Table S3 Top Ten GO Processes Differentially Regulated Between Virus and Mock Treatments

Table S3 Top ten GO processes differentially regulated between virus and mock treatments in cells differentiated from NEP, independent of their of apoE genotype.

GO Process / Total genes in process / p value / Number of genes in active data / Genes in data
1 / type I interferon-mediated signaling pathway / 85 / 4.830E-37 / 45 / IRF7, MHC class I, IFI17, IFP 35, OAS1, MxA, STAT2, OAS3, HLA-E, HLA-F, HLA-Cw3, IRF9, IFITM2, 1B57_HUMAN, IRF3, OAS2, HLA-G, HLA-A3, IFI27, HLA-C, PSMB8(LMP7), HLA-Cw4, HLA-B, HLA-B27, ISG15, HLA-A2, HLA-A, IFI6, 1B35_HUMAN, 1B08_HUMAN, ISGF3, IFITM3, IFI56, HLA-B7, ADAR1, HLAB, HLA-Cw7, SOCS3, 2'-5'-oligoadenylate synthetase, HLA-A11, STAT1, RIG-G, USP18, GBP2, STAT1/STAT2
2 / cellular response to type I interferon / 86 / 9.680E-37 / 45 / IRF7, MHC class I, IFI17, IFP 35, OAS1, MxA, STAT2, OAS3, HLA-E, HLA-F, HLA-Cw3, IRF9, IFITM2, 1B57_HUMAN, IRF3, OAS2, HLA-G, HLA-A3, IFI27, HLA-C, PSMB8(LMP7), HLA-Cw4, HLA-B, HLA-B27, ISG15, HLA-A2, HLA-A, IFI6, 1B35_HUMAN, 1B08_HUMAN, ISGF3, IFITM3, IFI56, HLA-B7, ADAR1, HLAB, HLA-Cw7, SOCS3, 2'-5'-oligoadenylate synthetase, HLA-A11, STAT1, RIG-G, USP18, GBP2, STAT1/STAT2
3 / response to type I interferon / 87 / 1.916E-36 / 45 / IRF7, MHC class I, IFI17, IFP 35, OAS1, MxA, STAT2, OAS3, HLA-E, HLA-F, HLA-Cw3, IRF9, IFITM2, 1B57_HUMAN, IRF3, OAS2, HLA-G, HLA-A3, IFI27, HLA-C, PSMB8(LMP7), HLA-Cw4, HLA-B, HLA-B27, ISG15, HLA-A2, HLA-A, IFI6, 1B35_HUMAN, 1B08_HUMAN, ISGF3, IFITM3, IFI56, HLA-B7, ADAR1, HLAB, HLA-Cw7, SOCS3, 2'-5'-oligoadenylate synthetase, HLA-A11, STAT1, RIG-G, USP18, GBP2, STAT1/STAT2
4 / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / 22 / 5.782E-25 / 20 / MHC class I, Beta-2-microglobulin, HLA-E, HLA-F, HLA-Cw3, 1B57_HUMAN, HLA-G, HLA-A3, HLA-C, HLA-Cw4, HLA-B, HLA-B27, HLA-A2, HLA-A, 1B35_HUMAN, 1B08_HUMAN, HLA-B7, HLAB, HLA-Cw7, HLA-A11
5 / interferon-gamma-mediated signaling pathway / 95 / 1.234E-24 / 37 / CIITA, MHC class II alpha chain, IRF7, MHC class I, OAS1, Beta-2-microglobulin, OAS3, GBP1, HLA-E, HLA-F, HLA-Cw3, IRF9, HLA-DRA1, 1B57_HUMAN, IRF3, OAS2, HLA-G, HLA-A3, HLA-C, HLA-Cw4, HLA-B, PKC, HLA-B27, HLA-A2, HLA-A, 1B35_HUMAN, 1B08_HUMAN, ISGF3, HLA-B7, HLAB, HLA-Cw7, SOCS3, 2'-5'-oligoadenylate synthetase, HLA-A11, STAT1, GBP2, STAT1/STAT2
