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1 Figure S1. Histone modification profiles near transcription start sites. The overall histone modification around transcription start sites (TSSs) was calculated. Histone modification levels of genes were separated by their expression levels; 2,000 high, medium, and low genes.
2 Figure S2. Histone modification enrichment patterns at the integration sites of HIV-1. (a) Two HIV-1 integration sites in NCHA1 cells were marked by arrows in chr2 and chrx. (b) In ACH2 cells, the HIV-1 was integrated in chr7 and marked by arrow. (c) The integrated HIV- 1 genome itself was also subjected to enrichment analysis of histone H3K9ac. 1: Gag-Pol (336-4,642), 2: Gag (336-1,838), 3: Vif (4,587-5,165), 4: Vpr (5,105-5,396), 5: Tat (5,377-7,970), 6: Rev (5,516-8,199), 7: Vpu (5,608-5,856), 8: Env (5,771-8,341), 9: Nef (8,343-8,963).
3 Figure S3. Histone modification enrichment patterns of NFAT family genes. Histone modifications, H3K4me3 and H3K9ac of NFATC4 (a) and NFATC2 (b) loci were displayed on the UCSC genome browser.
4 Table S1. The top 10 significantly enriched GO terms with down-regulated cluster genes. GO ID GO terms p-val corr p- val cluster frequency total frequency Cluster cell surface receptor linked signaling 7.47E E-10 17/ % 1281/ % interspecies interaction between organisms 2.61E E-09 11/ % 328/ % 1775 cell activation 1.54E E-09 10/ % 276/ % T cell activation 1.86E E-09 8/ % 120/ % leukocyte activation 1.17E E-08 9/ % 234/ % signaling 1.61E E-08 18/ % 2101/ % 2684 positive regulation of immune system 3.66E E-08 9/ % 266/ % lymphocyte activation 6.56E E-08 8/ % 187/ % signaling 1.02E E-08 20/ % 3132/ % 2682 regulation of immune system 1.06E E-08 10/ % 425/ % Cluster response to chemical stimulus 7.92E E-14 27/ % 1465/ % 7166 cell surface receptor linked signaling 8.68E E-12 24/ % 1281/ % signaling 6.62E E-10 27/ % 2101/ % response to organic substance 1.29E E-10 19/ % 870/ % regulation of molecular function 4.09E E-09 20/ % 1063/ % 7626 locomotory behavior 1.73E E-09 12/ % 274/ % signaling 2.48E E-09 30/ % 3132/ % regulation of phosphorylation 1.71E E-08 14/ % 519/ % response to stimulus 1.72E E-08 31/ % 3634/ % regulation of phosphorus metabolic 3.10E E-08 14/ % 543/ % regulation of phosphate metabolic 3.10E E-08 14/ % 543/ % Cluster cell death 2.36E E-08 15/ % 698/ % death 2.60E E-08 15/ % 703/ % response to chemical stimulus 2.63E E-08 20/ % 1465/ % 60 protein import into nucleus, translocation 2.78E E-08 6/ % 32/ % positive regulation of molecular function 8.67E E-07 14/ % 639/ % positive regulation of catalytic activity 1.77E E-07 13/ % 554/ % 7166 cell surface receptor linked signaling 2.05E E-07 18/ % 1281/ % response to organic substance 4.92E E-07 15/ % 870/ % positive regulation of cellular protein metabolic 5.16E E-07 10/ % 291/ % regulation of molecular function 8.88E E-06 16/ % 1063/ %
5 Cluster positive regulation of calcium-mediated 3.16E E-06 4/ % signaling 18/ % regulation of calcium-mediated signaling 6.18E E-06 4/ % 21/ % 2684 positive regulation of immune system 6.87E E-06 7/ % 265/ % 2376 immune system 8.66E E-06 10/ % 948/ % 7165 signal transduction 2.77E E-06 12/ % 1878/ % signaling 4.31E E-06 14/ % 3131/ % signal transmission 1.35E E-05 12/ % 2157/ % signaling 1.35E E-05 12/ % 2157/ % 2682 regulation of immune system 1.74E E-05 7/ % 424/ % positive regulation of cytokine biosynthetic 2.53E E-05 4/ % 51/ % Cluster negative regulation of signaling 8.99E E-02 3/ % 262/ % 7165 signal transduction 1.30E E-02 6/ % 1878/ % 6275 regulation of DNA replication 1.41E E-02 2/ % 74/ % negative regulation of cell communication 1.72E E-02 3/ % 328/ % regulation of Wnt receptor signaling 1.94E E-02 2/ % 87/ % 6435 threonyl-trna aminoacylation 2.31E E-02 1/11 9.0% 3/ % negative regulation of epithelial cell migration 2.31E E-02 1/11 9.0% 3/ % signal transmission 2.72E E-02 6/ % 2157/ % signaling 2.72E E-02 6/ % 2157/ % nucleic acid metabolic 3.00E E-02 5/ % 1460/ % Significant GO terms were identified by BiNGO plugin of Cytoscape with hypergeometric test. Most significantly enriched terms were selected according to their p-value.
