PEACHi
GeneSet Cell Cycle (Pathways_-_Reactome.gmt.txt) is enriched in the following clusters
Cluster log(P) Qvalue Observed in Background Observed in Cluster Expected in Cluster
o--b -3.2 0.01223 260.0 54.0 35.92
oo- -2.4 0.03396 260.0 11.0 4.95
o+o -2.8 0.01955 260.0 27.0 15.39
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
ENSG00000102977 ACD o+-
ENSG00000138107 ACTR1A ---
ENSG00000153207 AHCTF1 o--b
ENSG00000127914 AKAP9 NonAssociatedWithProgression
ENSG00000116127 ALMS1 NonAssociatedWithProgression
ENSG00000153107 ANAPC1 o--a
ENSG00000164162 ANAPC10 o++b
ENSG00000141552 ANAPC11 NonAssociatedWithProgression
ENSG00000176248 ANAPC2 NonAssociatedWithProgression
ENSG00000053900 ANAPC4 NonAssociatedWithProgression
ENSG00000089053 ANAPC5 o++a
ENSG00000196510 ANAPC7 o++b
ENSG00000175279 APITD1 NonAssociatedWithProgression
ENSG00000149311 ATM NonAssociatedWithProgression
ENSG00000175054 ATR NonAssociatedWithProgression
ENSG00000164053 ATRIP NonAssociatedWithProgression
ENSG00000087586 AURKA +-o
ENSG00000178999 AURKB o--b
ENSG00000141577 AZI1 ---
ENSG00000123810 B9D2 -o-
ENSG00000089685 BIRC5 ---
ENSG00000012048 BRCA1 NonAssociatedWithProgression
ENSG00000166167 BTRC --o
ENSG00000169679 BUB1 -o-
ENSG00000156970 BUB1B +oo
ENSG00000154473 BUB3 o--a
ENSG00000040275 CCDC99 o+-
ENSG00000145386 CCNA2 o--b
ENSG00000134057 CCNB1 oo-
ENSG00000157456 CCNB2 oo-
ENSG00000112576 CCND3 o--b
ENSG00000105173 CCNE1 o--b
ENSG00000175305 CCNE2 NonAssociatedWithProgression
ENSG00000134480 CCNH -o-
ENSG00000079335 CDC14A o+o
ENSG00000130177 CDC16 NonAssociatedWithProgression
ENSG00000094880 CDC23 NonAssociatedWithProgression
ENSG00000164045 CDC25A o--b
ENSG00000101224 CDC25B o--a
ENSG00000158402 CDC25C o-+
ENSG00000176386 CDC26 NonAssociatedWithProgression
ENSG00000004897 CDC27 NonAssociatedWithProgression
ENSG00000093009 CDC45 o++b
ENSG00000094804 CDC6 NonAssociatedWithProgression
ENSG00000097046 CDC7 NonAssociatedWithProgression
ENSG00000134690 CDCA8 o--a
ENSG00000170312 CDK1 o-+
ENSG00000008128 CDK11A o-o
ENSG00000123374 CDK2 oo-
ENSG00000135446 CDK4 o--a
ENSG00000136861 CDK5RAP2 o-o
ENSG00000105810 CDK6 o--a
ENSG00000134058 CDK7 o+o
ENSG00000124762 CDKN1A oo-
ENSG00000111276 CDKN1B +o+
ENSG00000123080 CDKN2C o-o
ENSG00000115163 CENPA o-o
ENSG00000145241 CENPC1 NonAssociatedWithProgression
ENSG00000138778 CENPE NonAssociatedWithProgression
ENSG00000117724 CENPF o--a
ENSG00000153044 CENPH oo-
ENSG00000102384 CENPI o-+
ENSG00000151849 CENPJ o+o
ENSG00000123219 CENPK o+o
ENSG00000120334 CENPL o--b
ENSG00000100162 CENPM o--a
ENSG00000166451 CENPN o+-
ENSG00000138092 CENPO o-+
ENSG00000188312 CENPP -oo
ENSG00000031691 CENPQ o--b
ENSG00000102901 CENPT o--b
ENSG00000174799 CEP135 +oo
ENSG00000101639 CEP192 o-+
ENSG00000126001 CEP250 o-o
ENSG00000198707 CEP290 -oo
