1.34 0.000120 GAPDH GAPDH 209230_s_at −2.44 0.000232 P8 p8 Protein (candidate of metastasis 1) 
202638_s_at 1.50 0.000145 ICAM1 Intercellular adhesion molecule 1 (CD54), human rhinovirus receptor 209831_x_at −1.35 0.000235 DNASE2 Deoxyribonuclease II, lysosomal 
208799_at 1.34 0.000145 PSMB5 Proteasome (prosome, macropain) subunit, β type, 5 203717_at −1.35 0.000241 DPP4 Dipeptidyl-peptidase 4 (CD26, adenosine deaminase complexing protein 2) 
218755_at 4.62 0.000152 KIF20A Kinesin family member 20A 204891_s_at −1.31 0.000244 LCK Lymphocyte-specific protein tyrosine kinase 
(Table continues
Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
UP-REGULATED GENES     DOWN-REGULATED GENES     
209773_s_at 2.06 0.000002 RRM2 Ribonucleotide reductase M2 polypeptide 201005_at −1.82 0.00000007 CD9 CD9 Ag (p24) 
208921_s_at 1.48 0.000004 SRI Sorcin 201029_s_at −1.30 0.000002 CD99 CD99 Ag 
201487_at 1.52 0.000006 CTSC Cathepsin C 205695_at −2.51 0.000009 SDS Serine dehydratase 
200039_s_at 1.34 0.000010 PSMB2 Proteasome (prosome, macropain) subunit, β type, 2 203509_at −1.71 0.000012 SORL1 sortilin-related receptor, L(DLR class) A repeats-containing 
210164_at 2.33 0.000015 GZMB Granzyme B (granzyme 2, cytotoxic T lymphocyte-associated serine esterase 1) 201591_s_at −1.51 0.000020 NISCH Nischarin 
210354_at 2.57 0.000022 IFNG IFN-γ 209390_at −1.36 0.000023 TSC1 Tuberous sclerosis 1 
204127_at 1.78 0.000022 RFC3 Replication factor C (activator 1) 3, 38 kDa 221558_s_at −1.36 0.000026 LEF1 Lymphoid enhancer-binding factor 1 
204777_s_at 1.65 0.000030 MAL Mal, T cell differentiation protein 201743_at −2.46 0.000031 CD14 CD14 Ag 
217848_s_at 1.86 0.000048 PPA1 Pyrophosphatase (inorganic) 1 203979_at −2.14 0.000032 CYP27A1 Cytochrome p450, family 27, subfamily A, polypeptide 1 
201274_at 1.39 0.000049 PSMA5 Proteasome (prosome, macropain) subunit, α type, 5 204647_at −1.99 0.000056 HOMER3 Homer homolog 3 (Drosophila
205404_at 3.49 0.000052 HSD11B1 Hydroxysteroid (11-β) dehydrogenase 1 205891_at −1.69 0.000077 ADORA2B Adenosine A2b receptor 
210029_at 2.47 0.000058 INDO Indoleamine-pyrrole 2,3-dioxygenase 205960_at −2.80 0.000082 PDK4 Pyruvate dehydrogenase kinase, isozyme 4 
219210_s_at 1.40 0.000063 RAB8B Rab8b, member ras oncogene family 211284_s_at −1.52 0.000082 GRN Granulin 
205582_s_at 3.90 0.000065 GGTLA1 γ-Glutamyltransferase-like activity 1 203695_s_at −1.82 0.000089 DFNA5 Deafness, autosomal dominant 5 
216268_s_at 1.51 0.000077 JAG1 Jagged 1 (Alagille syndrome) 214198_s_at −1.34 0.000101 DGCR2 KIAA0163 gene product 
202760_s_at 1.58 0.000082 AKAP2 ///PALM2-AKAP2 A kinase (PRKA) anchor protein 2 204134_at −2.87 0.000153 PDE2A Phosphodiesterase 2A, cGMP-stimulated 
210163_at 2.39 0.000086 CXCL11 Chemokine (C-X-C motif) ligand 11 222240_s_at −1.36 0.000158 ISYNA1 Myo-inositol 1-phosphate synthase A1 
203471_s_at 1.40 0.000087 PLEK Pleckstrin 203382_s_at −2.95 0.000183 APOE Apolipoprotein E 
202941_at 1.34 0.000092 NDUFV2 NADH dehydrogenase (ubiquinone) flavoprotein 2, 24 kDa 204906_at −1.36 0.000190 RPS6KA2 Ribosomal protein S6 kinase, 90 kDa, polypeptide 2 
209765_at 1.77 0.000096 ADAM19 ADAM metallopeptidase domain 19 (meltrin β) 52940_at −1.52 0.000204 SIGIRR Single Ig and Toll-IL-1R (TIR) domain 
208203_x_at 2.11 0.000110 KIR2DS5 Killer cell Ig-like receptor, two domains, long cytoplasmic tail, 2 219889_at −1.41 0.000207 FRAT1 Rrequently rearranged in advanced T cell lymphomas 
212581_x_at 1.34 0.000120 GAPDH GAPDH 209230_s_at −2.44 0.000232 P8 p8 Protein (candidate of metastasis 1) 
202638_s_at 1.50 0.000145 ICAM1 Intercellular adhesion molecule 1 (CD54), human rhinovirus receptor 209831_x_at −1.35 0.000235 DNASE2 Deoxyribonuclease II, lysosomal 
208799_at 1.34 0.000145 PSMB5 Proteasome (prosome, macropain) subunit, β type, 5 203717_at −1.35 0.000241 DPP4 Dipeptidyl-peptidase 4 (CD26, adenosine deaminase complexing protein 2) 
218755_at 4.62 0.000152 KIF20A Kinesin family member 20A 204891_s_at −1.31 0.000244 LCK Lymphocyte-specific protein tyrosine kinase 
(Table continues
Table IIIA.

(Continued)

Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
203217_s_at 1.35 0.000152 ST3GAL5 ST3 β-galactoside α-2,3-sialyltransferase 5 202054_s_at −1.48 0.000256 ALDH3A2 Dldehyde dehydrogenase 3 family, member A2 
201037_at 1.52 0.000167 PFKP Phosphofructokinase, platelet 219697_at −2.64 0.000260 HS3ST2 Heparan sulfate (glucosamine) 3-O-sulfotransferase 2 
205692_s_at 1.92 0.000181 CD38 CD38 Ag (p45) 208626_s_at −1.30 0.000269 VAT1 Vesicle amine transport protein 1 homolog (T. californica
217771_at 3.13 0.000200 GOLPH2 Golgi phosphoprotein 2 204466_s_at −1.58 0.000286 SNCA Synuclein, α (non-A4 component of amyloid precursor) 
213011_s_at 1.32 0.000211 TPI1 Triosephosphate isomerase 1 205859_at −1.45 0.000340 LY86 Lymphocyte Ag 86 
201761_at 1.42 0.000226 MTHFD2 Methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase 203591_s_at −1.44 0.000355 CSF3R CSF3R (granulocyte) 
202589_at 1.75 0.000226 TYMS Thymidylate synthetase 221872_at −2.32 0.000403 RARRES1 Retinoic acid receptor responder (tazarotene induced) 1 
202352_s_at 1.35 0.000231 PSMD12 Proteasome (prosome, macropain) 26S subunit, non-ATPase, 12 219445_at −1.58 0.000404 GLTSCR1 Glioma tumor suppressor candidate region gene 1 
201323_at 1.43 0.000244 EBNA1BP2 EBNA1 binding protein 2 204867_at −1.75 0.000408 GCHFR GTP cyclohydrolase I feedback regulator 
209146_at 1.39 0.000247 SC4MOL Sterol-C4-methyl oxidase-like 201853_s_at −1.36 0.000428 CDC25B Cell division cycle 25b 
201786_s_at 1.37 0.000249 ADAR Adenosine deaminase, RNA-specific 200878_at −1.59 0.000443 EPAS1 Endothelial PAS domain protein 1 
209805_at 1.93 0.000257 PMS2 /// PMS2CL PMS2 postmeiotic segregation increased 2 (S. cerevisiae), PMS2-c terminal-like 220776_at −1.89 0.000452 KCNJ14 Potassium inwardly rectifying channel, subfamily J, member 14 
205569_at 1.66 0.000283 LAMP3 Lysosomal-associated membrane protein 3 201278_at −1.52 0.000496 DAB2 Disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila
205207_at 2.18 0.000295 IL6 IL-6 (IFN-β2) 209122_at −1.60 0.000511 ADFP Adipose differentiation-related protein 
207906_at 4.03 0.000303 IL3 IL-3 (CSF, multiple) 200766_at −1.54 0.000544 CTSD Cathepsin D (lysosomal aspartyl peptidase) 
218009_s_at 1.92 0.000321 PRC1 Protein regulator of cytokinesis 1 60528_at −1.34 0.000546 PLA2G4B Phospholipase A2, group IVB (cytosolic) 
219841_at 2.91 0.000333 AICDA Activation-induced cytidine deaminase 203665_at −1.61 0.000564 HMOX1 Heme oxygenase (decycling) 1 
214210_at 1.79 0.000349 SLC25A17 Solute carrier family 25 (mitochondrial carrier; peroxisomal membrane protein, 34 kDa), member 17 218831_s_at −1.68 0.000678 FCGRT Fc fragment of IgG, receptor, transporter, α 
202705_at 1.66 0.000377 CCNB2 Cyclin B2 212774_at −1.54 0.000688 ZNF238 Zinc finger protein 238 
200953_s_at 1.42 0.000378 CCND2 Cyclin D2 202500_at −1.50 0.000695 DNAJB2 DnaJ (HSP40) homolog, subfamily B, member 2 
201317_s_at 1.41 0.000395 PSMA2 Proteasome (prosome, macropain) subunit, α type, 2 203055_s_at −1.36 0.000724 ARHGEF1 Rho guanine nucleotide exchange factor (GEF) 1 
203376_at 1.34 0.000400 CDC40 Cell division cycle 40 homolog (yeast) 214780_s_at −1.42 0.000801 MYO9B Myosin IXB 
212185_x_at 1.72 0.000417 MT2A Metallothionein 2A 219113_x_at −1.51 0.000846 DHRS10 Dehydrogenase/reductase (SDR family) member 10 
(Table continues
Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
203217_s_at 1.35 0.000152 ST3GAL5 ST3 β-galactoside α-2,3-sialyltransferase 5 202054_s_at −1.48 0.000256 ALDH3A2 Dldehyde dehydrogenase 3 family, member A2 
201037_at 1.52 0.000167 PFKP Phosphofructokinase, platelet 219697_at −2.64 0.000260 HS3ST2 Heparan sulfate (glucosamine) 3-O-sulfotransferase 2 
205692_s_at 1.92 0.000181 CD38 CD38 Ag (p45) 208626_s_at −1.30 0.000269 VAT1 Vesicle amine transport protein 1 homolog (T. californica
217771_at 3.13 0.000200 GOLPH2 Golgi phosphoprotein 2 204466_s_at −1.58 0.000286 SNCA Synuclein, α (non-A4 component of amyloid precursor) 
213011_s_at 1.32 0.000211 TPI1 Triosephosphate isomerase 1 205859_at −1.45 0.000340 LY86 Lymphocyte Ag 86 
201761_at 1.42 0.000226 MTHFD2 Methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase 203591_s_at −1.44 0.000355 CSF3R CSF3R (granulocyte) 
202589_at 1.75 0.000226 TYMS Thymidylate synthetase 221872_at −2.32 0.000403 RARRES1 Retinoic acid receptor responder (tazarotene induced) 1 
202352_s_at 1.35 0.000231 PSMD12 Proteasome (prosome, macropain) 26S subunit, non-ATPase, 12 219445_at −1.58 0.000404 GLTSCR1 Glioma tumor suppressor candidate region gene 1 
201323_at 1.43 0.000244 EBNA1BP2 EBNA1 binding protein 2 204867_at −1.75 0.000408 GCHFR GTP cyclohydrolase I feedback regulator 
209146_at 1.39 0.000247 SC4MOL Sterol-C4-methyl oxidase-like 201853_s_at −1.36 0.000428 CDC25B Cell division cycle 25b 
201786_s_at 1.37 0.000249 ADAR Adenosine deaminase, RNA-specific 200878_at −1.59 0.000443 EPAS1 Endothelial PAS domain protein 1 
209805_at 1.93 0.000257 PMS2 /// PMS2CL PMS2 postmeiotic segregation increased 2 (S. cerevisiae), PMS2-c terminal-like 220776_at −1.89 0.000452 KCNJ14 Potassium inwardly rectifying channel, subfamily J, member 14 
205569_at 1.66 0.000283 LAMP3 Lysosomal-associated membrane protein 3 201278_at −1.52 0.000496 DAB2 Disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila
205207_at 2.18 0.000295 IL6 IL-6 (IFN-β2) 209122_at −1.60 0.000511 ADFP Adipose differentiation-related protein 
207906_at 4.03 0.000303 IL3 IL-3 (CSF, multiple) 200766_at −1.54 0.000544 CTSD Cathepsin D (lysosomal aspartyl peptidase) 
218009_s_at 1.92 0.000321 PRC1 Protein regulator of cytokinesis 1 60528_at −1.34 0.000546 PLA2G4B Phospholipase A2, group IVB (cytosolic) 
219841_at 2.91 0.000333 AICDA Activation-induced cytidine deaminase 203665_at −1.61 0.000564 HMOX1 Heme oxygenase (decycling) 1 
214210_at 1.79 0.000349 SLC25A17 Solute carrier family 25 (mitochondrial carrier; peroxisomal membrane protein, 34 kDa), member 17 218831_s_at −1.68 0.000678 FCGRT Fc fragment of IgG, receptor, transporter, α 
202705_at 1.66 0.000377 CCNB2 Cyclin B2 212774_at −1.54 0.000688 ZNF238 Zinc finger protein 238 
200953_s_at 1.42 0.000378 CCND2 Cyclin D2 202500_at −1.50 0.000695 DNAJB2 DnaJ (HSP40) homolog, subfamily B, member 2 
201317_s_at 1.41 0.000395 PSMA2 Proteasome (prosome, macropain) subunit, α type, 2 203055_s_at −1.36 0.000724 ARHGEF1 Rho guanine nucleotide exchange factor (GEF) 1 
203376_at 1.34 0.000400 CDC40 Cell division cycle 40 homolog (yeast) 214780_s_at −1.42 0.000801 MYO9B Myosin IXB 
212185_x_at 1.72 0.000417 MT2A Metallothionein 2A 219113_x_at −1.51 0.000846 DHRS10 Dehydrogenase/reductase (SDR family) member 10 
(Table continues
Table IIIB.

