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. Author manuscript; available in PMC: 2011 Dec 1.
Published in final edited form as: J Acquir Immune Defic Syndr. 2010 Dec 1;55(4):428–438. doi: 10.1097/QAI.0b013e3181ef4963

Table 2.

Down-regulation of 53 genes at all time points with HIV therapy

Gene Symbol Gene Expression Adjusted P-value1 Entrez Gene ID Gene Ontology Process Ref Gene Name
Percentile Avg % Decrease
Immune Activation Genes
OASL 97.4 67.9 1.1 ×10--5 8638 Im 5, 6, 26 2’-5’-oligoadenylate synthetase-like
SIGLEC1 85.5 71.9 4.6 ×10-6 6614 Im 27, 28 Sialic acid binding Ig-like lectin 1, sialoadhesin
OAS2 98.1 67.5 5.3 ×10-6 4939 Im 2, 5,6 2’-5’-oligoadenylate synthetase 2
ZBP1 91.5 47.7 5.3 ×10-5 81030 Im Z-DNA binding protein 1
IFI44L 98.6 82.9 4.9 ×10-6 10964 Im 2, 4, 6, 10 Interferon-induced protein 44-like
MX1 98.9 70.4 6.6 ×10-6 4599 Im 2, 4, 5, 10 Myxovirus (influenza) resistance 1, IFN-inducible protein p78
OAS1 99.2 68.3 6.2 ×10-6 4938 Im 2, 5, 6, 10 2’,5’-oligoadenylate synthetase 1
IRF7 99.1 60.2 2.1 ×10-5 3665 Im 2, 5, 6 Interferon regulatory factor 7
OAS3 94.6 63.4 2.2 ×10-5 4940 Im 5, 6, 29 2’-5’-oligoadenylate synthetase 3
IFI6 99.1 69.3 5.1 ×10-5 2537 Im 2, 6 Interferon, alpha-inducible protein 6
RSAD2 98.3 78.9 1.4 ×10-5 91543 Im Radical S-adenosyl methionine domain containing 2
IFI27 98.8 85.9 3.7 ×10-6 3429 Im 2, 4, 6 Interferon, α-inducible protein 27
IFIT3 98.9 68.9 4.5 ×10-5 3437 Im 6 Interferon-induced protein with tetratricopeptide repeats 3
IFI35 96.7 55.2 1.2 ×10-4 3430 Im 2, 6 Interferon-induced protein 35
SERPING1 94.8 63.0 5.5 ×10-5 710 Im 6 Serpin peptidase inhibitor, clade G (C1 inhibitor)
IFI44 91.0 71.2 2.1 ×10-5 10561 Im 4 Interferon-induced protein 44
LY6E 98.5 64.6 1.3 ×10-4 4061 Im Lymphocyte antigen 6 complex, E
CD38 90.1 39.9 4.5 ×10-3 952 Im 4, 6, 10, 30-32 CD38, surface activation marker of T-cells
BST2 97.0 45.4 2.2 ×10-4 684 Im, Sig Bone marrow stromal cell antigen 2
APOL6 95.3 34.4 6.3 ×10-4 80830 Im, Mito Apolipoprotein L, 6
CCL8 60.0 29.4 2.8 ×10-3 6355 Im, Sig 10 Chemokine (C-C motif) ligand 8
IFIH1 89.3 61.8 1.3 ×10-5 64135 Im 33 Interferon induced with helicase C domain 1
MX2 98.4 53.3 3.4 ×10-5 4600 Im 6, 10, 34 Myxovirus (influenza virus) resistance 2 (mouse)
IL1RN 97.2 52.1 9.1 ×10-4 3557 Im 35 Interleukin 1 receptor antagonist
Cell Cycle Genes
NTNG2 85.8 45.1 2.6 ×10-4 84628 Cycle Netrin G2
LAMP3 66.3 45.8 5.0 ×10-5 27074 Cycle 6 Lysosomal-associated membrane protein 3
FOXO6 51.0 22.8 1.5 ×10-3 100132074 Cycle Forkhead box protein O6
SOCS1 80.9 35.4 3.1 ×10-3 8651 Cycle 36 Suppressor of cytokine signaling 1
XAF1 94.4 65.4 2.7 ×10-5 54739 Cycle 6 XIAP associated factor 1
SHISA5 98.9 40.0 8.4 ×10-4 51246 Cycle Shisa homolog 5 (Xenopus laevis)
Ubiquitin Cycle of Protein degradation Genes
