PEACHi
Cluster -+o is enriched in the following gene classes
GeneSet DB Hit Count
Pathways_-_KEGGBioCarta.gmt.txt 4
GO_-_Cellular_Component.gmt.txt 4
Pathways_-_Reactome.gmt.txt 15
TarBase_6beta.gmt.txt 1
GO_-_Biological_Process.gmt.txt 1
Chromosomal_Bands.gmt.txt 8
TFmiRNA_Targets.gmt.txt 1
GeneSet Name GeneSet DB log(P) Qvalue Observed in Background Observed in Cluster Expected in Cluster
ACTIN POLYMERIZATION AND OR DEPOLYMERIZATION GO_-_Biological_Process.gmt.txt -3.6 0.02851 8.0 3.0 0.37
BASOLATERAL PLASMA MEMBRANE GO_-_Cellular_Component.gmt.txt -2.8 0.03238 12.0 3.0 0.56
BIOCARTA ACTINY PATHWAY Pathways_-_KEGGBioCarta.gmt.txt -2.6 0.03739 13.0 3.0 0.61
BIOCARTA PROTEASOME PATHWAY Pathways_-_KEGGBioCarta.gmt.txt -2.4 0.0481 15.0 3.0 0.7
CELL JUNCTION GO_-_Cellular_Component.gmt.txt -3.0 0.02394 18.0 4.0 0.84
CELL MATRIX JUNCTION GO_-_Cellular_Component.gmt.txt -4.6 0.00173 5.0 3.0 0.23
Cell junction organization Pathways_-_Reactome.gmt.txt -3.8 0.00666 19.0 5.0 0.89
Cell-Cell communication Pathways_-_Reactome.gmt.txt -2.2 0.0428 36.0 5.0 1.68
G alpha (z) signalling events Pathways_-_Reactome.gmt.txt -2.4 0.035 15.0 3.0 0.7
INTEGRATOR COMPLEX GO_-_Cellular_Component.gmt.txt -2.9 0.02435 11.0 3.0 0.51
KEGG PROTEASOME Pathways_-_KEGGBioCarta.gmt.txt -2.7 0.0349 29.0 5.0 1.35
KEGG PURINE METABOLISM Pathways_-_KEGGBioCarta.gmt.txt -3.3 0.02028 72.0 10.0 3.36
Metabolism of nucleotides Pathways_-_Reactome.gmt.txt -2.9 0.01918 37.0 6.0 1.73
Metabolism of vitamins and cofactors Pathways_-_Reactome.gmt.txt -2.5 0.03156 32.0 5.0 1.49
Metabolism of water-soluble vitamins and cofactors Pathways_-_Reactome.gmt.txt -2.5 0.03156 32.0 5.0 1.49
NRAGE signals death through JNK Pathways_-_Reactome.gmt.txt -2.7 0.02203 20.0 4.0 0.93
Post-translational modification: synthesis of GPI-anchored proteins Pathways_-_Reactome.gmt.txt -2.2 0.04602 17.0 3.0 0.79
Purine metabolism Pathways_-_Reactome.gmt.txt -3.2 0.01179 16.0 4.0 0.75
RNA Polymerase III Chain Elongation Pathways_-_Reactome.gmt.txt -3.1 0.01339 10.0 3.0 0.47
RNA Polymerase III Transcription Initiation From Type 1 Promoter Pathways_-_Reactome.gmt.txt -2.3 0.04119 16.0 3.0 0.75
RNA Polymerase III Transcription Initiation From Type 2 Promoter Pathways_-_Reactome.gmt.txt -2.4 0.035 15.0 3.0 0.7
RNA Polymerase III Transcription Initiation From Type 3 Promoter Pathways_-_Reactome.gmt.txt -2.3 0.04119 16.0 3.0 0.75
RNA Polymerase III Transcription Termination Pathways_-_Reactome.gmt.txt -3.1 0.01339 10.0 3.0 0.47
V$OCT1 07 TFmiRNA_Targets.gmt.txt -5.2 0.01046 38.0 9.0 1.77
chr11p13 Chromosomal_Bands.gmt.txt -2.6 0.02304 13.0 3.0 0.61
chr12q14 Chromosomal_Bands.gmt.txt -2.3 0.03202 16.0 3.0 0.75