(Continued)

Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
206181_at 1.42 0.000468 SLAMF1 Signaling lymphocytic activation molecule family member 1 204638_at −1.39 0.000861 ACP5 Acid phosphatase 5, tartrate resistant 
203915_at 1.91 0.000507 CXCL9 Chemokine (C-X-C motif) ligand 9 218855_at −1.51 0.000959 GPR175 Seven transmembrane domain orphan receptor 
208581_x_at 1.94 0.000511 MT1X Metallothionein 1X 204046_at −1.42 0.001080 PLCB2 Phospholipase C,β2 
209803_s_at 1.84 0.000566 PHLDA2 Pleckstrin homology-like domain, family A, member 2 221601_s_at −1.41 0.001082 FAIM3 Fas apoptotic inhibitory molecule 3 
205633_s_at 1.60 0.000591 ALAS1 aminolevulinate, δ-, synthase 1 40225_at −1.34 0.001110 GAK Cyclin G-associated kinase 
221521_s_at 3.50 0.000599 GINS2 DNA replication complex GINS protein Psf2 201185_at −1.53 0.001140 HTRA1 HtrA serine peptidase 1 
204962_s_at 1.76 0.000638 CENPA Centromere protein A, 17 kDa 221579_s_at −1.33 0.001161 NUDT3 Diphosphoinositol polyphosphate phosphohydrolase 
207113_s_at 1.81 0.000638 TNF TNF (TNF superfamily, member 2) 221675_s_at −1.48 0.001196 CHPT1 Choline phosphotransferase 1 
205126_at 1.45 0.000693 VRK2 Vaccinia-related kinase 2 217963_s_at −1.63 0.001204 NGFRAP1 Nerve growth factor receptor (TNFR superfamily16)-associated protein 1 
209642_at 2.16 0.000754 BUB1 BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast) 218555_at −1.47 0.001284 ANAPC2 Anaphase-promoting complex subunit 2 
205488_at 1.59 0.000755 GZMA Granzyme A (granzyme 1, cytotoxic T lymphocyte-associated serine esterase 3) 219452_at −2.48 0.001417 DPEP2 Dipeptidase 2 
202953_at 1.59 0.000775 C1QB complement component 1, q subcomponent, B chain 35626_at −1.32 0.001587 SGSH N-sulfoglucosamine sulfohydrolase (sulfamidase) 
209267_s_at 1.68 0.000802 SLC39A8 Solute carrier family 39 (zinc transporter), member 8 201819_at −1.35 0.001596 SCARB1 Scavenger receptor class B, member 1 
204326_x_at 1.77 0.000952 MT1X Metallothionein 1X 211110_s_at −2.00 0.001806 AR Androgen receptor (dihydrotestosterone receptor; testicular feminization; spinal and bulbar muscular atrophy; Kennedy disease) 
205992_s_at 1.32 0.000979 IL15 IL-15 209774_x_at −1.76 0.002054 CXCL2 Chemokine (C-X-C motif) ligand 2 
205174_s_at 2.29 0.001056 QPCT Glutaminyl-peptide cyclotransferase (glutaminyl cyclase) 206608_s_at −1.36 0.002175 RPGRIP1 Retinitis pigmentosa GRPase regulator interacting protein 1 
219960_s_at 1.30 0.001160 UCHL5 Ubiquitin carboxyl-terminal hydrolase l5 204949_at −1.34 0.002253 ICAM3 ICAM3 
208864_s_at 1.34 0.001162 TXN thioredoxin 214414_x_at −1.59 0.002301 HBA2 Hemoglobin, α1 
203213_at 2.50 0.001193 CDC2 Cell division cycle 2, G1 to S and G2 to M 219549_s_at −1.32 0.002316 RTN3 Reticulon 3 
210229_s_at 3.34 0.001253 CSF2 CSF2 (granulocyte-macrophage) 205382_s_at −1.84 0.002559 CFD Complement factor C (adipsin) 
205676_at 2.38 0.001331 CYP27B1 Cytochrome p450, family 27, subfamily B, polypeptide 1 216092_s_at −1.48 0.002565 SLC7A8 Solute carrier family 7 (cationic amino acid transporter, y+ system), member 8 
217979_at 1.51 0.001398 TSPAN13 Tetraspanin 13 202449_s_at −1.31 0.002571 RXRA Retinoid X receptor, α 
202421_at 1.59 0.001460 IGSF3 Ig superfamily, member 3 205090_s_at −1.30 0.002597 NAGPA N-acetylglucosamine-1-phosphodiester α-N-acetylglucosaminidase 
207277_at 1.65 0.001460 CD209 CD209 Ag 218427_at −1.50 0.002685 SDCCAG3 Serologically defined colon cancer Ag 3 
(Table continues
Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
206181_at 1.42 0.000468 SLAMF1 Signaling lymphocytic activation molecule family member 1 204638_at −1.39 0.000861 ACP5 Acid phosphatase 5, tartrate resistant 
203915_at 1.91 0.000507 CXCL9 Chemokine (C-X-C motif) ligand 9 218855_at −1.51 0.000959 GPR175 Seven transmembrane domain orphan receptor 
208581_x_at 1.94 0.000511 MT1X Metallothionein 1X 204046_at −1.42 0.001080 PLCB2 Phospholipase C,β2 
209803_s_at 1.84 0.000566 PHLDA2 Pleckstrin homology-like domain, family A, member 2 221601_s_at −1.41 0.001082 FAIM3 Fas apoptotic inhibitory molecule 3 
205633_s_at 1.60 0.000591 ALAS1 aminolevulinate, δ-, synthase 1 40225_at −1.34 0.001110 GAK Cyclin G-associated kinase 
221521_s_at 3.50 0.000599 GINS2 DNA replication complex GINS protein Psf2 201185_at −1.53 0.001140 HTRA1 HtrA serine peptidase 1 
204962_s_at 1.76 0.000638 CENPA Centromere protein A, 17 kDa 221579_s_at −1.33 0.001161 NUDT3 Diphosphoinositol polyphosphate phosphohydrolase 
207113_s_at 1.81 0.000638 TNF TNF (TNF superfamily, member 2) 221675_s_at −1.48 0.001196 CHPT1 Choline phosphotransferase 1 
205126_at 1.45 0.000693 VRK2 Vaccinia-related kinase 2 217963_s_at −1.63 0.001204 NGFRAP1 Nerve growth factor receptor (TNFR superfamily16)-associated protein 1 
209642_at 2.16 0.000754 BUB1 BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast) 218555_at −1.47 0.001284 ANAPC2 Anaphase-promoting complex subunit 2 
205488_at 1.59 0.000755 GZMA Granzyme A (granzyme 1, cytotoxic T lymphocyte-associated serine esterase 3) 219452_at −2.48 0.001417 DPEP2 Dipeptidase 2 
202953_at 1.59 0.000775 C1QB complement component 1, q subcomponent, B chain 35626_at −1.32 0.001587 SGSH N-sulfoglucosamine sulfohydrolase (sulfamidase) 
209267_s_at 1.68 0.000802 SLC39A8 Solute carrier family 39 (zinc transporter), member 8 201819_at −1.35 0.001596 SCARB1 Scavenger receptor class B, member 1 
204326_x_at 1.77 0.000952 MT1X Metallothionein 1X 211110_s_at −2.00 0.001806 AR Androgen receptor (dihydrotestosterone receptor; testicular feminization; spinal and bulbar muscular atrophy; Kennedy disease) 
205992_s_at 1.32 0.000979 IL15 IL-15 209774_x_at −1.76 0.002054 CXCL2 Chemokine (C-X-C motif) ligand 2 
205174_s_at 2.29 0.001056 QPCT Glutaminyl-peptide cyclotransferase (glutaminyl cyclase) 206608_s_at −1.36 0.002175 RPGRIP1 Retinitis pigmentosa GRPase regulator interacting protein 1 
219960_s_at 1.30 0.001160 UCHL5 Ubiquitin carboxyl-terminal hydrolase l5 204949_at −1.34 0.002253 ICAM3 ICAM3 
208864_s_at 1.34 0.001162 TXN thioredoxin 214414_x_at −1.59 0.002301 HBA2 Hemoglobin, α1 
203213_at 2.50 0.001193 CDC2 Cell division cycle 2, G1 to S and G2 to M 219549_s_at −1.32 0.002316 RTN3 Reticulon 3 
210229_s_at 3.34 0.001253 CSF2 CSF2 (granulocyte-macrophage) 205382_s_at −1.84 0.002559 CFD Complement factor C (adipsin) 
205676_at 2.38 0.001331 CYP27B1 Cytochrome p450, family 27, subfamily B, polypeptide 1 216092_s_at −1.48 0.002565 SLC7A8 Solute carrier family 7 (cationic amino acid transporter, y+ system), member 8 
217979_at 1.51 0.001398 TSPAN13 Tetraspanin 13 202449_s_at −1.31 0.002571 RXRA Retinoid X receptor, α 
202421_at 1.59 0.001460 IGSF3 Ig superfamily, member 3 205090_s_at −1.30 0.002597 NAGPA N-acetylglucosamine-1-phosphodiester α-N-acetylglucosaminidase 
207277_at 1.65 0.001460 CD209 CD209 Ag 218427_at −1.50 0.002685 SDCCAG3 Serologically defined colon cancer Ag 3 
(Table continues
Table IIIC.

(Continued)

Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
205505_at 1.54 0.001515 GCNT1 Glucosaminyl (N-acetyl) transferase 1, core 2 (β -1,6-N-acetylglucosaminyl-transferase) 207105_s_at −1.49 0.002882 PIK3R2 PI3K, regulatory subunit 2 (p85 β) 
211269_s_at 1.51 0.001562 IL2RA IL-2Rα 212346_s_at −1.38 0.002913 MXD4 MAX dimerization protein 4 
220358_at 2.21 0.001584 SNFT Jun dimerization protein p21SNFT 212552_at −1.32 0.002917 HPCAL1 hippocalcin-like 1 
209825_s_at 1.57 0.001612 UCK2 Uridine-cytidine kinase 2 201427_s_at −4.80 0.002990 SEPP1 Selenoprotein P, plasma, 1 
207900_at 2.43 0.001637 CCL17 Chemokine (C-C motif) ligand 17 209409_at −1.50 0.002998 GRB10 Growth factor receptor-bound protein 10 
205890_s_at 2.17 0.001649 GABBR1 /// UBD Ubiquitin D 207574_s_at −1.31 0.003015 GADD45B Growth arrest and DNA-damage-inducible, β 
201897_s_at 1.45 0.001660 CKS1B CDC28 protein kinase regulatory subunit 1B 200710_at −1.38 0.003071 ACADVL Acyl-coenzyme A dehydrogenase, very long chain 
203200_s_at 1.36 0.001691 MTRR 5-methyltetrahydrofolate-homocysteine methyltransferase reductase 206471_s_at −1.58 0.003112 PLXNC1 Plexin C1 
201013_s_at 1.33 0.001713 PAICS Phosphoribosylamino-imidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase 205466_s_at −2.39 0.003130 HS3ST1 Heparan sulfate (glucosamine) 3-O-sulfotransferase 1 
221331_x_at 2.49 0.001713 CTLA4 Cytotoxic T lymphocyte-associated protein 4 210980_s_at −1.39 0.003134 ASAH1 N-acylsphingosine amidohydrolase (acid ceramidase) 1 
37145_at 1.31 0.001870 GNLY Granulysin 200965_s_at −1.37 0.003340 ABLIM1 Actin-binding LIM protein 1 
207849_at 3.91 0.001871 IL2 IL-2 204955_at −1.40 0.003354 SRPX Sushi-repeat-containing protein, X-linked 
202675_at 1.35 0.001876 SDHB Succinate dehydrogenase complex, subunit B, iron sulfur (Ip) 202481_at −1.31 0.003365 DHRS3 Dehydrogenase/reductase (SDR family) member 3 
202688_at 1.55 0.001887 TNFSF10 TNF (ligand) superfamily, member 10 205182_s_at −1.86 0.003400 ZNF324 Zinc finger protein 324 
204924_at 1.36 0.001944 TLR2 TLR2 205683_x_at, 207741_x_at −2.07 0.003403 TPSAB1 Tryptase, α 
201157_s_at 1.34 0.002035 NMT1 N-myristoyltransferase 1 207826_s_at −1.69 0.003407 ID3 Inhibitor of DNA binding 3, dominant negative helix-loop-helix protein 
209610_s_at 1.49 0.002047 SLC1A4 Solute carrier family 1 (glutamate/neutral amino acid transporter), member 4 221748_s_at −1.41 0.003427 TNS1 Tensin 1 
210001_s_at 1.60 0.002354 SOCS1 Suppressor of cytokine signaling 1 221210_s_at −1.36 0.003450 NPL N-acetylneuraminate pyruvate lyase (dihydrodipicolinate synthase) 
33304_at 1.46 0.002364 ISG20 IFN-stimulated exonuclease gene, 20 kDa 204446_s_at −1.45 0.003510 ALOX5 Arachidonate 5-lipoxygenase 
201625_s_at 1.57 0.002371 INSIG1 Insulin-induced gene 1 206368_at −3.15 0.003566 CPLX2 Complexin 2 
203097_s_at 1.33 0.002475 RAPGEF2 Rap guanine nucleotide exchange factor (GEF) 2 206644_at −2.17 0.003579 NR0B1 Nuclear receptor subfamily 0, group B, member 1 
204279_at 1.39 0.002485 PSMB9 Proteasome (prosome, macropain) subunit, β type, 9 (large multifunctional peptidase 2) 209782_s_at −1.66 0.003585 DBP D site of albumin promoter (albumin D-box)-binding protein 
(Table continues
Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
205505_at 1.54 0.001515 GCNT1 Glucosaminyl (N-acetyl) transferase 1, core 2 (β -1,6-N-acetylglucosaminyl-transferase) 207105_s_at −1.49 0.002882 PIK3R2 PI3K, regulatory subunit 2 (p85 β) 
211269_s_at 1.51 0.001562 IL2RA IL-2Rα 212346_s_at −1.38 0.002913 MXD4 MAX dimerization protein 4 
220358_at 2.21 0.001584 SNFT Jun dimerization protein p21SNFT 212552_at −1.32 0.002917 HPCAL1 hippocalcin-like 1 
209825_s_at 1.57 0.001612 UCK2 Uridine-cytidine kinase 2 201427_s_at −4.80 0.002990 SEPP1 Selenoprotein P, plasma, 1 
207900_at 2.43 0.001637 CCL17 Chemokine (C-C motif) ligand 17 209409_at −1.50 0.002998 GRB10 Growth factor receptor-bound protein 10 
205890_s_at 2.17 0.001649 GABBR1 /// UBD Ubiquitin D 207574_s_at −1.31 0.003015 GADD45B Growth arrest and DNA-damage-inducible, β 
201897_s_at 1.45 0.001660 CKS1B CDC28 protein kinase regulatory subunit 1B 200710_at −1.38 0.003071 ACADVL Acyl-coenzyme A dehydrogenase, very long chain 
203200_s_at 1.36 0.001691 MTRR 5-methyltetrahydrofolate-homocysteine methyltransferase reductase 206471_s_at −1.58 0.003112 PLXNC1 Plexin C1 
201013_s_at 1.33 0.001713 PAICS Phosphoribosylamino-imidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase 205466_s_at −2.39 0.003130 HS3ST1 Heparan sulfate (glucosamine) 3-O-sulfotransferase 1 
221331_x_at 2.49 0.001713 CTLA4 Cytotoxic T lymphocyte-associated protein 4 210980_s_at −1.39 0.003134 ASAH1 N-acylsphingosine amidohydrolase (acid ceramidase) 1 
37145_at 1.31 0.001870 GNLY Granulysin 200965_s_at −1.37 0.003340 ABLIM1 Actin-binding LIM protein 1 
207849_at 3.91 0.001871 IL2 IL-2 204955_at −1.40 0.003354 SRPX Sushi-repeat-containing protein, X-linked 
202675_at 1.35 0.001876 SDHB Succinate dehydrogenase complex, subunit B, iron sulfur (Ip) 202481_at −1.31 0.003365 DHRS3 Dehydrogenase/reductase (SDR family) member 3 
202688_at 1.55 0.001887 TNFSF10 TNF (ligand) superfamily, member 10 205182_s_at −1.86 0.003400 ZNF324 Zinc finger protein 324 
204924_at 1.36 0.001944 TLR2 TLR2 205683_x_at, 207741_x_at −2.07 0.003403 TPSAB1 Tryptase, α 
201157_s_at 1.34 0.002035 NMT1 N-myristoyltransferase 1 207826_s_at −1.69 0.003407 ID3 Inhibitor of DNA binding 3, dominant negative helix-loop-helix protein 
209610_s_at 1.49 0.002047 SLC1A4 Solute carrier family 1 (glutamate/neutral amino acid transporter), member 4 221748_s_at −1.41 0.003427 TNS1 Tensin 1 
210001_s_at 1.60 0.002354 SOCS1 Suppressor of cytokine signaling 1 221210_s_at −1.36 0.003450 NPL N-acetylneuraminate pyruvate lyase (dihydrodipicolinate synthase) 
33304_at 1.46 0.002364 ISG20 IFN-stimulated exonuclease gene, 20 kDa 204446_s_at −1.45 0.003510 ALOX5 Arachidonate 5-lipoxygenase 
201625_s_at 1.57 0.002371 INSIG1 Insulin-induced gene 1 206368_at −3.15 0.003566 CPLX2 Complexin 2 
203097_s_at 1.33 0.002475 RAPGEF2 Rap guanine nucleotide exchange factor (GEF) 2 206644_at −2.17 0.003579 NR0B1 Nuclear receptor subfamily 0, group B, member 1 
204279_at 1.39 0.002485 PSMB9 Proteasome (prosome, macropain) subunit, β type, 9 (large multifunctional peptidase 2) 209782_s_at −1.66 0.003585 DBP D site of albumin promoter (albumin D-box)-binding protein 
(Table continues
Table IIID.

