PEACHi
Cluster o-+ is enriched in the following gene classes
GeneSet DB Hit Count
Pathways_-_Reactome.gmt.txt 8
GO_-_Molecular_Function.gmt.txt 2
Chromosomal_Bands.gmt.txt 5
GeneSet Name GeneSet DB log(P) Qvalue Observed in Background Observed in Cluster Expected in Cluster
E2F mediated regulation of DNA replication Pathways_-_Reactome.gmt.txt -2.2 0.04333 26.0 3.0 0.75
G2/M Transition Pathways_-_Reactome.gmt.txt -2.4 0.035 54.0 5.0 1.55
Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell Pathways_-_Reactome.gmt.txt -2.8 0.01955 18.0 3.0 0.52
Interferon alpha/beta signaling Pathways_-_Reactome.gmt.txt -2.6 0.02804 21.0 3.0 0.6
MAP kinase activation in TLR cascade Pathways_-_Reactome.gmt.txt -2.9 0.0181 29.0 4.0 0.83
Mitotic G2-G2/M phases Pathways_-_Reactome.gmt.txt -2.3 0.03937 56.0 5.0 1.6
NFkB and MAP kinases activation mediated by TLR4 signaling repertoire Pathways_-_Reactome.gmt.txt -2.2 0.04598 42.0 4.0 1.2
PHOSPHORIC DIESTER HYDROLASE ACTIVITY GO_-_Molecular_Function.gmt.txt -3.9 0.01669 10.0 3.0 0.29
PHOSPHORIC ESTER HYDROLASE ACTIVITY GO_-_Molecular_Function.gmt.txt -3.5 0.03238 61.0 7.0 1.75
TRAF6 Mediated Induction of proinflammatory cytokines Pathways_-_Reactome.gmt.txt -2.3 0.041 40.0 4.0 1.15
chr15q15 Chromosomal_Bands.gmt.txt -2.5 0.02637 22.0 3.0 0.63
chr18p11 Chromosomal_Bands.gmt.txt -3.4 0.0089 23.0 4.0 0.66
chr3p22 Chromosomal_Bands.gmt.txt -2.8 0.01797 18.0 3.0 0.52
chr4p15 Chromosomal_Bands.gmt.txt -3.7 0.00681 11.0 3.0 0.32
chr6p22 Chromosomal_Bands.gmt.txt -2.2 0.03815 27.0 3.0 0.77
Gene expression pattern
Figure: Temporal expression patterns were grouped into clusters with differential expression profiles at three phases of the viral life cycle, namely reverse transcription, integration, and late phase. Boxplots on the left show the distribution of the normalized regression weights for each viral phase used in clustering. Expression change pattern of each gene over time is plotted for mock and HIV samples (dotted orange lines) along with the cluster median (bold red line).
List of genes
Ensembl ID Name Cluster
ENSG00000167637 AC008733.1 o-+
ENSG00000253918 AC010207.2 o-+
ENSG00000198637 AC016596.1 o-+
ENSG00000235225 AC016712.2 o-+
ENSG00000235655 AC018890.1 o-+
ENSG00000227973 AC023356.3 o-+
ENSG00000166503 AC024270.1 o-+
ENSG00000143429 AC027612.6 o-+
ENSG00000162836 ACP6 o-+
ENSG00000186063 AIDA o-+
ENSG00000106524 ANKMY2 o-+
ENSG00000224334 AP000357.4 o-+
ENSG00000240771 ARHGEF25 o-+
ENSG00000032219 ARID4A o-+
ENSG00000143862 ARL8A o-+
ENSG00000204147 ASAH2B o-+
ENSG00000177981 ASB8 o-+
ENSG00000177556 ATOX1 o-+
ENSG00000143515 ATP8B2 o-+
ENSG00000112983 BRD8 o-+
ENSG00000096070 BRPF3 o-+
ENSG00000165511 C10orf25 o-+
ENSG00000129534 C14orf106 o-+
ENSG00000119705 C14orf156 o-+
ENSG00000140688 C16orf58 o-+
