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