chr15q21 Chromosomal_Bands.gmt.txt -2.4 0.02814 24.0 4.0 1.12
chr16q12 Chromosomal_Bands.gmt.txt -2.5 0.02637 14.0 3.0 0.65
chr2p21 Chromosomal_Bands.gmt.txt -2.4 0.028 15.0 3.0 0.7
chr2q31 Chromosomal_Bands.gmt.txt -3.6 0.00754 28.0 6.0 1.31
chr3q26 Chromosomal_Bands.gmt.txt -3.0 0.01685 18.0 4.0 0.84
chr6q21 Chromosomal_Bands.gmt.txt -2.1 0.04167 18.0 3.0 0.84
hsa-miR-335-5p targets TarBase_6beta.gmt.txt -3.0 0.03599 605.0 44.0 28.24
p75 NTR receptor-mediated signalling Pathways_-_Reactome.gmt.txt -2.2 0.04176 47.0 6.0 2.19
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
ENSG00000134864 A2LD1 -+o
ENSG00000157426 AASDH -+o
ENSG00000158201 ABHD3 -+o
ENSG00000164241 AC004507.1 -+o
ENSG00000229113 AC005795.1 -+o
ENSG00000239322 AC007040.7 -+o
ENSG00000227855 AC007276.5 -+o
ENSG00000204334 AC007405.7 -+o
ENSG00000212884 AC011841.1 -+o
ENSG00000245206 AC012184.1 -+o
ENSG00000225973 AC018926.1 -+o
ENSG00000214857 AC026726.1 -+o
ENSG00000237883 AC073046.4 -+o
ENSG00000213963 AC074286.1 -+o
ENSG00000218761 AC093227.1 -+o
ENSG00000234663 AC104820.2 -+o
ENSG00000238035 AC138035.1 -+o
ENSG00000167315 ACAA2 -+o
ENSG00000112304 ACOT13 -+o
ENSG00000072110 ACTN1 -+o
ENSG00000170634 ACYP2 -+o
ENSG00000008277 ADAM22 -+o
ENSG00000121281 ADCY7 -+o
ENSG00000156110 ADK -+o
ENSG00000239900 ADSL -+o
ENSG00000162688 AGL -+o
ENSG00000168710 AHCYL1 -+o
ENSG00000063438 AHRR -+o
ENSG00000155085 AKD1 -+o
ENSG00000235194 AL049829.1 -+o
ENSG00000251327 AL109917.2 -+o
ENSG00000247181 AL137244.1 -+o
ENSG00000250255 AL359643.2 -+o
ENSG00000240038 AMY2B -+o
ENSG00000164331 ANKRA2 -+o
ENSG00000133302 ANKRD32 -+o
ENSG00000169604 ANTXR1 -+o
ENSG00000164111 ANXA5 -+o
ENSG00000138279 ANXA7 -+o
ENSG00000242553 AP001432.14 -+o
ENSG00000228463 AP006222.2 -+o
ENSG00000182287 AP1S2 -+o
ENSG00000075884 ARHGAP15 -+o
ENSG00000132694 ARHGEF11 -+o
ENSG00000170632 ARMC10 -+o
ENSG00000130429 ARPC1B -+o
ENSG00000113273 ARSB -+o
ENSG00000164291 ARSK -+o
ENSG00000107669 ATE1 -+o
ENSG00000182220 ATP6AP2 -+o
ENSG00000124406 ATP8A1 -+o
ENSG00000146776 ATXN7L1 -+o
ENSG00000187676 B3GALTL -+o
ENSG00000123636 BAZ2B -+o
ENSG00000122507 BBS9 -+o
ENSG00000114439 BBX -+o
ENSG00000107949 BCCIP -+o
ENSG00000198908 BHLHB9 -+o
ENSG00000115760 BIRC6 -+o
ENSG00000060762 BRP44L -+o
ENSG00000133678 C10orf57 -+o
ENSG00000166323 C11orf65 -+o
ENSG00000151135 C12orf23 -+o
ENSG00000166262 C15orf33 -+o
ENSG00000242028 C15orf63 -+o
ENSG00000121486 C1orf25 -+o
ENSG00000157181 C1orf27 -+o
ENSG00000163946 C3orf63 -+o
ENSG00000168538 C4orf41 -+o
ENSG00000204564 C6orf136 -+o
ENSG00000107020 C9orf46 -+o
ENSG00000176007 C9orf51 -+o
ENSG00000102547 CAB39L -+o
ENSG00000180881 CAPS2 -+o
ENSG00000121691 CAT -+o