(Continued)

Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
204929_s_at 1.66 0.002546 VAMP5 Vesicle-associated membrane protein 5 (myobrevin) 203803_at −3.43 0.003661 PCYOX1 prenylcysteine oxidase 1 
205159_at 1.40 0.002596 CSF2RB CSF2R, β, low affinity (granulocyte-macrophage) 205728_at −2.76 0.003665 ODZ1 Odz, odd Oz/ten-m homolog 1 (Drosophila
204033_at 1.61 0.002694 TRIP13 Thyroid hormone receptor interactor 13 209355_s_at −1.80 0.003724 PPAP2B Phosphatidic acid phosphatase type 2B 
207500_at 2.31 0.002995 CASP5 Caspase 5, apoptosis-related cysteine peptidase 202790_at −2.17 0.003926 CLDN7 Claudin 7 
204103_at 1.47 0.002996 CCL4 Chemokine (C-C motif) ligand 4 213553_x_at −1.83 0.004021 APOC1 Apolipoprotein C-I 
205220_at 2.72 0.003027 GPR109B G protein-coupled receptor 109G 220491_at −1.57 0.004027 HAMP Hepcidin antimicrobial peptide 
216834_at 2.24 0.003485 RGS1 Regulator of G-protein signaling 1 204359_at −1.83 0.004188 FLRT2 Fibronectin leucine-rich transmembrane protein 2 
206745_at 1.80 0.003645 HOXC11 Homeobox C11 217807_s_at −1.48 0.004252 GLTSCR2 Glioma tumor suppressor candidate region gene 2 
204254_s_at 1.58 0.003671 VDR Vitamin D (1,25-dihydroxyvitamin D3) receptor 219952_s_at −1.51 0.004269 MCOLN1 Mucolipin 1 
200054_at 1.34 0.003724 ZNF259 Zinc finger protein 259 214369_s_at −1.36 0.004357 RASGRP2 RAS guanyl releasing protein 2 (calcium and DAG-regulated) 
202267_at 2.48 0.003954 LAMC2 Laminin, γ2 209616_s_at −1.96 0.004451 CES1 Carboxylesterase 1 (monocyte/macrophage serine esterase 1) 
207952_at 4.12 0.003994 IL5 IL-5 (CSF, eosinophil) 203167_at −1.53 0.004531 TIMP2 TIMP metallopeptidase inhibitor 2 
208450_at 3.03 0.004025 LGALS2 Lectin, galactoside-binding, soluble, 2 (galectin 2) 218718_at −1.74 0.004611 PDGFC Spinal cord-derived growth factor; secretory growth factor-like protein fallotein 
218239_s_at 1.38 0.004091 GTPBP4 GTP-binding protein 4 205222_at −2.53 0.004683 EHHADH Enoyl-coenzyme A, hydratase/3-hydroxyacyl coenzyme A dehydrogenase 
210511_s_at 5.01 0.004176 INHBA Inhibin, β A (activin A, activin AB α polypeptide) 204394_at −1.37 0.004684 SLC43A1 Solute carrier family 43, member 1 
210015_s_at 2.32 0.004275 MAP2 Microtubule-associated protein 2 40569_at −1.30 0.004743 ZNF42 Zinc finger protein 42 (myeloid-specific retinoic acid-responsive) 
201292_at 2.09 0.004316 TOP2A Topoisomerase (DNA) II α, 170 kDa 219267_at −1.41 0.004851 GLTP Glycolipid transfer protein 
202847_at 1.30 0.004351 PCK2 Phosphoenolpyruvate carboxykinase 2 (mitochondrial) 206339_at −1.71 0.004861 CART Cocaine- and amphetamine-regulated transcript 
206632_s_at 1.59 0.004372 APOBEC3B Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B 221364_at −2.28 0.004933 GRID2 Glutamate receptor, ionotropic, δ2 
208002_s_at 1.43 0.004425 ACOT7 Acyl-CoA thioesterase 7 214132_at −1.36 0.004975 ATP5C1 ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1 
202252_at 1.33 0.004492 RAB13 RAB13, member RAS oncogene family 202391_at −1.37 0.005083 BASP1 Brain-abundant, membrane-attached signal protein 1 
205242_at 3.37 0.004539 CXCL13 Chemokine (C-X-X motif) ligand 13 (B cell chemoattractant) 209990_s_at −2.51 0.005271 GABBR2 γ -Aminobutyric acid (GABA) B receptor, 2 
206513_at 1.37 0.004563 AIM2 Absent in melanoma 2 207345_at −1.94 0.005697 FST Follistatin 
204580_at 2.69 0.004759 MMP12 Matrix metallopeptidase 12 (macrophage elastase) 214743_at −1.35 0.005728 CUTL1 Cut-like 1, CCAAT displacement protein (Drosophila
(Table continues
Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
204929_s_at 1.66 0.002546 VAMP5 Vesicle-associated membrane protein 5 (myobrevin) 203803_at −3.43 0.003661 PCYOX1 prenylcysteine oxidase 1 
205159_at 1.40 0.002596 CSF2RB CSF2R, β, low affinity (granulocyte-macrophage) 205728_at −2.76 0.003665 ODZ1 Odz, odd Oz/ten-m homolog 1 (Drosophila
204033_at 1.61 0.002694 TRIP13 Thyroid hormone receptor interactor 13 209355_s_at −1.80 0.003724 PPAP2B Phosphatidic acid phosphatase type 2B 
207500_at 2.31 0.002995 CASP5 Caspase 5, apoptosis-related cysteine peptidase 202790_at −2.17 0.003926 CLDN7 Claudin 7 
204103_at 1.47 0.002996 CCL4 Chemokine (C-C motif) ligand 4 213553_x_at −1.83 0.004021 APOC1 Apolipoprotein C-I 
205220_at 2.72 0.003027 GPR109B G protein-coupled receptor 109G 220491_at −1.57 0.004027 HAMP Hepcidin antimicrobial peptide 
216834_at 2.24 0.003485 RGS1 Regulator of G-protein signaling 1 204359_at −1.83 0.004188 FLRT2 Fibronectin leucine-rich transmembrane protein 2 
206745_at 1.80 0.003645 HOXC11 Homeobox C11 217807_s_at −1.48 0.004252 GLTSCR2 Glioma tumor suppressor candidate region gene 2 
204254_s_at 1.58 0.003671 VDR Vitamin D (1,25-dihydroxyvitamin D3) receptor 219952_s_at −1.51 0.004269 MCOLN1 Mucolipin 1 
200054_at 1.34 0.003724 ZNF259 Zinc finger protein 259 214369_s_at −1.36 0.004357 RASGRP2 RAS guanyl releasing protein 2 (calcium and DAG-regulated) 
202267_at 2.48 0.003954 LAMC2 Laminin, γ2 209616_s_at −1.96 0.004451 CES1 Carboxylesterase 1 (monocyte/macrophage serine esterase 1) 
207952_at 4.12 0.003994 IL5 IL-5 (CSF, eosinophil) 203167_at −1.53 0.004531 TIMP2 TIMP metallopeptidase inhibitor 2 
208450_at 3.03 0.004025 LGALS2 Lectin, galactoside-binding, soluble, 2 (galectin 2) 218718_at −1.74 0.004611 PDGFC Spinal cord-derived growth factor; secretory growth factor-like protein fallotein 
218239_s_at 1.38 0.004091 GTPBP4 GTP-binding protein 4 205222_at −2.53 0.004683 EHHADH Enoyl-coenzyme A, hydratase/3-hydroxyacyl coenzyme A dehydrogenase 
210511_s_at 5.01 0.004176 INHBA Inhibin, β A (activin A, activin AB α polypeptide) 204394_at −1.37 0.004684 SLC43A1 Solute carrier family 43, member 1 
210015_s_at 2.32 0.004275 MAP2 Microtubule-associated protein 2 40569_at −1.30 0.004743 ZNF42 Zinc finger protein 42 (myeloid-specific retinoic acid-responsive) 
201292_at 2.09 0.004316 TOP2A Topoisomerase (DNA) II α, 170 kDa 219267_at −1.41 0.004851 GLTP Glycolipid transfer protein 
202847_at 1.30 0.004351 PCK2 Phosphoenolpyruvate carboxykinase 2 (mitochondrial) 206339_at −1.71 0.004861 CART Cocaine- and amphetamine-regulated transcript 
206632_s_at 1.59 0.004372 APOBEC3B Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B 221364_at −2.28 0.004933 GRID2 Glutamate receptor, ionotropic, δ2 
208002_s_at 1.43 0.004425 ACOT7 Acyl-CoA thioesterase 7 214132_at −1.36 0.004975 ATP5C1 ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1 
202252_at 1.33 0.004492 RAB13 RAB13, member RAS oncogene family 202391_at −1.37 0.005083 BASP1 Brain-abundant, membrane-attached signal protein 1 
205242_at 3.37 0.004539 CXCL13 Chemokine (C-X-X motif) ligand 13 (B cell chemoattractant) 209990_s_at −2.51 0.005271 GABBR2 γ -Aminobutyric acid (GABA) B receptor, 2 
206513_at 1.37 0.004563 AIM2 Absent in melanoma 2 207345_at −1.94 0.005697 FST Follistatin 
204580_at 2.69 0.004759 MMP12 Matrix metallopeptidase 12 (macrophage elastase) 214743_at −1.35 0.005728 CUTL1 Cut-like 1, CCAAT displacement protein (Drosophila
(Table continues
Table IIIE.

(Continued)

Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
220865_s_at 1.37 0.004829 PDSS1 Prenyl (decaprenyl) diphosphate synthase, subunit 1 213812_s_at −1.38 0.006040 CAMKK2 Calcium/calmodulin-dependent protein kinase kinase 2, β 
219761_at 2.14 0.004855 CLEC1A C-type lectin domain family 1, member A 205486_at −1.33 0.006059 TESK2 Testis-specific kinase 2 
206749_at 2.91 0.004909 CD1B CD1B Ag 203136_at −1.60 0.006081 RABAC1 Rab acceptor 1 (prenylated) 
201170_s_at 1.38 0.004946 BHLHB2 Basic helix-loop-helix domain containing, class B, 2 204131_s_at −1.51 0.006086 FOXO3A Forkhead box O3A 
218866_s_at 1.42 0.004968 POLR3K Polymerase (RNA) III (DNA directed) polypeptide K, 12.3 kDa 209158_s_at −1.35 0.006206 PSCD2 Pleckstrin homology, Sec7 and coiled-coil domains 2 (cytohesin-2) 
201798_s_at 1.34 0.005042 FER1L3 Fer-1-like 3, myoferlin (C. elegans221246_x_at, 221748_s_at −1.42 0.006314 TNS1 Tensin 1 
200629_at 1.50 0.005046 WARS IFN-induced protein 53 202108_at −1.30 0.006356 PEPD Peptidase d 
213415_at 1.90 0.005165 CLIC2 Chloride intracellular channel 2 204360_s_at −1.44 0.006377 NAGLU N-acetylglucosaminidase, α-(Sanfilippo disease iiib) 
203275_at 1.32 0.005360 IRF2 IFN regulatory factor 2 217865_at −1.32 0.006628 RNF130 Ring finger protein 130 
214512_s_at 1.38 0.005550 SUB1 SUB1 homolog (S. cerevisiae219371_s_at −1.53 0.006725 KLF2 Kruppel-like factor 2 (lung) 
206461_x_at 1.51 0.005684 MT1H Metallothionein 1H 202256_at −1.46 0.007049 CD2BP2 CD2 Ag (cytoplasmic tail) binding protein 2 
211333_s_at 1.48 0.005789 FASLG Fas ligand (TNF superfamily, member 6) 211145_x_at −2.22 0.007309 IFNA21 IFN, α21 
210538_s_at 1.45 0.005790 BIRC3 Baculoviral IAP repeat-containing 3 221649_s_at −1.35 0.007423 PPAN Peter pan homolog (Drosophila
204224_s_at 1.49 0.006013 GCH1 GTP cyclohydrolase 1 (dopa-responsive dystonia) 221378_at −1.31 0.007478 CER1 Cerberus 1, cysteine knot superfamily, homolog (Xenopus laevis
203564_at 1.52 0.006110 FANCG Fanconi anemia, complementation group G 206171_at −1.51 0.007505 ADORA3 Adenosine A3 receptor 
207586_at 2.08 0.006245 SHH Sonic hedgehog homolog (Drosophila205206_at −1.72 0.007576 KAL1 Kallmann syndrome 1 sequence 
221463_at 2.63 0.006382 CCL24 Chemokine (C-C motif) ligand 24 203414_at −1.38 0.007979 MMD Monocyte to macrophage differentiation-associated 
204748_at 2.60 0.006552 PTGS2 Prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) 209541_at −1.76 0.008232 IGF1 Insulin-like growth factor 1 (somatomedin C) 
202743_at 1.39 0.006584 PIK3R3 PI3K, regulatory subunit 3 (p55, γ) 221065_s_at −1.81 0.008237 CHST8 Carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 8 
209785_s_at 1.35 0.006692 PLA2G4C Phospholipase A2, group IVC (cytosolic, calcium-independent) 208610_s_at −1.41 0.008280 SRRM2 Serine/arginine repetitive matrix 2 
206975_at 3.99 0.006853 LTA Lymphotoxin α (TNF superfamily, member 1) 213592_at −1.91 0.008299 AGTRL1 Angiotensin II receptor-like 1 
202499_s_at 1.39 0.006958 SLC2A3 Solute carrier family 2 (facilitated glucose transporter), member 3 201141_at −1.44 0.008837 GPNMB Glycoprotein (transmembrane) NMB 
201329_s_at 1.49 0.006989 ETS2 V-ets erythroblastosis virus e26 oncogene homolog 2 (avian) 220068_at −2.11 0.009019 VPREB3 Pre-B lymphocyte gene 3 
204205_at 1.35 0.007064 APOBEC3G Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G 201186_at −1.39 0.009581 LRPAP1 Low-density lipoprotein receptor-related protein-associated protein 1 
(Table continues
Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
220865_s_at 1.37 0.004829 PDSS1 Prenyl (decaprenyl) diphosphate synthase, subunit 1 213812_s_at −1.38 0.006040 CAMKK2 Calcium/calmodulin-dependent protein kinase kinase 2, β 
219761_at 2.14 0.004855 CLEC1A C-type lectin domain family 1, member A 205486_at −1.33 0.006059 TESK2 Testis-specific kinase 2 
206749_at 2.91 0.004909 CD1B CD1B Ag 203136_at −1.60 0.006081 RABAC1 Rab acceptor 1 (prenylated) 
201170_s_at 1.38 0.004946 BHLHB2 Basic helix-loop-helix domain containing, class B, 2 204131_s_at −1.51 0.006086 FOXO3A Forkhead box O3A 
218866_s_at 1.42 0.004968 POLR3K Polymerase (RNA) III (DNA directed) polypeptide K, 12.3 kDa 209158_s_at −1.35 0.006206 PSCD2 Pleckstrin homology, Sec7 and coiled-coil domains 2 (cytohesin-2) 
201798_s_at 1.34 0.005042 FER1L3 Fer-1-like 3, myoferlin (C. elegans221246_x_at, 221748_s_at −1.42 0.006314 TNS1 Tensin 1 
200629_at 1.50 0.005046 WARS IFN-induced protein 53 202108_at −1.30 0.006356 PEPD Peptidase d 
213415_at 1.90 0.005165 CLIC2 Chloride intracellular channel 2 204360_s_at −1.44 0.006377 NAGLU N-acetylglucosaminidase, α-(Sanfilippo disease iiib) 
203275_at 1.32 0.005360 IRF2 IFN regulatory factor 2 217865_at −1.32 0.006628 RNF130 Ring finger protein 130 
214512_s_at 1.38 0.005550 SUB1 SUB1 homolog (S. cerevisiae219371_s_at −1.53 0.006725 KLF2 Kruppel-like factor 2 (lung) 
206461_x_at 1.51 0.005684 MT1H Metallothionein 1H 202256_at −1.46 0.007049 CD2BP2 CD2 Ag (cytoplasmic tail) binding protein 2 
211333_s_at 1.48 0.005789 FASLG Fas ligand (TNF superfamily, member 6) 211145_x_at −2.22 0.007309 IFNA21 IFN, α21 
210538_s_at 1.45 0.005790 BIRC3 Baculoviral IAP repeat-containing 3 221649_s_at −1.35 0.007423 PPAN Peter pan homolog (Drosophila
204224_s_at 1.49 0.006013 GCH1 GTP cyclohydrolase 1 (dopa-responsive dystonia) 221378_at −1.31 0.007478 CER1 Cerberus 1, cysteine knot superfamily, homolog (Xenopus laevis
203564_at 1.52 0.006110 FANCG Fanconi anemia, complementation group G 206171_at −1.51 0.007505 ADORA3 Adenosine A3 receptor 
207586_at 2.08 0.006245 SHH Sonic hedgehog homolog (Drosophila205206_at −1.72 0.007576 KAL1 Kallmann syndrome 1 sequence 
221463_at 2.63 0.006382 CCL24 Chemokine (C-C motif) ligand 24 203414_at −1.38 0.007979 MMD Monocyte to macrophage differentiation-associated 
204748_at 2.60 0.006552 PTGS2 Prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) 209541_at −1.76 0.008232 IGF1 Insulin-like growth factor 1 (somatomedin C) 
202743_at 1.39 0.006584 PIK3R3 PI3K, regulatory subunit 3 (p55, γ) 221065_s_at −1.81 0.008237 CHST8 Carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 8 
209785_s_at 1.35 0.006692 PLA2G4C Phospholipase A2, group IVC (cytosolic, calcium-independent) 208610_s_at −1.41 0.008280 SRRM2 Serine/arginine repetitive matrix 2 
206975_at 3.99 0.006853 LTA Lymphotoxin α (TNF superfamily, member 1) 213592_at −1.91 0.008299 AGTRL1 Angiotensin II receptor-like 1 
202499_s_at 1.39 0.006958 SLC2A3 Solute carrier family 2 (facilitated glucose transporter), member 3 201141_at −1.44 0.008837 GPNMB Glycoprotein (transmembrane) NMB 
201329_s_at 1.49 0.006989 ETS2 V-ets erythroblastosis virus e26 oncogene homolog 2 (avian) 220068_at −2.11 0.009019 VPREB3 Pre-B lymphocyte gene 3 
204205_at 1.35 0.007064 APOBEC3G Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G 201186_at −1.39 0.009581 LRPAP1 Low-density lipoprotein receptor-related protein-associated protein 1 
(Table continues
Table IIIF.

(Continued)

Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
218039_at 1.35 0.007138 NUSAP1 Nucleolar and spindle-associated protein 1 204824_at −1.56 0.009682 ENDOG Endonuclease G 
214567_s_at 1.51 0.007306 XCL1 /// XCL2 Chemokine (C motif) ligand 2, chemokine (C motif) ligand 1 220762_s_at −1.46 0.009853 GNB1L Guanine nucleotide-binding protein (G protein), β polypeptide 1-like 
206278_at 1.46 0.007320 PTAFR Platelet-activating factor receptor 209215_at −1.33 0.009935 TETRAN Tetracycline transporter-like protein 
204026_s_at 1.35 0.007406 ZWINT ZW10 interactor 219963_at −1.60 0.010000 DUSP13 Dual specificity phosphatase 13 
211138_s_at 1.42 0.007457 KMO Kynurenine 3-monooxygenase (kynurenine 3-hydroxylase) 202838_at −2.05 0.010039 FUCA1 fucosidase, α-L-1, tissue 
201948_at 1.48 0.007689 GNL2 Guanine nucleotide-binding protein-like 2 (nucleolar) 202477_s_at −1.36 0.010213 TUBGCP2 Tubulin, γ complex-associated protein 2 
202284_s_at 1.51 0.007786 CDKN1A Cyclin-dependent kinase inhibitor 1a (p21, Cip1) 206739_at −2.24 0.010378 HOXC5 Homeobox C5 
202357_s_at 1.82 0.007826 CFB Complement factor B 203113_s_at −1.53 0.010380 EEF1D Eukaryotic translation elongation factor 1 δ (guanine nucleotide exchange protein) 
214022_s_at 1.35 0.007980 IFITM1 IFN-induced transmembrane protein 1 (9–27) 210123_s_at −2.12 0.010514 CHRNA7 /// CHRFAM7A /// LOC652740 Cholinergic receptor, nicotinic, α 7 
203975_s_at 1.54 0.008000 CHAF1A Chromatin assembly factor 1, subunit A (p150) 32837_at −1.34 0.010565 AGPAT2 1-Acylglycerol-3-phosphate-O-acyltransferase 2 (lysophosphatidic acid acyltransferase, β) 
206547_s_at 2.70 0.008057 PPEF1 Protein phosphatase, EF-hand calcium-binding domain 1 217969_at −1.34 0.010748 C11orf2 Chromosome 11 open reading frame 2 
208075_s_at 2.35 0.008074 CCL7 Chemokine (C-C motif) ligand 7 204862_s_at −1.38 0.010803 NME3 Nonmetastatic cells 3, protein expressed in 
206508_at 2.28 0.008142 TNFSF7 TNF (ligand) superfamily, member 7 210205_at −1.35 0.010859 B3GALT4 UDP-Gal:β GlcNAc β 1,3-galactosyltransferase, polypeptide 4 
35150_at 1.63 0.008147 CD40 CD40 Ag (TNF receptor superfamily member 5) 203980_at −1.83 0.011023 FABP4 Fatty acid binding protein 4, adipocyte 
204070_at 1.33 0.008335 RARRES3 Retinoic acid receptor responder (tazarotene induced) 3 202201_at −1.44 0.011165 BLVRB Biliverdin reductase B (flavin reductase (NADPH)) 
204440_at 1.31 0.008599 CD83 CD83 Ag (activated B lymphocytes, Ig superfamily) 217983_s_at −1.53 0.011188 RNASET2 Ribonuclease T2 
209392_at 1.57 0.008806 ENPP2 Ectonucleotide pyrophosphatase/phosphodiesterase 2 (autotaxin) 209236_at −1.34 0.011251 SLC23A2 Solute carrier family 23 (nucleobase transporters), member 2 
214933_at 1.36 0.008923 CACNA1A Calcium channel, voltage-dependent, P/Q type, α 1A subunit 221116_at −2.18 0.011341 PPARL Pparl 
205266_at 2.00 0.009015 LIF Leukemia inhibitory factor (cholinergic differentiation factor) 207839_s_at −1.33 0.012331 C9orf127 Chromosome 9 open reading frame 127 
201614_s_at 1.35 0.009016 RUVBL1 RuvB-like 1 (E. coli201820_at −2.00 0.012345 KRT5 Keratin 4 
218662_s_at 1.65 0.009357 HCAP-G Chromosome condensation protein G 221830_at −1.38 0.012420 RAP2A RAP2A, member of RAS oncogene family 
220665_at 2.32 0.009580 LUZP4 Leucine zipper protein 4 204749_at −2.44 0.012608 NAP1L3 Nucleosome assembly protein 1-like 3 
(Table continues
Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
218039_at 1.35 0.007138 NUSAP1 Nucleolar and spindle-associated protein 1 204824_at −1.56 0.009682 ENDOG Endonuclease G 
214567_s_at 1.51 0.007306 XCL1 /// XCL2 Chemokine (C motif) ligand 2, chemokine (C motif) ligand 1 220762_s_at −1.46 0.009853 GNB1L Guanine nucleotide-binding protein (G protein), β polypeptide 1-like 
206278_at 1.46 0.007320 PTAFR Platelet-activating factor receptor 209215_at −1.33 0.009935 TETRAN Tetracycline transporter-like protein 
204026_s_at 1.35 0.007406 ZWINT ZW10 interactor 219963_at −1.60 0.010000 DUSP13 Dual specificity phosphatase 13 
211138_s_at 1.42 0.007457 KMO Kynurenine 3-monooxygenase (kynurenine 3-hydroxylase) 202838_at −2.05 0.010039 FUCA1 fucosidase, α-L-1, tissue 
201948_at 1.48 0.007689 GNL2 Guanine nucleotide-binding protein-like 2 (nucleolar) 202477_s_at −1.36 0.010213 TUBGCP2 Tubulin, γ complex-associated protein 2 
202284_s_at 1.51 0.007786 CDKN1A Cyclin-dependent kinase inhibitor 1a (p21, Cip1) 206739_at −2.24 0.010378 HOXC5 Homeobox C5 
202357_s_at 1.82 0.007826 CFB Complement factor B 203113_s_at −1.53 0.010380 EEF1D Eukaryotic translation elongation factor 1 δ (guanine nucleotide exchange protein) 
214022_s_at 1.35 0.007980 IFITM1 IFN-induced transmembrane protein 1 (9–27) 210123_s_at −2.12 0.010514 CHRNA7 /// CHRFAM7A /// LOC652740 Cholinergic receptor, nicotinic, α 7 
203975_s_at 1.54 0.008000 CHAF1A Chromatin assembly factor 1, subunit A (p150) 32837_at −1.34 0.010565 AGPAT2 1-Acylglycerol-3-phosphate-O-acyltransferase 2 (lysophosphatidic acid acyltransferase, β) 
206547_s_at 2.70 0.008057 PPEF1 Protein phosphatase, EF-hand calcium-binding domain 1 217969_at −1.34 0.010748 C11orf2 Chromosome 11 open reading frame 2 
208075_s_at 2.35 0.008074 CCL7 Chemokine (C-C motif) ligand 7 204862_s_at −1.38 0.010803 NME3 Nonmetastatic cells 3, protein expressed in 
206508_at 2.28 0.008142 TNFSF7 TNF (ligand) superfamily, member 7 210205_at −1.35 0.010859 B3GALT4 UDP-Gal:β GlcNAc β 1,3-galactosyltransferase, polypeptide 4 
35150_at 1.63 0.008147 CD40 CD40 Ag (TNF receptor superfamily member 5) 203980_at −1.83 0.011023 FABP4 Fatty acid binding protein 4, adipocyte 
204070_at 1.33 0.008335 RARRES3 Retinoic acid receptor responder (tazarotene induced) 3 202201_at −1.44 0.011165 BLVRB Biliverdin reductase B (flavin reductase (NADPH)) 
204440_at 1.31 0.008599 CD83 CD83 Ag (activated B lymphocytes, Ig superfamily) 217983_s_at −1.53 0.011188 RNASET2 Ribonuclease T2 
209392_at 1.57 0.008806 ENPP2 Ectonucleotide pyrophosphatase/phosphodiesterase 2 (autotaxin) 209236_at −1.34 0.011251 SLC23A2 Solute carrier family 23 (nucleobase transporters), member 2 
214933_at 1.36 0.008923 CACNA1A Calcium channel, voltage-dependent, P/Q type, α 1A subunit 221116_at −2.18 0.011341 PPARL Pparl 
205266_at 2.00 0.009015 LIF Leukemia inhibitory factor (cholinergic differentiation factor) 207839_s_at −1.33 0.012331 C9orf127 Chromosome 9 open reading frame 127 
201614_s_at 1.35 0.009016 RUVBL1 RuvB-like 1 (E. coli201820_at −2.00 0.012345 KRT5 Keratin 4 
218662_s_at 1.65 0.009357 HCAP-G Chromosome condensation protein G 221830_at −1.38 0.012420 RAP2A RAP2A, member of RAS oncogene family 
220665_at 2.32 0.009580 LUZP4 Leucine zipper protein 4 204749_at −2.44 0.012608 NAP1L3 Nucleosome assembly protein 1-like 3 
(Table continues
Table IIIG.