ENSG00000170222 C17orf48 o-+
ENSG00000144647 C3orf39 o-+
ENSG00000130023 C6orf70 o-+
ENSG00000157693 C9orf91 o-+
ENSG00000162545 CAMK2N1 o-+
ENSG00000213995 CARKD o-+
ENSG00000145439 CBR4 o-+
ENSG00000177352 CCDC71 o-+
ENSG00000177697 CD151 o-+
ENSG00000158402 CDC25C o-+
ENSG00000170312 CDK1 o-+
ENSG00000102384 CENPI o-+
ENSG00000138092 CENPO o-+
ENSG00000101639 CEP192 o-+
ENSG00000131873 CHSY1 o-+
ENSG00000131148 COX4NB o-+
ENSG00000111775 COX6A1 o-+
ENSG00000226976 COX6A1P2 o-+
ENSG00000157184 CPT2 o-+
ENSG00000140577 CRTC3 o-+
ENSG00000159176 CSRP1 o-+
ENSG00000233937 CTC-338M12.4 o-+
ENSG00000250705 CTC-470C15.1 o-+
ENSG00000251118 CTC-505O3.1 o-+
ENSG00000243297 CTD-2525J15.1 o-+
ENSG00000175215 CTDSP2 o-+
ENSG00000174080 CTSF o-+
ENSG00000083097 DOPEY1 o-+
ENSG00000108861 DUSP3 o-+
ENSG00000140598 EFTUD1 o-+
ENSG00000132205 EMILIN2 o-+
ENSG00000178567 EPM2AIP1 o-+
ENSG00000135476 ESPL1 o-+
ENSG00000221968 FADS3 o-+
ENSG00000248019 FAM13AOS o-+
ENSG00000182646 FAM156A o-+
ENSG00000179304 FAM156B o-+
ENSG00000221909 FAM200A o-+
ENSG00000119812 FAM98A o-+
ENSG00000156860 FBRS o-+
ENSG00000118564 FBXL5 o-+
ENSG00000135108 FBXO21 o-+
ENSG00000147364 FBXO25 o-+
ENSG00000109536 FRG1 o-+
ENSG00000107164 FUBP3 o-+
ENSG00000001036 FUCA2 o-+
ENSG00000137731 FXYD2 o-+
ENSG00000147536 GINS4 o-+
ENSG00000090863 GLG1 o-+
ENSG00000250571 GLI4 o-+
ENSG00000144230 GPR17 o-+
ENSG00000160360 GPSM1 o-+
ENSG00000137106 GRHPR o-+
ENSG00000197448 GSTK1 o-+
ENSG00000220875 H3F3AP1 o-+
ENSG00000137814 HAUS2 o-+
ENSG00000126264 HCST o-+
ENSG00000013583 HEBP1 o-+
ENSG00000197238 HIST1H4J o-+
ENSG00000197914 HIST1H4K o-+
ENSG00000234745 HLA-B o-+
ENSG00000204525 HLA-C o-+
ENSG00000189159 HN1 o-+
ENSG00000126945 HNRNPH2 o-+
ENSG00000136231 IGF2BP3 o-+
ENSG00000148384 INPP5E o-+
ENSG00000125629 INSIG2 o-+
ENSG00000183856 IQGAP3 o-+
ENSG00000187608 ISG15 o-+
ENSG00000165572 KBTBD6 o-+
ENSG00000155729 KCTD18 o-+
ENSG00000168502 KIAA0802 o-+
ENSG00000237649 KIFC1 o-+
ENSG00000167702 KIFC2 o-+
ENSG00000102554 KLF5 o-+
ENSG00000005893 LAMP2 o-+
ENSG00000100068 LRP5L o-+
ENSG00000168904 LRRC28 o-+
ENSG00000183011 LSMD1 o-+
ENSG00000111144 LTA4H o-+
ENSG00000102897 LYRM1 o-+
ENSG00000102158 MAGT1 o-+
ENSG00000198909 MAP3K3 o-+
ENSG00000047849 MAP4 o-+
ENSG00000123066 MED13L o-+
ENSG00000118579 MED28 o-+
ENSG00000105429 MEGF8 o-+
ENSG00000037749 MFAP3 o-+
ENSG00000198840 MT-ND3 o-+
ENSG00000163719 MTMR14 o-+
ENSG00000139505 MTMR6 o-+
ENSG00000118513 MYB o-+
ENSG00000198951 NAGA o-+
ENSG00000134265 NAPG o-+
ENSG00000175701 NCRNA00116 o-+
ENSG00000065518 NDUFB4 o-+
ENSG00000125820 NKX2-2 o-+
ENSG00000091592 NLRP1 o-+
ENSG00000106100 NOD1 o-+
ENSG00000170485 NPAS2 o-+
ENSG00000149308 NPAT o-+
ENSG00000173566 NUDT18 o-+
ENSG00000164978 NUDT2 o-+
ENSG00000198836 OPA1 o-+
ENSG00000085465 OVGP1 o-+