6 Table S2. The top 10 significantly enriched GO terms with up-regulated cluster genes. GO ID GO terms p-val corr p- val cluster frequency total frequency Cluster regulation of cell cycle 1.36E E-21 22/ % 450/ % positive regulation of cellular 1.76E E-17 30/ % 2007/ % negative regulation of cellular 4.62E E-17 29/ % 1848/ % positive regulation of biological 2.98E E-17 30/ % 2211/ % positive regulation of macromolecule metabolic 5.40E E-16 23/ % 943/ % negative regulation of biological 5.99E E-16 29/ % 2024/ % regulation of cell proliferation 1.44E E-16 22/ % 851/ % 9893 positive regulation of metabolic 3.12E E-16 23/ % 1020/ % negative regulation of cell cycle 4.13E E-16 14/ % 179/ % negative regulation of cellular metabolic 7.54E E-16 21/ % 790/ % Cluster second-messenger-mediated signaling 8.78E E-08 8/ % 231/ % lipid phosphorylation 6.71E E-08 4/ % 12/ % phosphoinositide phosphorylation 6.71E E-08 4/ % 12/ % 9755 hormone-mediated signaling 3.12E E-07 5/ % 52/ % activation of protein kinase A activity 3.22E E-07 4/ % 17/ % lipid modification 9.82E E-07 5/ % 65/ % phosphoinositide metabolic 2.49E E-06 5/ % 78/ % 6644 phospholipid metabolic 6.89E E-06 6/ % 197/ % organophosphate metabolic 9.52E E-06 6/ % 208/ % 7193 inhibition of adenylate cyclase activity by G-protein signaling 1.21E E-06 4/ % 40/ % Cluster positive regulation of metabolic 6.43E E-17 30/ % 1017/ % positive regulation of cellular metabolic 2.44E E-17 29/ % 965/ % interspecies interaction between organisms 1.36E E-17 20/ % 327/ % positive regulation of biological 1.76E E-17 38/ % 2206/ % positive regulation of cellular 1.02E E-16 36/ % 2003/ % regulation of cellular metabolic 1.80E E-16 45/ % 3734/ % 6357 regulation of transcription from RNA polymerase II promoter 2.39E E-16 25/ % 747/ % positive regulation of macromolecule metabolic 2.94E E-16 27/ % 940/ % regulation of macromolecule metabolic 4.87E E-16 43/ % 3375/ % response to organic substance 6.05E E-15 26/ % 869/ % Cluster regulation of cell cycle 1.03E E-23 30/ % 451/ %
7 51716 cellular response to stimulus 2.95E E-19 35/ % 991/ % positive regulation of cellular 1.20E E-18 44/ % 2008/ % negative regulation of cellular 4.79E E-17 42/ % 1849/ % positive regulation of biological 6.12E E-17 45/ % 2212/ % positive regulation of macromolecule metabolic 1.34E E-17 32/ % 944/ % regulation of cell proliferation 1.00E E-16 30/ % 852/ % 9893 positive regulation of metabolic 1.38E E-16 32/ % 1021/ % negative regulation of biological 1.52E E-16 42/ % 2025/ % negative regulation of cellular metabolic 1.57E E-16 29/ % 791/ % Cluster translational elongation 2.46E E-03 3/9 33.3% 97/ % negative regulation of centrosome cycle 6.29E E-02 1/9 11.1% 1/ % negative regulation of centriole replication 6.29E E-02 1/9 11.1% 1/ % 6412 translation 6.39E E-02 3/9 33.3% 291/ % regulation of centriole replication 1.89E E-02 1/9 11.1% 3/ % response to indole-3-methanol 3.14E E-02 1/9 11.1% 5/ % cellular response to indole-3-methanol 3.14E E-02 1/9 11.1% 5/ % 6729 tetrahydrobiopterin biosynthetic 3.77E E-02 1/9 11.1% 6/ % protein K6-linked ubiquitination 4.40E E-02 1/9 11.1% 7/ % tetrahydrobiopterin metabolic 4.40E E-02 1/9 11.1% 7/ % Cluster cellular macromolecule metabolic 2.80E E-05 20/ % 3508/ % cellular metabolic 2.49E E-05 22/ % 4990/ % macromolecule metabolic 3.23E E-05 20/ % 4017/ % interspecies interaction between organisms 1.38E E-04 7/ % 327/ % cellular protein metabolic 4.72E E-04 14/ % 2153/ % primary metabolic 6.18E E-04 21/ % 5288/ % 8152 metabolic 8.30E E-03 22/ % 5959/ % intracellular signaling 1.85E E-03 10/ % 1158/ % 6461 protein complex assembly 2.46E E-03 7/ % 507/ % protein complex biogenesis 2.46E E-03 7/ % 507/ % Significant GO terms were identified by BiNGO plugin of Cytoscape with hypergeometric test. Most significantly enriched terms were selected according to their p-value.
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