(Continued)

Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
205570_at 1.31 0.009613 PIP5K2A Phosphatidylinositol-4-phosphate 5-kinase, type II, α 219264_s_at −1.60 0.012642 PPP2R3B Protein phosphatase 2 (formerly 2A), regulatory subunit B”, β 
217892_s_at 1.31 0.009635 LIMA1 LIM domain and actin binding 1 204595_s_at −1.33 0.012951 STC1 Stanniocalcin 1 
204444_at 1.62 0.009826 KIF11 Kinesin family member 11 208013_s_at −1.42 0.013342 ACRV1 Acrosomal vesicle protein 1 
201263_at 1.35 0.009908 TARS Threonyl-tRNA synthetase 200665_s_at −1.82 0.013513 SPARC Secreted protein, acidic, cysteine-rich (osteonectin) 
202068_s_at 1.33 0.010149 LDLR Low-density lipoprotein receptor (familial hypercholesterolemia) 207643_s_at −1.32 0.013568 TNFRSF1A TNFR superfamily, member 1A 
212378_at 1.32 0.010160 GART Phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase 203126_at −1.34 0.013930 IMPA2 Inositol(myo)-1(or 4)-monophosphatase 2 
204959_at 1.31 0.010219 MNDA Myeloid cell nuclear differentiation Ag 221666_s_at −1.31 0.013942 PYCARD PYD and CARD domain containing 
218350_s_at 1.30 0.010640 GMNN Geminin, DNA replication inhibitor 217996_at −1.44 0.014560 PHLDA1 Pleckstrin homology-like domain, family A, member 1 
219255_x_at 1.68 0.010644 IL17RB IL-17RB 219403_s_at −1.44 0.014588 HPSE Heparanase 
205476_at 2.47 0.011419 CCL20 Chemokine (C-C motif) ligand 20 61874_at −1.52 0.014677 C9orf7 Chromosome 9 open reading frame 7 
208892_s_at 1.38 0.011479 DUSP6 Dual specificity phosphatase 6 208130_s_at −1.78 0.014684 TBXAS1 Thromboxane A synthase 1 (platelet, cytochrome p450, family 5, subfamily A) 
204023_at 1.31 0.011734 RFC4 Replication factor C (activator 1) 4, 37 kDa 200785_s_at −1.47 0.014746 LRP1 Low-density lipoprotein-related protein 1 (α-2-macroglobulin receptor) 
220957_at 1.33 0.012024 CTAGE1 Dutaneous T cell lymphoma-associated Ag 1 207117_at −2.16 0.014850 H-plk Krueppel-related zinc finger protein 
203105_s_at 1.34 0.012173 DNM1L Dynamin 1-like 206028_s_at −1.50 0.014914 MERTK cCmer proto-oncogene tyrosine kinase 
220658_s_at 1.56 0.012531 ARNTL2 Aryl hydrocarbon receptor nuclear translocator-like 2 209354_at −1.32 0.014997 TNFRSF14 TNFR superfamily, member 14 (herpesvirus entry mediator) 
204998_s_at 1.34 0.012554 ATF5 Activating transcription factor 5 201064_s_at −1.32 0.015387 PABPC4 Poly(A) binding protein, cytoplasmic 4 (inducible form) 
204170_s_at 1.44 0.013296 CKS2 CDC28 protein kinase regulatory subunit 2 204857_at −1.39 0.015779 MAD1L1 MAD1 mitotic arrest deficient-like 1 (yeast) 
209726_at 1.56 0.013322 CA11 Carbonic anhydrase XI 221287_at −1.84 0.015826 RNASEL Ribonuclease l (2′,5′-oligoisoadenylate synthetase-dependent) 
202069_s_at 1.38 0.013436 IDH3A Isocitrate dehydrogenase 3 (NAD+) α 209185_s_at −1.38 0.016378 IRS2 Insulin receptor substrate 2 
204531_s_at 1.82 0.013582 BRCA1 Breast cancer 1, early onset 220727_at −1.49 0.016475 KCNK10 Potassium channel, subfamily K, member 10 
221209_s_at 1.90 0.013776 OTOR Otoraplin 201785_at −1.97 0.016745 RNASE1 ribonuclease, RNase A family, 1 (pancreatic) 
201315_x_at 1.34 0.014191 IFITM2 IFN-induced transmembrane protein 2 (1–8D) 209458_x_at, 214414_x_at −1.52 0.017735 HBA1 /// HBA2 Hemoglobin, α1 
208881_x_at 1.33 0.014408 IDI1 Isopentenyl-diphosphate δ isomerase 1 201876_at −1.61 0.017903 PON2 Paraoxonase 2 
200886_s_at 1.30 0.014546 PGAM1 /// LOC642969 ///LOC643576 Phosphoglycerate mutase 1 (brain) 216924_s_at −1.97 0.018447 DRD2 Dopamine receptor D2 
203350_at 1.42 0.014818 AP1G1 Adaptor-related protein complex 1, δ1 subunit 206196_s_at −1.81 0.018469 RPIP8 RaP2 interacting protein 8 
(Table continues
Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
205570_at 1.31 0.009613 PIP5K2A Phosphatidylinositol-4-phosphate 5-kinase, type II, α 219264_s_at −1.60 0.012642 PPP2R3B Protein phosphatase 2 (formerly 2A), regulatory subunit B”, β 
217892_s_at 1.31 0.009635 LIMA1 LIM domain and actin binding 1 204595_s_at −1.33 0.012951 STC1 Stanniocalcin 1 
204444_at 1.62 0.009826 KIF11 Kinesin family member 11 208013_s_at −1.42 0.013342 ACRV1 Acrosomal vesicle protein 1 
201263_at 1.35 0.009908 TARS Threonyl-tRNA synthetase 200665_s_at −1.82 0.013513 SPARC Secreted protein, acidic, cysteine-rich (osteonectin) 
202068_s_at 1.33 0.010149 LDLR Low-density lipoprotein receptor (familial hypercholesterolemia) 207643_s_at −1.32 0.013568 TNFRSF1A TNFR superfamily, member 1A 
212378_at 1.32 0.010160 GART Phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase 203126_at −1.34 0.013930 IMPA2 Inositol(myo)-1(or 4)-monophosphatase 2 
204959_at 1.31 0.010219 MNDA Myeloid cell nuclear differentiation Ag 221666_s_at −1.31 0.013942 PYCARD PYD and CARD domain containing 
218350_s_at 1.30 0.010640 GMNN Geminin, DNA replication inhibitor 217996_at −1.44 0.014560 PHLDA1 Pleckstrin homology-like domain, family A, member 1 
219255_x_at 1.68 0.010644 IL17RB IL-17RB 219403_s_at −1.44 0.014588 HPSE Heparanase 
205476_at 2.47 0.011419 CCL20 Chemokine (C-C motif) ligand 20 61874_at −1.52 0.014677 C9orf7 Chromosome 9 open reading frame 7 
208892_s_at 1.38 0.011479 DUSP6 Dual specificity phosphatase 6 208130_s_at −1.78 0.014684 TBXAS1 Thromboxane A synthase 1 (platelet, cytochrome p450, family 5, subfamily A) 
204023_at 1.31 0.011734 RFC4 Replication factor C (activator 1) 4, 37 kDa 200785_s_at −1.47 0.014746 LRP1 Low-density lipoprotein-related protein 1 (α-2-macroglobulin receptor) 
220957_at 1.33 0.012024 CTAGE1 Dutaneous T cell lymphoma-associated Ag 1 207117_at −2.16 0.014850 H-plk Krueppel-related zinc finger protein 
203105_s_at 1.34 0.012173 DNM1L Dynamin 1-like 206028_s_at −1.50 0.014914 MERTK cCmer proto-oncogene tyrosine kinase 
220658_s_at 1.56 0.012531 ARNTL2 Aryl hydrocarbon receptor nuclear translocator-like 2 209354_at −1.32 0.014997 TNFRSF14 TNFR superfamily, member 14 (herpesvirus entry mediator) 
204998_s_at 1.34 0.012554 ATF5 Activating transcription factor 5 201064_s_at −1.32 0.015387 PABPC4 Poly(A) binding protein, cytoplasmic 4 (inducible form) 
204170_s_at 1.44 0.013296 CKS2 CDC28 protein kinase regulatory subunit 2 204857_at −1.39 0.015779 MAD1L1 MAD1 mitotic arrest deficient-like 1 (yeast) 
209726_at 1.56 0.013322 CA11 Carbonic anhydrase XI 221287_at −1.84 0.015826 RNASEL Ribonuclease l (2′,5′-oligoisoadenylate synthetase-dependent) 
202069_s_at 1.38 0.013436 IDH3A Isocitrate dehydrogenase 3 (NAD+) α 209185_s_at −1.38 0.016378 IRS2 Insulin receptor substrate 2 
204531_s_at 1.82 0.013582 BRCA1 Breast cancer 1, early onset 220727_at −1.49 0.016475 KCNK10 Potassium channel, subfamily K, member 10 
221209_s_at 1.90 0.013776 OTOR Otoraplin 201785_at −1.97 0.016745 RNASE1 ribonuclease, RNase A family, 1 (pancreatic) 
201315_x_at 1.34 0.014191 IFITM2 IFN-induced transmembrane protein 2 (1–8D) 209458_x_at, 214414_x_at −1.52 0.017735 HBA1 /// HBA2 Hemoglobin, α1 
208881_x_at 1.33 0.014408 IDI1 Isopentenyl-diphosphate δ isomerase 1 201876_at −1.61 0.017903 PON2 Paraoxonase 2 
200886_s_at 1.30 0.014546 PGAM1 /// LOC642969 ///LOC643576 Phosphoglycerate mutase 1 (brain) 216924_s_at −1.97 0.018447 DRD2 Dopamine receptor D2 
203350_at 1.42 0.014818 AP1G1 Adaptor-related protein complex 1, δ1 subunit 206196_s_at −1.81 0.018469 RPIP8 RaP2 interacting protein 8 
(Table continues
Table IIIH.

(Continued)

Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
204015_s_at 2.04 0.014931 DUSP4 Dual specificity phosphatase 4 207922_s_at −1.31 0.018875 MAEA Macrophage erythroblast attacher 
203805_s_at 1.52 0.015213 FANCA Fanconi anemia, complementation group A 205911_at −1.69 0.018983 PTHR1 Parathyroid hormone receptor 1 
203502_at 1.38 0.015219 BPGM 2,3-Bisphosphoglycerate mutase 203910_at −1.31 0.019419 ARHGAP29 Rho GTPase activating protein 29 
206254_at 1.76 0.015446 EGF Epidermal growth factor (β- urogastrone) 204592_at −1.49 0.019475 DLG4 Discs, large homolog 4 (Drosophila
206096_at 1.39 0.015587 ZNF35 Zinc finger protein 35 (clone HF.10) 205744_at −2.07 0.019498 DOC2A Double C2-like domains, α 
207904_s_at 2.23 0.015741 LNPEP Leucyl/cystinyl aminopeptidase 206623_at −2.16 0.019526 PDE6A Phosphodiesterase 6A, cGMP-specific, rod, α 
208393_s_at 1.31 0.015769 RAD50 RAD50 homolog (S. cerevisiae212191_x_at −1.37 0.019681 RPL13 Ribosomal protein L13 
203276_at 1.49 0.016097 LMNB1 Lamin B1 204561_x_at −1.44 0.019846 APOC2 Apolipoprotein C-II 
206561_s_at 2.20 0.016231 AKR1B10 Aldo-keto reductase family 1, member b11 (aldose reductase-like) 201212_at −1.58 0.019878 LGMN Legumain 
210176_at 1.38 0.016450 TLR1 TLR1 202152_x_at −1.38 0.020121 USF2 Upstream transcription factor 2, c-fos interacting 
219148_at 1.39 0.016529 PBK PDZ binding kinase 208982_at −1.35 0.020229 PECAM1 Platelet/endothelial cell adhesion molecule (CD31 Ag) 
210367_s_at 1.40 0.016595 PTGES PGE synthase 206816_s_at −1.83 0.020456 SPAG8 Sperm-associated Ag 8 
205500_at 1.63 0.016907 C5 Complement component 5 221123_x_at −1.30 0.021205 ZNF395 Hypothetical protein DKFZp434K1210 
210007_s_at 1.45 0.017219 GPD2 Glycerol-3-phosphate dehydrogenase 2 (mitochondrial) 220066_at −1.33 0.021232 CARD15 Caspase recruitment domain family, member 15 
208204_s_at 1.83 0.017264 CAV3 Caveolin 3 219752_at −1.60 0.021342 RASAL1 RAS protein activator like 1 (GAP1 like) 
205403_at 2.46 0.017286 IL1R2 IL-1R, type II 216860_s_at −1.77 0.021418 GDF11 Growth differentiation factor 11 
218854_at 1.47 0.017922 SART2 Squamous cell carcinoma Ag recognized by T cells 2 209030_s_at −1.38 0.021664 IGSF4 Ig superfamily, member 4 
210072_at 1.82 0.017991 CCL19 Chemokine (C-C motif) ligand 19 202187_s_at −1.36 0.021770 PPP2R5A Protein phosphatase 2, regulatory subunit B (B56), α isoform 
203454_s_at 1.34 0.018216 ATOX1 ATX1 antioxidant protein 1 homolog (yeast) 207421_at −2.30 0.022313 CA5A Carbonic anhydrase VA, mitochondrial 
219866_at 2.10 0.018296 CLIC5 Chloride intracellular channel 5 205131_x_at −2.05 0.023117 CLEC11A C-type lectin domain family 11, member A 
214279_s_at 2.24 0.018713 NDRG2 NDRG family member 2 205498_at −2.27 0.023139 GHR Growth hormone receptor 
206682_at 1.46 0.018849 CLEC10A C-type lectin domain family 10, member A 207741_x_at −1.45 0.023415 TPSAB1 /// TPSB2 /// LOC652751 Tryptase β 2 
209714_s_at 1.55 0.019322 CDKN3 Cyclin-dependent kinase inhibitor 3 (CDK2-associated dual specificity phosphatase) 213213_at −1.44 0.023500 DIDO1 Death inducer-obliterator 1 
202518_at 1.30 0.019575 BCL7B B Cell CLL/lymphoma 7B 219799_s_at −1.42 0.023653 DHRS9 Dehydrogenase/reductase (SDR family) member 9 
211367_s_at 1.39 0.019698 CASP1 Caspase 1, apoptosis-related cysteine peptidase (IL-1, β, convertase) 220528_at −2.33 0.023827 VNN3 Vanin 3 
212671_s_at 1.40 0.020228 HLA-DQA1 /// HLA-DQA2 /// LOC650946 MHC, class II, DQ α 1 219607_s_at −1.86 0.024188 MS4A4A Membrane-spanning 4-domains, subfamily A, member 4 
(Table continues
Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
204015_s_at 2.04 0.014931 DUSP4 Dual specificity phosphatase 4 207922_s_at −1.31 0.018875 MAEA Macrophage erythroblast attacher 
203805_s_at 1.52 0.015213 FANCA Fanconi anemia, complementation group A 205911_at −1.69 0.018983 PTHR1 Parathyroid hormone receptor 1 
203502_at 1.38 0.015219 BPGM 2,3-Bisphosphoglycerate mutase 203910_at −1.31 0.019419 ARHGAP29 Rho GTPase activating protein 29 
206254_at 1.76 0.015446 EGF Epidermal growth factor (β- urogastrone) 204592_at −1.49 0.019475 DLG4 Discs, large homolog 4 (Drosophila
206096_at 1.39 0.015587 ZNF35 Zinc finger protein 35 (clone HF.10) 205744_at −2.07 0.019498 DOC2A Double C2-like domains, α 
207904_s_at 2.23 0.015741 LNPEP Leucyl/cystinyl aminopeptidase 206623_at −2.16 0.019526 PDE6A Phosphodiesterase 6A, cGMP-specific, rod, α 
208393_s_at 1.31 0.015769 RAD50 RAD50 homolog (S. cerevisiae212191_x_at −1.37 0.019681 RPL13 Ribosomal protein L13 
203276_at 1.49 0.016097 LMNB1 Lamin B1 204561_x_at −1.44 0.019846 APOC2 Apolipoprotein C-II 
206561_s_at 2.20 0.016231 AKR1B10 Aldo-keto reductase family 1, member b11 (aldose reductase-like) 201212_at −1.58 0.019878 LGMN Legumain 
210176_at 1.38 0.016450 TLR1 TLR1 202152_x_at −1.38 0.020121 USF2 Upstream transcription factor 2, c-fos interacting 
219148_at 1.39 0.016529 PBK PDZ binding kinase 208982_at −1.35 0.020229 PECAM1 Platelet/endothelial cell adhesion molecule (CD31 Ag) 
210367_s_at 1.40 0.016595 PTGES PGE synthase 206816_s_at −1.83 0.020456 SPAG8 Sperm-associated Ag 8 
205500_at 1.63 0.016907 C5 Complement component 5 221123_x_at −1.30 0.021205 ZNF395 Hypothetical protein DKFZp434K1210 
210007_s_at 1.45 0.017219 GPD2 Glycerol-3-phosphate dehydrogenase 2 (mitochondrial) 220066_at −1.33 0.021232 CARD15 Caspase recruitment domain family, member 15 
208204_s_at 1.83 0.017264 CAV3 Caveolin 3 219752_at −1.60 0.021342 RASAL1 RAS protein activator like 1 (GAP1 like) 
205403_at 2.46 0.017286 IL1R2 IL-1R, type II 216860_s_at −1.77 0.021418 GDF11 Growth differentiation factor 11 
218854_at 1.47 0.017922 SART2 Squamous cell carcinoma Ag recognized by T cells 2 209030_s_at −1.38 0.021664 IGSF4 Ig superfamily, member 4 
210072_at 1.82 0.017991 CCL19 Chemokine (C-C motif) ligand 19 202187_s_at −1.36 0.021770 PPP2R5A Protein phosphatase 2, regulatory subunit B (B56), α isoform 
203454_s_at 1.34 0.018216 ATOX1 ATX1 antioxidant protein 1 homolog (yeast) 207421_at −2.30 0.022313 CA5A Carbonic anhydrase VA, mitochondrial 
219866_at 2.10 0.018296 CLIC5 Chloride intracellular channel 5 205131_x_at −2.05 0.023117 CLEC11A C-type lectin domain family 11, member A 
214279_s_at 2.24 0.018713 NDRG2 NDRG family member 2 205498_at −2.27 0.023139 GHR Growth hormone receptor 
206682_at 1.46 0.018849 CLEC10A C-type lectin domain family 10, member A 207741_x_at −1.45 0.023415 TPSAB1 /// TPSB2 /// LOC652751 Tryptase β 2 
209714_s_at 1.55 0.019322 CDKN3 Cyclin-dependent kinase inhibitor 3 (CDK2-associated dual specificity phosphatase) 213213_at −1.44 0.023500 DIDO1 Death inducer-obliterator 1 
202518_at 1.30 0.019575 BCL7B B Cell CLL/lymphoma 7B 219799_s_at −1.42 0.023653 DHRS9 Dehydrogenase/reductase (SDR family) member 9 
211367_s_at 1.39 0.019698 CASP1 Caspase 1, apoptosis-related cysteine peptidase (IL-1, β, convertase) 220528_at −2.33 0.023827 VNN3 Vanin 3 
212671_s_at 1.40 0.020228 HLA-DQA1 /// HLA-DQA2 /// LOC650946 MHC, class II, DQ α 1 219607_s_at −1.86 0.024188 MS4A4A Membrane-spanning 4-domains, subfamily A, member 4 
(Table continues
Table IIII.

(Continued)

Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
203409_at 1.56 0.020373 DDB2 Damage-specific DNA-binding protein 2, 48 kDa 208472_at −1.42 0.024357 ZNFN1A4 Zinc finger protein, subfamily 1A, 4 (Eos) 
200986_at 1.36 0.021457 SERPING1 Serpin peptidase inhibitor, clade gG (C1 inhibitor), member 1 (angioedema, hereditary) 214636_at −1.55 0.024501 CALCB Calcitonin-related polypeptide, β 
220042_x_at 2.32 0.021477 HIVEP3 HIV type I enhancer-binding protein 3 203973_s_at −1.40 0.024666 CEBPD CCAAT/enhancer binding protein (C/EBP), δ 
204408_at 1.41 0.021502 APEX2 APEX nuclease (apurinic/apyrimidinic endonuclease) 2 202812_at −1.35 0.024799 GAA Glucosidase, α; acid (Pompe disease, glycogen storage disease type II) 
218036_x_at 1.30 0.021537 NMD3 NMD3 homolog (S. cerevisiae204042_at −1.32 0.025662 WASF3 WAS protein family, member 3 
221034_s_at 1.44 0.021674 TEX13B Testis-expressed sequence 13B 202450_s_at −1.34 0.025802 CTSK Cathepsin K (pycnodysostosis) 
205598_at 1.90 0.021893 TRAIP TRAF-interacting protein 201050_at −1.43 0.025854 PLD3 Phospholipase D family, member 3 
205347_s_at 1.39 0.021921 TMSL8 Thymosin-like 8 209978_s_at −2.28 0.025937 LPA /// PLG plasminogen, lipoprotein, Lp (a) 
220386_s_at 1.43 0.022175 EML4 Echinoderm microtubule-associated protein-like 4 201753_s_at −1.35 0.026385 ADD3 Adducin 3 (gamma) 
217738_at 1.35 0.022376 PBEF1 /// LOC646309 /// RP11-92J19.4 Pre-B cell colony-enhancing factor 1 219892_at −1.43 0.026459 TM6SF1 Transmembrane 6 superfamily member 1 
207662_at 1.64 0.023056 TBX1 T-box 1 205844_at −1.74 0.026498 VNN1 Vanin 1 
203362_s_at 1.41 0.023308 MAD2L1 MAD2 mitotic arrest deficient-like 1 (yeast) 207582_at −2.12 0.027216 PIN1L Protein (peptidylprolyl cis/trans isomerase) NIMA-interacting 1-like 
206325_at 1.83 0.023449 SERPINA6 Serpin peptidase inhibitor, clade A (α- 1 antiproteinase, antitrypsin), member 6 203729_at −1.41 0.027633 EMP3 Epithelial membrane protein 3 
220938_s_at 1.59 0.023571 GMEB1 Glucocorticoid modulatory element binding protein 1 204079_at −1.30 0.027635 TPST2 Tyrosylprotein sulfotransferase 2 
201202_at 1.40 0.023620 PCNA Croliferating cell nuclear Ag 208511_at −2.68 0.027688 PTTG3 Pituitary tumor-transforming 3 
201507_at 1.38 0.023999 PFDN1 Prefoldin subunit 1 209661_at −1.90 0.027937 KIFC3 Kinesin family member C3 
37950_at 1.36 0.024052 PREP Prolyl endopeptidase 206106_at −1.63 0.028087 MAPK12 MAPK12 
204835_at 1.66 0.024112 POLA Polymerase (DNA directed), α 203028_s_at −1.48 0.028274 CYBA Cytochrome B-245, α polypeptide 
202780_at 1.40 0.024117 OXCT1 3-Oxoacid CoA transferase 1 219440_at −2.54 0.028291 RAI2 Retinoic acid induced 2 
219424_at 1.97 0.024648 EBI3 EBV-induced gene 3 203996_s_at −1.71 0.028734 C21orf2 Chromosome 21 open reading frame 2 
204769_s_at 1.35 0.025000 TAP2 Transporter 2, ATP-binding cassette, subfamily B (MDR/TAP) 221061_at −2.63 0.029166 PKD2L1 Polycystic kidney disease 2-like 1 
210119_at 2.62 0.026057 KCNJ15 Potassium inwardly rectifying channel, subfamily J, member 15 204367_at −1.30 0.029203 SP2 Sp2 transcription factor 
207143_at 1.93 0.026156 CDK6 Cyclin-dependent kinase 6 213436_at −1.73 0.029349 CNR1 Cannabinoid receptor 1 (brain) 
218219_s_at 1.38 0.026250 LANCL2 LanC lantibiotic synthetase component C-like 2 (bacterial) 38157_at −1.64 0.030123 DOM3Z Dom-3 homolog C (C. elegans
219645_at 1.38 0.026851 CASQ1 Calsequestrin 1 (fast-twitch, skeletal muscle) 210423_s_at −1.56 0.030184 SLC11A1 Solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1 
201710_at 1.85 0.027145 MYBL2 V-myb myeloblastosis viral oncogene homolog (avian)-like 2 201911_s_at −2.04 0.031248 FARP1 FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived) 
(Table continues
Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
203409_at 1.56 0.020373 DDB2 Damage-specific DNA-binding protein 2, 48 kDa 208472_at −1.42 0.024357 ZNFN1A4 Zinc finger protein, subfamily 1A, 4 (Eos) 
200986_at 1.36 0.021457 SERPING1 Serpin peptidase inhibitor, clade gG (C1 inhibitor), member 1 (angioedema, hereditary) 214636_at −1.55 0.024501 CALCB Calcitonin-related polypeptide, β 
220042_x_at 2.32 0.021477 HIVEP3 HIV type I enhancer-binding protein 3 203973_s_at −1.40 0.024666 CEBPD CCAAT/enhancer binding protein (C/EBP), δ 
204408_at 1.41 0.021502 APEX2 APEX nuclease (apurinic/apyrimidinic endonuclease) 2 202812_at −1.35 0.024799 GAA Glucosidase, α; acid (Pompe disease, glycogen storage disease type II) 
218036_x_at 1.30 0.021537 NMD3 NMD3 homolog (S. cerevisiae204042_at −1.32 0.025662 WASF3 WAS protein family, member 3 
221034_s_at 1.44 0.021674 TEX13B Testis-expressed sequence 13B 202450_s_at −1.34 0.025802 CTSK Cathepsin K (pycnodysostosis) 
205598_at 1.90 0.021893 TRAIP TRAF-interacting protein 201050_at −1.43 0.025854 PLD3 Phospholipase D family, member 3 
205347_s_at 1.39 0.021921 TMSL8 Thymosin-like 8 209978_s_at −2.28 0.025937 LPA /// PLG plasminogen, lipoprotein, Lp (a) 
220386_s_at 1.43 0.022175 EML4 Echinoderm microtubule-associated protein-like 4 201753_s_at −1.35 0.026385 ADD3 Adducin 3 (gamma) 
217738_at 1.35 0.022376 PBEF1 /// LOC646309 /// RP11-92J19.4 Pre-B cell colony-enhancing factor 1 219892_at −1.43 0.026459 TM6SF1 Transmembrane 6 superfamily member 1 
207662_at 1.64 0.023056 TBX1 T-box 1 205844_at −1.74 0.026498 VNN1 Vanin 1 
203362_s_at 1.41 0.023308 MAD2L1 MAD2 mitotic arrest deficient-like 1 (yeast) 207582_at −2.12 0.027216 PIN1L Protein (peptidylprolyl cis/trans isomerase) NIMA-interacting 1-like 
206325_at 1.83 0.023449 SERPINA6 Serpin peptidase inhibitor, clade A (α- 1 antiproteinase, antitrypsin), member 6 203729_at −1.41 0.027633 EMP3 Epithelial membrane protein 3 
220938_s_at 1.59 0.023571 GMEB1 Glucocorticoid modulatory element binding protein 1 204079_at −1.30 0.027635 TPST2 Tyrosylprotein sulfotransferase 2 
201202_at 1.40 0.023620 PCNA Croliferating cell nuclear Ag 208511_at −2.68 0.027688 PTTG3 Pituitary tumor-transforming 3 
201507_at 1.38 0.023999 PFDN1 Prefoldin subunit 1 209661_at −1.90 0.027937 KIFC3 Kinesin family member C3 
37950_at 1.36 0.024052 PREP Prolyl endopeptidase 206106_at −1.63 0.028087 MAPK12 MAPK12 
204835_at 1.66 0.024112 POLA Polymerase (DNA directed), α 203028_s_at −1.48 0.028274 CYBA Cytochrome B-245, α polypeptide 
202780_at 1.40 0.024117 OXCT1 3-Oxoacid CoA transferase 1 219440_at −2.54 0.028291 RAI2 Retinoic acid induced 2 
219424_at 1.97 0.024648 EBI3 EBV-induced gene 3 203996_s_at −1.71 0.028734 C21orf2 Chromosome 21 open reading frame 2 
204769_s_at 1.35 0.025000 TAP2 Transporter 2, ATP-binding cassette, subfamily B (MDR/TAP) 221061_at −2.63 0.029166 PKD2L1 Polycystic kidney disease 2-like 1 
210119_at 2.62 0.026057 KCNJ15 Potassium inwardly rectifying channel, subfamily J, member 15 204367_at −1.30 0.029203 SP2 Sp2 transcription factor 
207143_at 1.93 0.026156 CDK6 Cyclin-dependent kinase 6 213436_at −1.73 0.029349 CNR1 Cannabinoid receptor 1 (brain) 
218219_s_at 1.38 0.026250 LANCL2 LanC lantibiotic synthetase component C-like 2 (bacterial) 38157_at −1.64 0.030123 DOM3Z Dom-3 homolog C (C. elegans
219645_at 1.38 0.026851 CASQ1 Calsequestrin 1 (fast-twitch, skeletal muscle) 210423_s_at −1.56 0.030184 SLC11A1 Solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1 
201710_at 1.85 0.027145 MYBL2 V-myb myeloblastosis viral oncogene homolog (avian)-like 2 201911_s_at −2.04 0.031248 FARP1 FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived) 
(Table continues
Table IIIJ.