ENSG00000152705 CATSPER3 -+o
ENSG00000136682 CBWD2 -+o
ENSG00000215126 CBWD7 -+o
ENSG00000123106 CCDC91 -+o
ENSG00000152669 CCNO -+o
ENSG00000004468 CD38 -+o
ENSG00000112149 CD83 -+o
ENSG00000064886 CHI3L2 -+o
ENSG00000128656 CHN1 -+o
ENSG00000144021 CIAO1 -+o
ENSG00000171365 CLCN5 -+o
ENSG00000187118 CMC1 -+o
ENSG00000145781 COMMD10 -+o
ENSG00000148444 COMMD3 -+o
ENSG00000184432 COPB2 -+o
ENSG00000110871 COQ5 -+o
ENSG00000088682 COQ9 -+o
ENSG00000119878 CRIPT -+o
ENSG00000245937 CTC-228N24.3 -+o
ENSG00000240729 CTD-2301A4.3 -+o
ENSG00000163510 CWC22 -+o
ENSG00000153015 CWC27 -+o
ENSG00000099749 CYorf15A -+o
ENSG00000213047 DENND1B -+o
ENSG00000162777 DENND2D -+o
ENSG00000108176 DNAJC12 -+o
ENSG00000172269 DPAGT1 -+o
ENSG00000173852 DPY19L1 -+o
ENSG00000188641 DPYD -+o
ENSG00000151914 DST -+o
ENSG00000125868 DSTN -+o
ENSG00000093144 ECHDC1 -+o
ENSG00000111361 EIF2B1 -+o
ENSG00000092847 EIF2C1 -+o
ENSG00000115459 ELMOD3 -+o
ENSG00000253337 ENSG00000253337 -+o
ENSG00000049167 ERCC8 -+o
ENSG00000171503 ETFDH -+o
ENSG00000143845 ETNK2 -+o
ENSG00000144036 EXOC6B -+o
ENSG00000113194 FAF2 -+o
ENSG00000055147 FAM114A2 -+o
ENSG00000144401 FAM119A -+o
ENSG00000156500 FAM122C -+o
ENSG00000205670 FAM165B -+o
ENSG00000222011 FAM185A -+o
ENSG00000198673 FAM19A2 -+o
ENSG00000102710 FAM48A -+o
ENSG00000188343 FAM92A1 -+o
ENSG00000132879 FBXO44 -+o
ENSG00000146192 FGD2 -+o
ENSG00000135723 FHOD1 -+o
ENSG00000106080 FKBP14 -+o
ENSG00000100442 FKBP3 -+o
ENSG00000059122 FLYWCH1 -+o
ENSG00000140718 FTO -+o
ENSG00000033170 FUT8 -+o
ENSG00000034713 GABARAPL2 -+o
ENSG00000128683 GAD1 -+o
ENSG00000023572 GLRX2 -+o
ENSG00000108010 GLRX3 -+o
ENSG00000100938 GMPR2 -+o
ENSG00000114450 GNB4 -+o
ENSG00000066455 GOLGA5 -+o
ENSG00000171723 GPHN -+o
ENSG00000125388 GRK4 -+o
ENSG00000197245 GRRP1 -+o
ENSG00000061918 GUCY1B3 -+o
ENSG00000155393 HEATR3 -+o
ENSG00000129493 HEATR5A -+o
ENSG00000118418 HMGN3 -+o
ENSG00000143889 HNRPLL -+o
ENSG00000133835 HSD17B4 -+o
ENSG00000119471 HSDL2 -+o
ENSG00000081870 HSPB11 -+o
ENSG00000119912 IDE -+o
ENSG00000169991 IFFO2 -+o
ENSG00000165948 IFI27L1 -+o
ENSG00000068885 IFT80 -+o
ENSG00000148950 IMMP1L -+o
ENSG00000203485 INF2 -+o
ENSG00000108506 INTS2 -+o
ENSG00000102786 INTS6 -+o
ENSG00000142856 ITGB3BP -+o
ENSG00000205726 ITSN1 -+o
ENSG00000163166 IWS1 -+o
ENSG00000152969 JAKMIP1 -+o
ENSG00000187486 KCNJ11 -+o
ENSG00000012817 KDM5D -+o
ENSG00000135709 KIAA0513 -+o
ENSG00000134313 KIDINS220 -+o
ENSG00000165115 KIF27 -+o
ENSG00000167487 KLHL26 -+o
ENSG00000139187 KLRG1 -+o
ENSG00000001631 KRIT1 -+o
ENSG00000135537 LACE1 -+o
ENSG00000002549 LAP3 -+o
ENSG00000172292 LASS6 -+o
ENSG00000174405 LIG4 -+o
ENSG00000050405 LIMA1 -+o