ENSG00000123360 PDE1B o-+
ENSG00000169299 PGM2 o-+
ENSG00000038210 PI4K2B o-+
ENSG00000143398 PIP5K1A o-+
ENSG00000137841 PLCB2 o-+
ENSG00000137713 PPP2R1B o-+
ENSG00000146143 PRIM2 o-+
ENSG00000125818 PSMF1 o-+
ENSG00000152229 PSTPIP2 o-+
ENSG00000110536 PTPMT1 o-+
ENSG00000101417 PXMP4 o-+
ENSG00000116260 QSOX1 o-+
ENSG00000169228 RAB24 o-+
ENSG00000161800 RACGAP1 o-+
ENSG00000006451 RALA o-+
ENSG00000049449 RCN1 o-+
ENSG00000168476 REEP4 o-+
ENSG00000101695 RNF125 o-+
ENSG00000219755 RP1-199J3.5 o-+
ENSG00000218510 RP1-224A6.4 o-+
ENSG00000226436 RP1-22N22.1 o-+
ENSG00000213598 RP11-112J1.1 o-+
ENSG00000235280 RP11-120K24.2 o-+
ENSG00000241853 RP11-147K6.1 o-+
ENSG00000230291 RP11-244J10.1 o-+
ENSG00000178458 RP11-308D13.2 o-+
ENSG00000241281 RP11-364M6.1 o-+
ENSG00000236534 RP11-393H6.2 o-+
ENSG00000250966 RP11-402J6.3 o-+
ENSG00000244740 RP11-463H24.1 o-+
ENSG00000230228 RP11-4M23.4 o-+
ENSG00000242295 RP11-522B15.1 o-+
ENSG00000213433 RP11-54C4.1 o-+
ENSG00000177359 RP11-551L14.1 o-+
ENSG00000213302 RP11-560I19.2 o-+
ENSG00000124399 RP11-663P9.2 o-+
ENSG00000231409 RP11-83J16.1 o-+
ENSG00000213470 RP11-972K6.1 o-+
ENSG00000236735 RP13-470G3.1 o-+
ENSG00000241680 RP3-424M6.1 o-+
ENSG00000071082 RPL31 o-+
ENSG00000214326 RPL31P1 o-+
ENSG00000230837 RPL31P2 o-+
ENSG00000198918 RPL39 o-+
ENSG00000214289 RPL39P5 o-+
ENSG00000083750 RRAGB o-+
ENSG00000205323 SARNP o-+
ENSG00000130489 SCO2 o-+
ENSG00000093183 SEC22C o-+
ENSG00000214765 SEPT7P2 o-+
ENSG00000164402 SEPT8 o-+
ENSG00000111897 SERINC1 o-+
ENSG00000187231 SESTD1 o-+
ENSG00000126821 SGPP1 o-+
ENSG00000111252 SH2B3 o-+
ENSG00000087266 SH3BP2 o-+
ENSG00000149577 SIDT2 o-+
ENSG00000100372 SLC25A17 o-+
ENSG00000102100 SLC35A2 o-+
ENSG00000166311 SMPD1 o-+
ENSG00000099940 SNAP29 o-+
ENSG00000148158 SNX30 o-+
ENSG00000134243 SORT1 o-+
ENSG00000144451 SPAG16 o-+
ENSG00000167881 SRP68 o-+
ENSG00000115525 ST3GAL5 o-+
ENSG00000204344 STK19 o-+
ENSG00000067221 STOML1 o-+
ENSG00000102125 TAZ o-+
ENSG00000137310 TCF19 o-+
ENSG00000100926 TM9SF1 o-+
ENSG00000134291 TMEM106C o-+
ENSG00000096092 TMEM14A o-+
ENSG00000166471 TMEM41B o-+
ENSG00000062716 TMEM49 o-+
ENSG00000116857 TMEM9 o-+
ENSG00000125827 TMX4 o-+
ENSG00000157873 TNFRSF14 o-+
ENSG00000107854 TNKS2 o-+
ENSG00000136925 TSTD2 o-+
ENSG00000037042 TUBG2 o-+
ENSG00000092445 TYRO3 o-+
ENSG00000159202 UBE2Z o-+
ENSG00000153560 UBP1 o-+
ENSG00000154978 VOPP1 o-+
ENSG00000085433 WDR47 o-+
ENSG00000105875 WDR91 o-+
ENSG00000174282 ZBTB4 o-+
ENSG00000122299 ZC3H7A o-+
ENSG00000168228 ZCCHC4 o-+
ENSG00000186908 ZDHHC17 o-+
ENSG00000131061 ZNF341 o-+
ENSG00000160094 ZNF362 o-+
ENSG00000215421 ZNF407 o-+
ENSG00000083817 ZNF416 o-+
ENSG00000229809 ZNF688 o-+
ENSG00000132485 ZRANB2 o-+
hsa-miR-3182 hsa-miR-3182 o-+
hsa-miR-4755-3p hsa-miR-4755-3p o-+