(Continued)

Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
203859_s_at 1.49 0.027287 PALM Paralemmin 220782_x_at −1.82 0.031968 KLK12 Kallikrein 12 
204297_at 1.32 0.027612 PIK3C3 PI3K, class 3 207482_at −1.62 0.032061 C20orf10 Chromosome 20 open reading frame 10 
219971_at 1.37 0.028335 IL21R IL-21$ 204697_s_at −2.06 0.032591 CHGA Chromogranin A (parathyroid secretory protein 1) 
211297_s_at 1.37 0.028415 CDK7 Cyclin-dependent kinase 7 (mo15 homolog, Xenopus laevis, cdk-activating kinase) 206873_at −1.68 0.032847 CA6 Carbonic anhydrase VI 
204126_s_at 2.09 0.028496 CDC45L CDC45 cell division cycle 45-like (S. cerevisiae207914_x_at −1.54 0.033022 EVX1 Eve, even-skipped homeobox homolog 1 (Drosophila
207455_at 1.46 0.028568 P2RY1 Purinergic receptor P2Y, G protein coupled, 1 218206_x_at −1.37 0.033390 SCAND1 SCAN domain containing 1 
206765_at 1.33 0.028640 KCNJ2 Potassium inwardly rectifying channel, subfamily J, member 2 217975_at −1.50 0.034679 WBP5 WW domain binding protein 5 
206175_x_at 2.21 0.028671 ZNF222 Zinc finger protein 222 219327_s_at −1.60 0.035562 GPRC5C G protein-coupled receptor, family C, group 5, member C 
206173_x_at 2.11 0.028761 GABPB2 GA-binding protein transcription factor, β subunit 1, 53 kDa 206206_at −1.39 0.035730 CD180 CD180 Ag 
205463_s_at 1.84 0.029164 PDGFA Platelet-derived growth factor α polypeptide 222239_s_at −1.31 0.035916 INTS6 DKFZp434B105 protein 
206407_s_at 2.20 0.029186 CCL13 Chemokine (C-C motif) ligand 13 220189_s_at −1.44 0.036040 MGAT4B Mannosyl (α -1,3-)-glycoprotein β -1,4-N-acetylglucosaminyltransferase, isozyme B 
210772_at 1.37 0.029514 FPRL1 Formyl peptide receptor-like 1 203476_at −1.59 0.036505 TPBG Trophoblast glycoprotein 
211200_s_at 2.47 0.029575 EFCAB2 EF-hand calcium-binding domain 2 221005_s_at −1.55 0.037185 PTDSS2 Phosphatidylserine synthase 2 
203592_s_at 1.54 0.029679 FSTL3 Follistatin-like 3 (secreted glycoprotein) 209822_s_at −1.37 0.037473 VLDLR Very low-density lipoprotein receptor 
203052_at 1.39 0.029744 C2 Complement component 2 205638_at −1.71 0.037898 BAI3 Brain-specific angiogenesis inhibitor 3 
211499_s_at 1.67 0.029863 MAPK11 MAPK11 220777_at −1.74 0.038565 KIF13A Kinesin family member 13A 
204162_at 1.99 0.030006 KNTC2 Kinetochore-associated 2 210139_s_at −1.33 0.038607 PMP22 Peripheral myelin protein 22 
201737_s_at 1.35 0.030278 MARCH6 Membrane-associated ring finger (C3HC4) 6 221324_at −1.32 0.038629 TAS2R1 Taste receptor, type 2, member 1 
210549_s_at 2.57 0.030537 CCL23 Chemokine (C-C motif) ligand 23 210884_s_at −1.62 0.039295 LOC653423 Sperm-associated Ag 11 
218931_at 1.90 0.030914 RAB17 RAB17, member RAS oncogene family 207739_s_at −2.22 0.039456 GAGE1 /// GAGE2 /// GAGE3 /// GAGE4 /// GAGE5 /// GAGE6 /// GAGE7 /// GAGE7B /// GAGE8 /// LOC645009 /// LOC645037 /// LOC645073 /// LOC645093 G Ag 1, G Ag 3, G Ag 4, G Ag 2, G Ag 5, G Ag 8, G AG 6 
204304_s_at 1.48 0.030950 PROM1 Prominin 1 209737_at −1.42 0.039512 MAGI2 Membrane-associated guanylate kinase, WW and PDZ domain containing 2 
205450_at 2.53 0.030967 PHKA1 Phosphorylase kinase, α 1 (muscle) 32094_at −1.72 0.039607 CHST3 Carbohydrate (chondroitin 6) sulfotransferase 3 
204504_s_at 1.55 0.031187 HIRIP3 HIRA-interacting protein 3 41660_at −1.79 0.039999 CELSR1 Cadherin, EGF LAG seven-pass G-type receptor 1 (flamingo homolog, Drosophila
(Table continues
Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
203859_s_at 1.49 0.027287 PALM Paralemmin 220782_x_at −1.82 0.031968 KLK12 Kallikrein 12 
204297_at 1.32 0.027612 PIK3C3 PI3K, class 3 207482_at −1.62 0.032061 C20orf10 Chromosome 20 open reading frame 10 
219971_at 1.37 0.028335 IL21R IL-21$ 204697_s_at −2.06 0.032591 CHGA Chromogranin A (parathyroid secretory protein 1) 
211297_s_at 1.37 0.028415 CDK7 Cyclin-dependent kinase 7 (mo15 homolog, Xenopus laevis, cdk-activating kinase) 206873_at −1.68 0.032847 CA6 Carbonic anhydrase VI 
204126_s_at 2.09 0.028496 CDC45L CDC45 cell division cycle 45-like (S. cerevisiae207914_x_at −1.54 0.033022 EVX1 Eve, even-skipped homeobox homolog 1 (Drosophila
207455_at 1.46 0.028568 P2RY1 Purinergic receptor P2Y, G protein coupled, 1 218206_x_at −1.37 0.033390 SCAND1 SCAN domain containing 1 
206765_at 1.33 0.028640 KCNJ2 Potassium inwardly rectifying channel, subfamily J, member 2 217975_at −1.50 0.034679 WBP5 WW domain binding protein 5 
206175_x_at 2.21 0.028671 ZNF222 Zinc finger protein 222 219327_s_at −1.60 0.035562 GPRC5C G protein-coupled receptor, family C, group 5, member C 
206173_x_at 2.11 0.028761 GABPB2 GA-binding protein transcription factor, β subunit 1, 53 kDa 206206_at −1.39 0.035730 CD180 CD180 Ag 
205463_s_at 1.84 0.029164 PDGFA Platelet-derived growth factor α polypeptide 222239_s_at −1.31 0.035916 INTS6 DKFZp434B105 protein 
206407_s_at 2.20 0.029186 CCL13 Chemokine (C-C motif) ligand 13 220189_s_at −1.44 0.036040 MGAT4B Mannosyl (α -1,3-)-glycoprotein β -1,4-N-acetylglucosaminyltransferase, isozyme B 
210772_at 1.37 0.029514 FPRL1 Formyl peptide receptor-like 1 203476_at −1.59 0.036505 TPBG Trophoblast glycoprotein 
211200_s_at 2.47 0.029575 EFCAB2 EF-hand calcium-binding domain 2 221005_s_at −1.55 0.037185 PTDSS2 Phosphatidylserine synthase 2 
203592_s_at 1.54 0.029679 FSTL3 Follistatin-like 3 (secreted glycoprotein) 209822_s_at −1.37 0.037473 VLDLR Very low-density lipoprotein receptor 
203052_at 1.39 0.029744 C2 Complement component 2 205638_at −1.71 0.037898 BAI3 Brain-specific angiogenesis inhibitor 3 
211499_s_at 1.67 0.029863 MAPK11 MAPK11 220777_at −1.74 0.038565 KIF13A Kinesin family member 13A 
204162_at 1.99 0.030006 KNTC2 Kinetochore-associated 2 210139_s_at −1.33 0.038607 PMP22 Peripheral myelin protein 22 
201737_s_at 1.35 0.030278 MARCH6 Membrane-associated ring finger (C3HC4) 6 221324_at −1.32 0.038629 TAS2R1 Taste receptor, type 2, member 1 
210549_s_at 2.57 0.030537 CCL23 Chemokine (C-C motif) ligand 23 210884_s_at −1.62 0.039295 LOC653423 Sperm-associated Ag 11 
218931_at 1.90 0.030914 RAB17 RAB17, member RAS oncogene family 207739_s_at −2.22 0.039456 GAGE1 /// GAGE2 /// GAGE3 /// GAGE4 /// GAGE5 /// GAGE6 /// GAGE7 /// GAGE7B /// GAGE8 /// LOC645009 /// LOC645037 /// LOC645073 /// LOC645093 G Ag 1, G Ag 3, G Ag 4, G Ag 2, G Ag 5, G Ag 8, G AG 6 
204304_s_at 1.48 0.030950 PROM1 Prominin 1 209737_at −1.42 0.039512 MAGI2 Membrane-associated guanylate kinase, WW and PDZ domain containing 2 
205450_at 2.53 0.030967 PHKA1 Phosphorylase kinase, α 1 (muscle) 32094_at −1.72 0.039607 CHST3 Carbohydrate (chondroitin 6) sulfotransferase 3 
204504_s_at 1.55 0.031187 HIRIP3 HIRA-interacting protein 3 41660_at −1.79 0.039999 CELSR1 Cadherin, EGF LAG seven-pass G-type receptor 1 (flamingo homolog, Drosophila
(Table continues
Table IIIK.

(Continued)

Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
209890_at 1.38 0.031529 TSPAN5 Tetraspanin 5 206610_s_at −1.92 0.040448 F11 Coagulation factor XI (plasma thromboplastin antecedent) 
34187_at 1.89 0.031861 RBMS2 RNA binding motif, single-stranded interacting protein 2 209988_s_at −1.57 0.040611 ASCL1 Achaete-scute complex-like 1 (Drosophila
218943_s_at 1.58 0.032067 DDX58 Dead (Asp-Glu-Ala-Asp) box polypeptide 58 219922_s_at −1.47 0.040966 LTBP3 Latent transforming growth factor β binding protein 3 
202240_at 1.53 0.032437 PLK1 Polo-like kinase 1 (Drosophila205054_at −1.78 0.041014 NEB Nebulin 
205716_at 1.39 0.033296 MCFP Mitochondrial carrier family protein 206404_at −1.45 0.041028 FGF9 Fibroblast growth factor 9 (glia-activating factor) 
208005_at 1.69 0.033662 NTN1 Netrin 1 203305_at −1.59 0.041286 F13A1 Coagulation factor XIII, A1 polypeptide 
220059_at 1.53 0.033861 BRDG1 BCR downstream signaling 1 201656_at −1.38 0.041995 ITGA6 Integrin, α 6 
204767_s_at 1.39 0.034527 FEN1 Flap structure-specific endonuclease 1 205384_at −1.96 0.042828 FXYD1 FXYD domain-containing ion transport regulator 1 (phospholemman) 
210280_at 2.18 0.034875 MPZ Myelin protein 0 (Charcot-Marie-Tooth neuropathy 1B) 203618_at −1.34 0.043195 FAIM2 Fas apoptotic inhibitory molecule 2 
213492_at 1.64 0.034876 COL2A1 Collagen, type II, α 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital) 210117_at −2.03 0.044321 SPAG1 Sperm-associated Ag 1 
212020_s_at 1.51 0.035187 MKI67 Ag identified by mAb Ki-67 206498_at −1.85 0.044628 OCA2 Oculocutaneous albinism II (pink-eye dilution homolog, mouse) 
206247_at 1.32 0.035337 MICB MHC class I polypeptide-related sequence B 202621_at −1.41 0.045125 IRF3 IFN regulatory factor 3 
212657_s_at 1.61 0.035551 IL1RN IL-R1 antagonist 205881_at −2.10 0.045147 ZNF74 Zinc finger protein 74 (Cos52) 
215171_s_at 1.31 0.035701 TIMM17A Translocase of inner mitochondrial membrane 17 homolog a (yeast) 204449_at −1.40 0.045296 PDCL Phosducin-like 
210048_at 1.31 0.036177 NAPG N-Ethylmaleimide-sensitive factor attachment protein, γ 209657_s_at −1.38 0.045366 HSF2 Heat shock transcription factor 2 
221507_at 1.35 0.036194 TNPO2 Transportin 2 (importin 3, karyopherin β 2b) 208000_at −1.41 0.045916 GML GPI-anchored molecule-like protein 
208118_x_at 1.31 0.036247 LAT1–3TM /// IMAA /// LOC440345 /// LOC440354 /// LOC595101 /// LOC641298 /// LOC646866 SLC7A5 pseudogene, hypothetical gene LOC283846, KIAA0220-like protein 206251_s_at −2.18 0.046131 AVPR1A Arginine vasopressin receptor 1A 
219125_s_at 1.35 0.036524 RAG1AP1 Recombination activating gene 1 activating protein 1 207503_at −2.22 0.046146 TCP10 T complex 10 (mouse) 
204092_s_at 1.49 0.037044 AURKA Aurora kinase a 202191_s_at −1.33 0.046843 GAS7 Growth arrest-specific 7 
202627_s_at 1.79 0.037267 SERPINE1 Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 205200_at −1.72 0.047002 CLEC3B Cc-type lectin domain family 3, member B 
208478_s_at 1.51 0.037303 BAX BCL2-associated X protein 202178_at −1.88 0.047241 PRKCZ Protein kinase c, ζ 
207473_at 1.40 0.037435 MLN Motilin 217871_s_at −1.31 0.047313 MIF Macrophage migration inhibitory factor (glycosylation-inhibiting factor) 
(Table continues
Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
209890_at 1.38 0.031529 TSPAN5 Tetraspanin 5 206610_s_at −1.92 0.040448 F11 Coagulation factor XI (plasma thromboplastin antecedent) 
34187_at 1.89 0.031861 RBMS2 RNA binding motif, single-stranded interacting protein 2 209988_s_at −1.57 0.040611 ASCL1 Achaete-scute complex-like 1 (Drosophila
218943_s_at 1.58 0.032067 DDX58 Dead (Asp-Glu-Ala-Asp) box polypeptide 58 219922_s_at −1.47 0.040966 LTBP3 Latent transforming growth factor β binding protein 3 
202240_at 1.53 0.032437 PLK1 Polo-like kinase 1 (Drosophila205054_at −1.78 0.041014 NEB Nebulin 
205716_at 1.39 0.033296 MCFP Mitochondrial carrier family protein 206404_at −1.45 0.041028 FGF9 Fibroblast growth factor 9 (glia-activating factor) 
208005_at 1.69 0.033662 NTN1 Netrin 1 203305_at −1.59 0.041286 F13A1 Coagulation factor XIII, A1 polypeptide 
220059_at 1.53 0.033861 BRDG1 BCR downstream signaling 1 201656_at −1.38 0.041995 ITGA6 Integrin, α 6 
204767_s_at 1.39 0.034527 FEN1 Flap structure-specific endonuclease 1 205384_at −1.96 0.042828 FXYD1 FXYD domain-containing ion transport regulator 1 (phospholemman) 
210280_at 2.18 0.034875 MPZ Myelin protein 0 (Charcot-Marie-Tooth neuropathy 1B) 203618_at −1.34 0.043195 FAIM2 Fas apoptotic inhibitory molecule 2 
213492_at 1.64 0.034876 COL2A1 Collagen, type II, α 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital) 210117_at −2.03 0.044321 SPAG1 Sperm-associated Ag 1 
212020_s_at 1.51 0.035187 MKI67 Ag identified by mAb Ki-67 206498_at −1.85 0.044628 OCA2 Oculocutaneous albinism II (pink-eye dilution homolog, mouse) 
206247_at 1.32 0.035337 MICB MHC class I polypeptide-related sequence B 202621_at −1.41 0.045125 IRF3 IFN regulatory factor 3 
212657_s_at 1.61 0.035551 IL1RN IL-R1 antagonist 205881_at −2.10 0.045147 ZNF74 Zinc finger protein 74 (Cos52) 
215171_s_at 1.31 0.035701 TIMM17A Translocase of inner mitochondrial membrane 17 homolog a (yeast) 204449_at −1.40 0.045296 PDCL Phosducin-like 
210048_at 1.31 0.036177 NAPG N-Ethylmaleimide-sensitive factor attachment protein, γ 209657_s_at −1.38 0.045366 HSF2 Heat shock transcription factor 2 
221507_at 1.35 0.036194 TNPO2 Transportin 2 (importin 3, karyopherin β 2b) 208000_at −1.41 0.045916 GML GPI-anchored molecule-like protein 
208118_x_at 1.31 0.036247 LAT1–3TM /// IMAA /// LOC440345 /// LOC440354 /// LOC595101 /// LOC641298 /// LOC646866 SLC7A5 pseudogene, hypothetical gene LOC283846, KIAA0220-like protein 206251_s_at −2.18 0.046131 AVPR1A Arginine vasopressin receptor 1A 
219125_s_at 1.35 0.036524 RAG1AP1 Recombination activating gene 1 activating protein 1 207503_at −2.22 0.046146 TCP10 T complex 10 (mouse) 
204092_s_at 1.49 0.037044 AURKA Aurora kinase a 202191_s_at −1.33 0.046843 GAS7 Growth arrest-specific 7 
202627_s_at 1.79 0.037267 SERPINE1 Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 205200_at −1.72 0.047002 CLEC3B Cc-type lectin domain family 3, member B 
208478_s_at 1.51 0.037303 BAX BCL2-associated X protein 202178_at −1.88 0.047241 PRKCZ Protein kinase c, ζ 
207473_at 1.40 0.037435 MLN Motilin 217871_s_at −1.31 0.047313 MIF Macrophage migration inhibitory factor (glycosylation-inhibiting factor) 
(Table continues
Table IIIL.

(Continued)

Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
207329_at 2.09 0.037908 MMP8 Matrix metallopeptidase 8 (neutrophil collagenase) 221309_at −1.90 0.047786 RBM17 RNA-binding motif protein 17 
219199_at 1.64 0.037979 AFF4 AF4/FMR2 family, member 4 205050_s_at −1.54 0.047840 MAPK8IP2 MAPK8-interacting protein 2 
38037_at 1.51 0.038257 HBEGF Heparin-binding EGF-like growth factor 203643_at −1.55 0.048239 ERF Ets2 repressor factor 
33767_at 1.39 0.038470 NEFH Neurofilament, heavy polypeptide, 200 kDa 203422_at −1.33 0.049132 POLD1 Polymerase (DNA directed), δ1, catalytic subunit 125 kDa 
207882_at 1.38 0.038622 HSAJ2425 p65 protein 204811_s_at −1.35 0.049138 CACNA2D2 Calcium channel, voltage-dependent, α 2/δ subunit 2 
204864_s_at 1.55 0.038725 IL6ST IL-6 signal transducer (gp130, oncostatin m receptor) 209264_s_at −1.54 0.049162 TSPAN4 Tetraspanin 4 
204668_at 1.39 0.039002 RNF24 Ring finger protein 24 207929_at −1.44 0.049398 GRPR Gastrin-releasing peptide receptor 
207016_s_at 1.50 0.039529 ALDH1A2 Aldehyde dehydrogenase 1 family, member A2 219714_s_at −1.90 0.049494 CACNA2D3 Calcium channel, voltage-dependent, α 2/δ3 subunit 
207346_at 2.21 0.039649 STX2 Epimorphin      
32128_at 1.50 0.039852 CCL18 Chemokine (C-C motif) ligand 18 (pulmonary and activation-regulated)      
206932_at 1.67 0.040074 CH25H Cholesterol 25-hydroxylase      
205225_at 1.33 0.040378 ESR1 Estrogen receptor 1      
202416_at 1.32 0.040835 DNAJC7 DnaJ (hsp40) homolog, subfamily C, member 7      
220315_at 1.36 0.041177 PARP11 Poly(ADP-ribose) polymerase family, member 11      
206999_at 2.28 0.041871 IL12RB2 IL-12R, β2      
220993_s_at 2.19 0.042266 GPR63 G protein-coupled receptor 63      
221170_at 1.60 0.042356 HRH4 Histamine receptor H4      
207845_s_at 1.39 0.042369 ANAPC10 Anaphase-promoting complex subunit 10      
204401_at 1.40 0.042558 KCNN4 Potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4      
207124_s_at 1.53 0.042696 GNB5 Guanine nucleotide-binding protein (G protein), β5      
219187_at 1.85 0.042908 FKBPL FK506 binding protein-like      
203952_at 1.76 0.042917 ATF6 Activating transcription factor 6      
36742_at 1.57 0.043363 TRIM15 Tripartite motif-containing 15      
218117_at 1.35 0.043508 RBX1 Ring-box 1      
208592_s_at 1.49 0.043731 CD1E CD1E Ag, E polypeptide      
221106_at 1.98 0.044473 SLC22A17 Solute carrier family 22 (organic cation transporter), member 17      
207275_s_at 1.34 0.044487 ACSL1 Fatty acid coenzyme A ligase, long chain 1      
202403_s_at 2.21 0.044527 COL1A2 Collagen, type I, α 2      
220633_s_at 1.30 0.044556 HP1BP3 Heterochromatin protein 1, binding protein 3      
208916_at 1.36 0.044687 SLC1A5 Solute carrier family 1 (neutral amino acid transporter), member 5      
203881_s_at 1.76 0.045235 DMD Dystrophin (muscular dystrophy, Duchenne and Becker types)      
(Table continues
Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
207329_at 2.09 0.037908 MMP8 Matrix metallopeptidase 8 (neutrophil collagenase) 221309_at −1.90 0.047786 RBM17 RNA-binding motif protein 17 
219199_at 1.64 0.037979 AFF4 AF4/FMR2 family, member 4 205050_s_at −1.54 0.047840 MAPK8IP2 MAPK8-interacting protein 2 
38037_at 1.51 0.038257 HBEGF Heparin-binding EGF-like growth factor 203643_at −1.55 0.048239 ERF Ets2 repressor factor 
33767_at 1.39 0.038470 NEFH Neurofilament, heavy polypeptide, 200 kDa 203422_at −1.33 0.049132 POLD1 Polymerase (DNA directed), δ1, catalytic subunit 125 kDa 
207882_at 1.38 0.038622 HSAJ2425 p65 protein 204811_s_at −1.35 0.049138 CACNA2D2 Calcium channel, voltage-dependent, α 2/δ subunit 2 
204864_s_at 1.55 0.038725 IL6ST IL-6 signal transducer (gp130, oncostatin m receptor) 209264_s_at −1.54 0.049162 TSPAN4 Tetraspanin 4 
204668_at 1.39 0.039002 RNF24 Ring finger protein 24 207929_at −1.44 0.049398 GRPR Gastrin-releasing peptide receptor 
207016_s_at 1.50 0.039529 ALDH1A2 Aldehyde dehydrogenase 1 family, member A2 219714_s_at −1.90 0.049494 CACNA2D3 Calcium channel, voltage-dependent, α 2/δ3 subunit 
207346_at 2.21 0.039649 STX2 Epimorphin      
32128_at 1.50 0.039852 CCL18 Chemokine (C-C motif) ligand 18 (pulmonary and activation-regulated)      
206932_at 1.67 0.040074 CH25H Cholesterol 25-hydroxylase      
205225_at 1.33 0.040378 ESR1 Estrogen receptor 1      
202416_at 1.32 0.040835 DNAJC7 DnaJ (hsp40) homolog, subfamily C, member 7      
220315_at 1.36 0.041177 PARP11 Poly(ADP-ribose) polymerase family, member 11      
206999_at 2.28 0.041871 IL12RB2 IL-12R, β2      
220993_s_at 2.19 0.042266 GPR63 G protein-coupled receptor 63      
221170_at 1.60 0.042356 HRH4 Histamine receptor H4      
207845_s_at 1.39 0.042369 ANAPC10 Anaphase-promoting complex subunit 10      
204401_at 1.40 0.042558 KCNN4 Potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4      
207124_s_at 1.53 0.042696 GNB5 Guanine nucleotide-binding protein (G protein), β5      
219187_at 1.85 0.042908 FKBPL FK506 binding protein-like      
203952_at 1.76 0.042917 ATF6 Activating transcription factor 6      
36742_at 1.57 0.043363 TRIM15 Tripartite motif-containing 15      
218117_at 1.35 0.043508 RBX1 Ring-box 1      
208592_s_at 1.49 0.043731 CD1E CD1E Ag, E polypeptide      
221106_at 1.98 0.044473 SLC22A17 Solute carrier family 22 (organic cation transporter), member 17      
207275_s_at 1.34 0.044487 ACSL1 Fatty acid coenzyme A ligase, long chain 1      
202403_s_at 2.21 0.044527 COL1A2 Collagen, type I, α 2      
220633_s_at 1.30 0.044556 HP1BP3 Heterochromatin protein 1, binding protein 3      
208916_at 1.36 0.044687 SLC1A5 Solute carrier family 1 (neutral amino acid transporter), member 5      
203881_s_at 1.76 0.045235 DMD Dystrophin (muscular dystrophy, Duchenne and Becker types)      
(Table continues
Table IIIM.

(Continued)

Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
203948_s_at 1.89 0.045239 MPO Myeloperoxidase      
203968_s_at 1.48 0.045435 CDC6 CDC6 cell division cycle 6 homolog (S. cerevisiae     
209546_s_at 1.46 0.045614 APOL1 Apolipoprotein l, 1      
217847_s_at 2.47 0.045686 THRAP3 Thyroid hormone receptor-associated protein 3      
206976_s_at 1.31 0.046433 HSPH1 Heat shock 105 kDa/110 kDa protein 1      
210133_at 1.87 0.046451 CCL11 Chemokine (C-C motif) ligand 11      
219540_at 1.31 0.046489 ZNF267 Zinc finger protein 267      
203287_at 1.33 0.046497 LAD1 Ladinin 1      
220091_at 1.49 0.047676 SLC2A6 Solute carrier family 2 (facilitated glucose transporter), member 6      
213800_at 2.30 0.047921 CFH Complement factor H      
200793_s_at 1.37 0.048667 ACO2 Aconitase 2, mitochondrial      
202732_at 1.34 0.048888 PKIG Protein kinase (camp-dependent, catalytic) inhibitor γ      
39402_at 1.56 0.049565 IL1B IL-1β      
Affymetrix IDFC Post- vs Pre-apGene SymbolGene NameAffymetrix IDFC Post- vs Pre-apGene SymbolGene Name
203948_s_at 1.89 0.045239 MPO Myeloperoxidase      
203968_s_at 1.48 0.045435 CDC6 CDC6 cell division cycle 6 homolog (S. cerevisiae     
209546_s_at 1.46 0.045614 APOL1 Apolipoprotein l, 1      
217847_s_at 2.47 0.045686 THRAP3 Thyroid hormone receptor-associated protein 3      
206976_s_at 1.31 0.046433 HSPH1 Heat shock 105 kDa/110 kDa protein 1      
210133_at 1.87 0.046451 CCL11 Chemokine (C-C motif) ligand 11      
219540_at 1.31 0.046489 ZNF267 Zinc finger protein 267      
203287_at 1.33 0.046497 LAD1 Ladinin 1      
220091_at 1.49 0.047676 SLC2A6 Solute carrier family 2 (facilitated glucose transporter), member 6      
213800_at 2.30 0.047921 CFH Complement factor H      
200793_s_at 1.37 0.048667 ACO2 Aconitase 2, mitochondrial      
202732_at 1.34 0.048888 PKIG Protein kinase (camp-dependent, catalytic) inhibitor γ      
39402_at 1.56 0.049565 IL1B IL-1β      
a

Fold change post- vs prevaccination.

The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

1

This project has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health (N01-CO-12400).

The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. Government.

4

Abbreviations used in this paper: HPV, human papillomavirus; ds-cDNA, double-stranded cDNA; RPLPO, ribosomal protein, large P0; VLP, virus-like particles.

5

The online version of this article contains supplemental material.

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