ENSG00000166037 CEP57 NonAssociatedWithProgression
ENSG00000182923 CEP63 NonAssociatedWithProgression
ENSG00000114107 CEP70 NonAssociatedWithProgression
ENSG00000112877 CEP72 +o+
ENSG00000101624 CEP76 o++b
ENSG00000148019 CEP78 NonAssociatedWithProgression
ENSG00000147400 CETN2 o--b
ENSG00000149554 CHEK1 o+o
ENSG00000183765 CHEK2 ---
ENSG00000175216 CKAP5 NonAssociatedWithProgression
ENSG00000173207 CKS1B NonAssociatedWithProgression
ENSG00000074054 CLASP1 NonAssociatedWithProgression
ENSG00000163539 CLASP2 +oo
ENSG00000130779 CLIP1 o+o
ENSG00000141551 CSNK1D o--a
ENSG00000213923 CSNK1E o--b
ENSG00000055130 CUL1 o++a
ENSG00000006634 DBF4 ---
ENSG00000204843 DCTN1 ---
ENSG00000175203 DCTN2 --o
ENSG00000228716 DHFR o++a
ENSG00000101191 DIDO1 o-o
ENSG00000130826 DKC1 o--b
ENSG00000138346 DNA2 o++b
ENSG00000149636 DSN1 NonAssociatedWithProgression
ENSG00000077380 DYNC1I2 o+o
ENSG00000088986 DYNLL1 --o
ENSG00000157540 DYRK1A NonAssociatedWithProgression
ENSG00000101412 E2F1 o--b
ENSG00000007968 E2F2 o--a
ENSG00000112242 E2F3 NonAssociatedWithProgression
ENSG00000205250 E2F4 ---
ENSG00000133740 E2F5 o--b
ENSG00000186871 ERCC6L o-o
ENSG00000112029 FBXO5 NonAssociatedWithProgression
ENSG00000168496 FEN1 NonAssociatedWithProgression
ENSG00000213066 FGFR1OP o+-
ENSG00000101003 GINS1 o+o
ENSG00000147536 GINS4 o-+
ENSG00000112312 GMNN NonAssociatedWithProgression
ENSG00000114745 GORASP1 NonAssociatedWithProgression
ENSG00000188486 H2AFX ---
ENSG00000164032 H2AFZ o-o
ENSG00000137814 HAUS2 o-+
ENSG00000116478 HDAC1 ---
ENSG00000137259 HIST1H2AB oo-
ENSG00000180573 HIST1H2AC NonAssociatedWithProgression
ENSG00000196226 HIST1H2BB o--b
ENSG00000158373 HIST1H2BD NonAssociatedWithProgression
ENSG00000197459 HIST1H2BH oo-
ENSG00000196176 HIST1H4A ---
ENSG00000183558 HIST2H2AA3 o--b
ENSG00000184678 HIST2H2BE NonAssociatedWithProgression
ENSG00000123485 HJURP o-o
ENSG00000080824 HSP90AA1 NonAssociatedWithProgression
ENSG00000136273 HUS1 o+o
ENSG00000142856 ITGB3BP -+o
ENSG00000121621 KIF18A NonAssociatedWithProgression
ENSG00000112984 KIF20A NonAssociatedWithProgression
ENSG00000137807 KIF23 o--a
ENSG00000068796 KIF2A o+o
ENSG00000142945 KIF2C o--b
ENSG00000184445 KNTC1 o+o
ENSG00000105486 LIG1 o--a
ENSG00000188223 LIN37 +o+
ENSG00000189308 LIN54 oo-
ENSG00000183814 LIN9 o+o
ENSG00000113368 LMNB1 o--b
ENSG00000002822 MAD1L1 o-o
ENSG00000164109 MAD2L1 NonAssociatedWithProgression
ENSG00000101367 MAPRE1 o--b
ENSG00000125952 MAX NonAssociatedWithProgression
ENSG00000065328 MCM10 NonAssociatedWithProgression
ENSG00000073111 MCM2 o--a
ENSG00000104738 MCM4 o--a
ENSG00000100297 MCM5 o--b
ENSG00000076003 MCM6 o--a
ENSG00000166508 MCM7 o--b
ENSG00000125885 MCM8 oo+
ENSG00000135679 MDM2 -o-
ENSG00000167842 MIS12 o+o
ENSG00000151725 MLF1IP NonAssociatedWithProgression
ENSG00000101057 MYBL2 o--b