ENSG00000169756 LIMS1 -+o
ENSG00000143013 LMO4 -+o
ENSG00000110031 LPXN -+o
ENSG00000144749 LRIG1 -+o
ENSG00000139263 LRIG3 -+o
ENSG00000171757 LRRC34 -+o
ENSG00000133739 LRRCC1 -+o
ENSG00000127603 MACF1 -+o
ENSG00000204406 MBD5 -+o
ENSG00000076770 MBNL3 -+o
ENSG00000078070 MCCC1 -+o
ENSG00000111877 MCM9 -+o
ENSG00000232119 MCTS1 -+o
ENSG00000085276 MECOM -+o
ENSG00000130772 MED18 -+o
ENSG00000169519 METT5D1 -+o
ENSG00000165819 METTL3 -+o
ENSG00000170854 MINA -+o
ENSG00000158411 MITD1 -+o
ENSG00000114978 MOBKL1B -+o
ENSG00000164172 MOCS2 -+o
ENSG00000135698 MPHOSPH6 -+o
ENSG00000178988 MRFAP1L1 -+o
ENSG00000108826 MRPL27 -+o
ENSG00000181610 MRPS23 -+o
ENSG00000134056 MRPS36 -+o
ENSG00000100714 MTHFD1 -+o
ENSG00000085760 MTIF2 -+o
ENSG00000005810 MYCBP2 -+o
ENSG00000128833 MYO5C -+o
ENSG00000145911 N4BP3 -+o
ENSG00000095380 NANS -+o
ENSG00000172915 NBEA -+o
ENSG00000213672 NCKIPSD -+o
ENSG00000189043 NDUFA4 -+o
ENSG00000183648 NDUFB1 -+o
ENSG00000069869 NEDD4 -+o
ENSG00000114904 NEK4 -+o
ENSG00000165030 NFIL3 -+o
ENSG00000123609 NMI -+o
ENSG00000112992 NNT -+o
ENSG00000124588 NQO2 -+o
ENSG00000078618 NRD1 -+o
ENSG00000141698 NT5C3L -+o
ENSG00000013374 NUB1 -+o
ENSG00000070081 NUCB2 -+o
ENSG00000111581 NUP107 -+o
ENSG00000139579 OBFC2B -+o
ENSG00000122417 ODF2L -+o
ENSG00000081087 OSTM1 -+o
ENSG00000083720 OXCT1 -+o
ENSG00000124507 PACSIN1 -+o
ENSG00000138801 PAPSS1 -+o
ENSG00000124171 PARD6B -+o
ENSG00000227345 PARG -+o
ENSG00000135749 PCNXL2 -+o
ENSG00000163110 PDLIM5 -+o
ENSG00000160209 PDXK -+o
ENSG00000078043 PIAS2 -+o
ENSG00000151665 PIGF -+o
ENSG00000142892 PIGK -+o
ENSG00000143315 PIGM -+o
ENSG00000102309 PIN4 -+o
ENSG00000087842 PIR -+o
ENSG00000123739 PLA2G12A -+o
ENSG00000182621 PLCB1 -+o
ENSG00000064933 PMS1 -+o
ENSG00000013503 POLR3B -+o
ENSG00000168495 POLR3D -+o
ENSG00000113356 POLR3G -+o
ENSG00000121577 POPDC2 -+o
ENSG00000163644 PPM1K -+o
ENSG00000108819 PPP1R9B -+o
ENSG00000163558 PRKCI -+o
ENSG00000160310 PRMT2 -+o
ENSG00000147471 PROSC -+o
ENSG00000041357 PSMA4 -+o
ENSG00000101182 PSMA7 -+o
ENSG00000108294 PSMB3 -+o
ENSG00000087191 PSMC5 -+o
ENSG00000117425 PTCH2 -+o
ENSG00000140043 PTGR2 -+o
ENSG00000155093 PTPRN2 -+o
ENSG00000130348 QRSL1 -+o
ENSG00000152061 RABGAP1L -+o
ENSG00000175097 RAG2 -+o
ENSG00000174373 RALGAPA1 -+o
ENSG00000141084 RANBP10 -+o
ENSG00000172575 RASGRP1 -+o
ENSG00000100320 RBFOX2 -+o
ENSG00000119446 RBM18 -+o
ENSG00000157916 RER1 -+o
ENSG00000145331 RG9MTD2 -+o
ENSG00000171700 RGS19 -+o
ENSG00000129667 RHBDF2 -+o
ENSG00000167257 RNF214 -+o
ENSG00000241255 RP1-89D4.1 -+o
ENSG00000247679 RP11-1277A3.1 -+o
ENSG00000249773 RP11-15K19.2 -+o
ENSG00000245954 RP11-18H21.1 -+o
ENSG00000230847 RP11-195E2.1 -+o