ISG15 99.2 82.1 2.4 ×10-6 9636 Ubq, Im 4 ISG15 ubiquitin-like modifier
USP18 87.3 62.6 6.1 ×10-6 11274 Ubq Ubiquitin specific peptidase 18
HERC6 89.8 59.3 1.8 ×10-5 55008 Ubq 6 Hect domain and RLD 6
HERC5 96.3 71.1 8.3 ×10-6 51191 Ubq 6 Hect domain and RLD 5
Transcriptional and Translation Regulation Genes
EIF2AK2 92.2 53.7 3.7 ×10-6 5610 TransC Eukaryotic translation initiation factor 2-alpha kinase 2
SAMD9L 95.8 56.5 1.4 ×10-5 219285 TransL 6 Sterile alpha motif domain containing 9-like
PRIC285 90.4 33.2 2.9 ×10-4 85441 TransC 6 Peroxisomal proliferator-activated receptor A interacting cplx 285
HES4 83.6 47.0 6.2 ×10-4 57801 TransC Hairy and enhancer of split 4
SAMD4A 49.5 27.9 1.6 ×10-3 23034 TransL Sterile alpha motif domain containing 4A
ZCCHC2 92.6 52.9 2.2 ×10-4 54877 Zinc finger, CCHC domain containing 2
Miscellaneous Genes
RTP4 94.2 58.9 6.3 ×10-6 64108 Pr bind Receptor (chemosensory) transporter protein 4
MT2A 99.2 36.1 2.6 ×10-4 4502 Met 6 Metallothionein 2A
TREX1 94.5 34.6 1.5 ×10-4 11277 Repair 10, 37 Three prime repair exonuclease 1
FANCA 70.0 21.7 1.1 ×10-2 2175 Repair Fanconi anemia, complementation group A
C18orf49 66.5 35.6 3.8 ×10-4 400653 Sig Zinc finger, CCHC domain containing 2
SCO2 98.0 50.5 8.0 ×10-4 9997 Mito SCO cytochrome oxidase deficient homolog 2
CNP 96.0 32.5 1.6 ×10-3 1267 38 2’,3’-cyclic nucleotide 3’ phosphodiesterase
EPSTI1 95.2 56.7 1.7 ×10-5 94240 6 Epithelial stromal interaction 1
LGALS3BP 85.3 49.6 3.0 ×10-5 3959 6 Lectin, galactoside-binding, soluble, 3 binding protein
KLHDC7B 90.3 54.5 2.2 ×10-5 113730 Kelch domain containing 7B

Percentile gene expression represents the relative degree of expression in peripheral blood compared to the entire genome. The mean percent decrease in gene expression compared to baseline (0%) is presented with the adjusted P-value. The selected genes are down-regulated at 4, 8, and 24 weeks as well across all time points (by linear regression) with adjusted P<.01.

1

The adjusted-p-value is generated by linear regression, testing the fold change over all weeks. The range of unadjusted P-values is between 1.5×10-3 to 1.5×10-9.

Genes listed in bold have been previously reported in humans in relation to HIV infection with the literature reference (Ref).

Gene Ontology Abbreviations: Im=immune response; Cycle = cell cycle; Met=metabolism; Mito=mitochondrial; Pr Bind=protein binding; Repair=DNA repair; Sig=cell signaling; TransC=transcription regulation; TransL=translation regulation; Ubq=ubiquitin cycle

After adjustment for CD4 change, all of the above genes and seven additional genes were significantly down-regulated across all time points by linear regression. The seven additional genes were: PARP9, PARP12, PARP14, PHF11, SPTLC2, MOV10, and BIRC5.