ENSG00000136997 MYC o--b
ENSG00000080986 NDC80 o++b
ENSG00000072864 NDE1 --o
ENSG00000166579 NDEL1 o++b
ENSG00000139350 NEDD1 o+o
ENSG00000117650 NEK2 o--b
ENSG00000145912 NHP2 o-o
ENSG00000101004 NINL o--a
ENSG00000181163 NPM1 o--b
ENSG00000117697 NSL1 o+-
ENSG00000090273 NUDC o--a
ENSG00000143228 NUF2 NonAssociatedWithProgression
ENSG00000137497 NUMA1 o--b
ENSG00000111581 NUP107 -+o
ENSG00000069248 NUP133 o+-
ENSG00000030066 NUP160 NonAssociatedWithProgression
ENSG00000075188 NUP37 NonAssociatedWithProgression
ENSG00000125450 NUP85 o--b
ENSG00000110713 NUP98 o--a
ENSG00000136811 ODF2 o--b
ENSG00000046651 OFD1 NonAssociatedWithProgression
ENSG00000104147 OIP5 -oo
ENSG00000085840 ORC1 o+o
ENSG00000115942 ORC2 o++b
ENSG00000135336 ORC3 o+o
ENSG00000115947 ORC4 o+-
ENSG00000164815 ORC5 o+o
ENSG00000091651 ORC6 o--a
ENSG00000007168 PAFAH1B1 o+-
ENSG00000078674 PCM1 o--a
ENSG00000132646 PCNA -o-
ENSG00000160299 PCNT o--a
ENSG00000127564 PKMYT1 +-o
ENSG00000166851 PLK1 o--a
ENSG00000142731 PLK4 o+-
ENSG00000160783 PMF1 o-o
ENSG00000101868 POLA1 NonAssociatedWithProgression
ENSG00000014138 POLA2 o++b
ENSG00000062822 POLD1 o--a
ENSG00000106628 POLD2 o--b
ENSG00000077514 POLD3 o+o
ENSG00000175482 POLD4 --o
ENSG00000177084 POLE o--b
ENSG00000100479 POLE2 -o-
ENSG00000128513 POT1 o++b
ENSG00000186298 PPP1CC o--b
ENSG00000113575 PPP2CA o--b
ENSG00000104695 PPP2CB +o+
ENSG00000105568 PPP2R1A o--b
ENSG00000137713 PPP2R1B o-+
ENSG00000221914 PPP2R2A o--b
ENSG00000167393 PPP2R3B o--a
ENSG00000066027 PPP2R5A o--b
ENSG00000068971 PPP2R5B NonAssociatedWithProgression
ENSG00000078304 PPP2R5C NonAssociatedWithProgression
ENSG00000112640 PPP2R5D o--a
ENSG00000154001 PPP2R5E o-o
ENSG00000198056 PRIM1 ---
ENSG00000146143 PRIM2 o-+
ENSG00000072062 PRKACA ---
ENSG00000129084 PSMA1 o--a
ENSG00000106588 PSMA2 o+o
ENSG00000100567 PSMA3 o+o
ENSG00000041357 PSMA4 -+o
ENSG00000143106 PSMA5 o--a
ENSG00000100902 PSMA6 NonAssociatedWithProgression
ENSG00000101182 PSMA7 -+o
ENSG00000008018 PSMB1 o-o
ENSG00000126067 PSMB2 oo-
ENSG00000108294 PSMB3 -+o
ENSG00000159377 PSMB4 NonAssociatedWithProgression
ENSG00000100804 PSMB5 o--b
ENSG00000142507 PSMB6 o-o
ENSG00000136930 PSMB7 NonAssociatedWithProgression
ENSG00000204264 PSMB8 o--b
ENSG00000240065 PSMB9 o-o
ENSG00000100764 PSMC1 NonAssociatedWithProgression
ENSG00000161057 PSMC2 o+o
ENSG00000165916 PSMC3 o-o
ENSG00000013275 PSMC4 NonAssociatedWithProgression
ENSG00000087191 PSMC5 -+o
ENSG00000100519 PSMC6 o+o
ENSG00000173692 PSMD1 NonAssociatedWithProgression
ENSG00000101843 PSMD10 o+o
ENSG00000108671 PSMD11 NonAssociatedWithProgression
ENSG00000197170 PSMD12 oo-
ENSG00000185627 PSMD13 o--b
ENSG00000115233 PSMD14 o+o
ENSG00000175166 PSMD2 ---
ENSG00000108344 PSMD3 ---
ENSG00000159352 PSMD4 NonAssociatedWithProgression
ENSG00000095261 PSMD5 o++b