6 / cytokine-mediated signaling pathway / 434 / 2.426E-23 / 76 / CIITA, MHC class II alpha chain, Ubiquitin, IRF7, SOCS5, MHC class I, Importin (karyopherin)-alpha, IFI17, UBB, Pyk2(FAK2), IFP 35, OAS1, Beta-2-microglobulin, Galpha(i)-specific peptide GPCRs, MxA, STAT2, Ceb1, OAS3, Importin (karyopherin)-beta, GBP1, HLA-E, NUP43, HLA-F, HLA-Cw3, IRF9, HLA-DRA1, IFITM2, 1B57_HUMAN, IRF3, OAS2, Galpha(q)-specific peptide GPCRs, HLA-G, HLA-A3, IFI27, UBE1L, CD74, HLA-C, NUP133, NUP62, PSMB8(LMP7), HLA-Cw4, HLA-B, PRMT2, PKC, HLA-B27, ISG15, UBCH8, HLA-A2, CCL2, Karyopherin alpha 2, APOER2, HLA-A, IFI6, 1B35_HUMAN, 1B08_HUMAN, CSF2RA, ISGF3, IFITM3, TXNL5, IFI56, HLA-B7, ADAR1, HLAB, GPR17(Amida), NUP50, HLA-Cw7, TFF2, SOCS3, CCR2, 2'-5'-oligoadenylate synthetase, HLA-A11, STAT1, RIG-G, USP18, GBP2, STAT1/STAT2
7 / response to interferon-gamma / 160 / 7.383E-23 / 45 / CIITA, MHC class II alpha chain, BST2, IRF7, MHC class I, IFI17, OAS1, Beta-2-microglobulin, OAS3, GBP1, HLA-E, HLA-F, HLA-Cw3, IRF9, HLA-DRA1, IFITM2, 1B57_HUMAN, IRF3, OAS2, HLA-G, HLA-A3, HLA-C, HLA-Cw4, HLA-B, PKC, GBP4, HLA-B27, HLA-A2, HMGB1, CCL2, HLA-A, 1B35_HUMAN, 1B08_HUMAN, ISGF3, IFITM3, HMG1,2, HLA-B7, HLAB, HLA-Cw7, SOCS3, 2'-5'-oligoadenylate synthetase, HLA-A11, STAT1, GBP2, STAT1/STAT2
8 / antigen processing and presentation of endogenous antigen / 27 / 1.772E-21 / 20 / MHC class I, TAP1 (PSF1), HLA-E, HLA-F, HLA-Cw3, 1B57_HUMAN, TAPBPL, CD74, HLA-C, HLA-Cw4, HLA-B, HLA-B27, HLA-A, 1B35_HUMAN, 1B08_HUMAN, TAP, HLA-B7, HLAB, HLA-Cw7, TAP2 (PSF2)
9 / cellular response to cytokine stimulus / 595 / 4.370E-21 / 87 / CIITA, MHC class II alpha chain, Ubiquitin, IRF7, SOCS5, MHC class I, Importin (karyopherin)-alpha, IFI17, UBB, Guanylate cyclase, Pyk2(FAK2), IFP 35, OAS1, Beta-2-microglobulin, Galpha(i)-specific peptide GPCRs, MxA, GLCM, STAT2, Ceb1, OAS3, Importin (karyopherin)-beta, GBP1, HLA-E, NUP43, HLA-F, HLA-Cw3, IRF9, HLA-DRA1, IFITM2, 1B57_HUMAN, IRF3, OAS2, Galpha(q)-specific peptide GPCRs, Gas6, HLA-G, HLA-A3, IFI27, UBE1L, CD74, HLA-C, NUP133, NUP62, PSMB8(LMP7), HLA-Cw4, HLA-B, PRMT2, PKC, GBP4, HYAL1, Neprilysin, HLA-B27, ISG15, UBCH8, HLA-A2, HMGB1, CCL2, PDE, Karyopherin alpha 2, HIF1A, APOER2, HLA-A, IFI6, 1B35_HUMAN, 1B08_HUMAN, CSF2RA, ISGF3, IFITM3, HMG1,2, TXNL5, IFI56, HLA-B7, Lymphotactin, ADAR1, HLAB, GPR17(Amida), NUP50, HLA-Cw7, TFF2, SOCS3, CCR2, 2'-5'-oligoadenylate synthetase, HLA-A11, STAT1, RIG-G, USP18, GBP2, STAT1/STAT2
10 / cellular response to interferon-gamma / 131 / 5.737E-21 / 39 / CIITA, MHC class II alpha chain, IRF7, MHC class I, OAS1, Beta-2-microglobulin, OAS3, GBP1, HLA-E, HLA-F, HLA-Cw3, IRF9, HLA-DRA1, 1B57_HUMAN, IRF3, OAS2, HLA-G, HLA-A3, HLA-C, HLA-Cw4, HLA-B, PKC, GBP4, HLA-B27, HLA-A2, CCL2, HLA-A, 1B35_HUMAN, 1B08_HUMAN, ISGF3, HLA-B7, HLAB, HLA-Cw7, SOCS3, 2'-5'-oligoadenylate synthetase, HLA-A11, STAT1, GBP2, STAT1/STAT2

Genes were analyzed for GO processes using the MetaCore software on GeneGo from Thomson Reuters, including genes differentially expressed when comparing HIV-exposed vs. mock-exposed cultures. All cultures were included in this analysis, regardless of apoE genotype. p≤0.01