ENSG00000225519 RP11-236B18.2 -+o
ENSG00000250091 RP11-380L11.1 -+o
ENSG00000240024 RP11-393B14.1 -+o
ENSG00000241506 RP11-436J20.2 -+o
ENSG00000188002 RP11-43F13.1 -+o
ENSG00000243256 RP11-453M1.1 -+o
ENSG00000246090 RP11-696N14.1 -+o
ENSG00000243020 RP11-766N7.1 -+o
ENSG00000219532 RP3-323K23.3 -+o
ENSG00000237096 RP4-782G3.1 -+o
ENSG00000240043 RPS27P26 -+o
ENSG00000048392 RRM2B -+o
ENSG00000182010 RTKN2 -+o
ENSG00000119042 SATB2 -+o
ENSG00000173611 SCAI -+o
ENSG00000140386 SCAPER -+o
ENSG00000143653 SCCPDH -+o
ENSG00000151466 SCLT1 -+o
ENSG00000196876 SCN8A -+o
ENSG00000144306 SCRN3 -+o
ENSG00000188404 SELL -+o
ENSG00000163536 SERPINI1 -+o
ENSG00000154447 SH3RF1 -+o
ENSG00000127922 SHFM1 -+o
ENSG00000105738 SIPA1L3 -+o
ENSG00000120519 SLC10A7 -+o
ENSG00000141469 SLC14A1 -+o
ENSG00000171612 SLC25A33 -+o
ENSG00000151229 SLC2A13 -+o
ENSG00000104154 SLC30A4 -+o
ENSG00000080493 SLC4A4 -+o
ENSG00000065923 SLC9A7 -+o
ENSG00000138375 SMARCAL1 -+o
ENSG00000136824 SMC2 -+o
ENSG00000064652 SNX24 -+o
ENSG00000115904 SOS1 -+o
ENSG00000100883 SRP54 -+o
ENSG00000124783 SSR1 -+o
ENSG00000138134 STAMBPL1 -+o
ENSG00000172345 STARD5 -+o
ENSG00000166900 STX3 -+o
ENSG00000164506 STXBP5 -+o
ENSG00000136143 SUCLA2 -+o
ENSG00000165416 SUGT1 -+o
ENSG00000059588 TARBP1 -+o
ENSG00000162065 TBC1D24 -+o
ENSG00000133138 TBC1D8B -+o
ENSG00000213123 TCTEX1D2 -+o
ENSG00000135605 TEC -+o
ENSG00000173451 THAP2 -+o
ENSG00000161277 THAP8 -+o
ENSG00000241043 TIGD1L2 -+o
ENSG00000180346 TIGD2 -+o
ENSG00000100575 TIMM9 -+o
ENSG00000150455 TIRAP -+o
ENSG00000170417 TMEM182 -+o
ENSG00000149582 TMEM25 -+o
ENSG00000109133 TMEM33 -+o
ENSG00000128872 TMOD2 -+o
ENSG00000125657 TNFSF9 -+o
ENSG00000154310 TNIK -+o
ENSG00000116783 TNNI3K -+o
ENSG00000196511 TPK1 -+o
ENSG00000131323 TRAF3 -+o
ENSG00000106477 TSGA14 -+o
ENSG00000156298 TSPAN7 -+o
ENSG00000165914 TTC7B -+o
ENSG00000184811 TUSC5 -+o
ENSG00000252288 U6.1114 -+o
ENSG00000206744 U6.443 -+o
ENSG00000207072 U6.571 -+o
ENSG00000184182 UBE2F -+o
ENSG00000116750 UCHL5 -+o
ENSG00000101019 UQCC -+o
ENSG00000048028 USP28 -+o
ENSG00000152818 UTRN -+o
ENSG00000078668 VDAC3 -+o
ENSG00000187650 VMAC -+o
ENSG00000132549 VPS13B -+o
ENSG00000206530 WDR52 -+o
ENSG00000248334 WHAMML2 -+o
ENSG00000115935 WIPF1 -+o
ENSG00000100219 XBP1 -+o
ENSG00000143324 XPR1 -+o
ENSG00000093217 XYLB -+o
ENSG00000139800 ZIC5 -+o
ENSG00000188629 ZNF177 -+o
ENSG00000197857 ZNF44 -+o
ENSG00000165655 ZNF503 -+o
ENSG00000198453 ZNF568 -+o
ENSG00000173041 ZNF680 -+o
ENSG00000197782 ZNF780A -+o
ENSG00000182318 ZSCAN22 -+o
hsa-miR-10a hsa-miR-10a -+o
hsa-miR-135a hsa-miR-135a -+o
hsa-miR-3150a-5p hsa-miR-3150a-5p -+o
hsa-miR-342-5p hsa-miR-342-5p -+o