ENSG00000163636 PSMD6 o+o
ENSG00000099341 PSMD8 o--b
ENSG00000110801 PSMD9 o--b
ENSG00000100911 PSME2 NonAssociatedWithProgression
ENSG00000131467 PSME3 o-o
ENSG00000068878 PSME4 o--b
ENSG00000125818 PSMF1 o-+
ENSG00000164611 PTTG1 NonAssociatedWithProgression
ENSG00000113456 RAD1 NonAssociatedWithProgression
ENSG00000152942 RAD17 o--a
ENSG00000164754 RAD21 o--b
ENSG00000172613 RAD9A o--b
ENSG00000153201 RANBP2 o+o
ENSG00000100401 RANGAP1 o-o
ENSG00000139687 RB1 NonAssociatedWithProgression
ENSG00000162521 RBBP4 NonAssociatedWithProgression
ENSG00000102054 RBBP7 o-o
ENSG00000080839 RBL1 +o+
ENSG00000103479 RBL2 NonAssociatedWithProgression
ENSG00000179051 RCC2 o--b
ENSG00000035928 RFC1 o--b
ENSG00000049541 RFC2 o--b
ENSG00000133119 RFC3 -oo
ENSG00000163918 RFC4 o--a
ENSG00000111445 RFC5 -oo
ENSG00000143207 RFWD2 o++a
ENSG00000117748 RPA2 oo-
ENSG00000106399 RPA3 o++b
ENSG00000177954 RPS27 o-o
ENSG00000143947 RPS27A o+o
ENSG00000171848 RRM2 o--a
ENSG00000048649 RSF1 +-o
ENSG00000175792 RUVBL1 ---
ENSG00000183207 RUVBL2 o--a
ENSG00000054282 SDCCAG8 ---
ENSG00000157020 SEC13 --o
ENSG00000085415 SEH1L o-o
ENSG00000198089 SFI1 NonAssociatedWithProgression
ENSG00000129810 SGOL1 NonAssociatedWithProgression
ENSG00000163535 SGOL2 NonAssociatedWithProgression
ENSG00000154839 SKA1 o-o
ENSG00000182628 SKA2 +-o
ENSG00000113558 SKP1 ---
ENSG00000145604 SKP2 o++b
ENSG00000072501 SMC1A o--a
ENSG00000108055 SMC3 NonAssociatedWithProgression
ENSG00000161888 SPC24 o--a
ENSG00000176101 SSNA1 NonAssociatedWithProgression
ENSG00000118007 STAG1 NonAssociatedWithProgression
ENSG00000101972 STAG2 o--b
ENSG00000066923 STAG3 o--b
ENSG00000164828 SUN1 o--a
ENSG00000100242 SUN2 o-o
ENSG00000161860 SYCE2 o--a
ENSG00000131018 SYNE1 o++b
ENSG00000054654 SYNE2 o--b
ENSG00000147601 TERF1 NonAssociatedWithProgression
ENSG00000132604 TERF2 o--a
ENSG00000166848 TERF2IP o--b
ENSG00000198176 TFDP1 -o-
ENSG00000114126 TFDP2 o--b
ENSG00000092330 TINF2 o--b
ENSG00000166548 TK2 o++b
ENSG00000131747 TOP2A o--b
ENSG00000141510 TP53 o--a
ENSG00000167552 TUBA1A +oo
ENSG00000127824 TUBA4A NonAssociatedWithProgression
ENSG00000196230 TUBB o--a
ENSG00000131462 TUBG1 --o
ENSG00000037042 TUBG2 o-+
ENSG00000126216 TUBGCP3 o-o
ENSG00000153575 TUBGCP5 o-o
ENSG00000128159 TUBGCP6 o--a
ENSG00000176890 TYMS NonAssociatedWithProgression
ENSG00000221983 UBA52 o--a
ENSG00000170315 UBB ---
ENSG00000175063 UBE2C o-o
ENSG00000072401 UBE2D1 NonAssociatedWithProgression
ENSG00000170142 UBE2E1 o--b
ENSG00000103275 UBE2I o--a
ENSG00000166483 WEE1 NonAssociatedWithProgression
ENSG00000141499 WRAP53 ---
ENSG00000082898 XPO1 o-o
ENSG00000108953 YWHAE NonAssociatedWithProgression
ENSG00000170027 YWHAG o+-
ENSG00000086827 ZW10 NonAssociatedWithProgression
ENSG00000174442 ZWILCH NonAssociatedWithProgression
ENSG00000122952 ZWINT o-o