PEACHi
Cluster --o is enriched in the following gene classes
GeneSet DB Hit Count
Pathways_-_KEGGBioCarta.gmt.txt 5
GO_-_Cellular_Component.gmt.txt 12
Pathways_-_Reactome.gmt.txt 5
TarBase_6beta.gmt.txt 1
GO_-_Biological_Process.gmt.txt 4
HIV_Collection.gmt.txt 1
Chromosomal_Bands.gmt.txt 5
GO_-_Molecular_Function.gmt.txt 7
GeneSet Name GeneSet DB log(P) Qvalue Observed in Background Observed in Cluster Expected in Cluster
CATION CHANNEL ACTIVITY GO_-_Molecular_Function.gmt.txt -3.2 0.03238 14.0 3.0 0.43
CYTOPLASMIC PART GO_-_Cellular_Component.gmt.txt -3.4 0.01209 709.0 37.0 21.74
ENVELOPE GO_-_Cellular_Component.gmt.txt -3.1 0.01889 98.0 9.0 3.0
ER GOLGI INTERMEDIATE COMPARTMENT GO_-_Cellular_Component.gmt.txt -2.9 0.02435 16.0 3.0 0.49
FATTY ACID METABOLIC PROCESS GO_-_Biological_Process.gmt.txt -3.1 0.0415 25.0 4.0 0.77
GATED CHANNEL ACTIVITY GO_-_Molecular_Function.gmt.txt -3.2 0.03238 14.0 3.0 0.43
GTPASE BINDING GO_-_Molecular_Function.gmt.txt -2.7 0.04505 18.0 3.0 0.55
HIV human PPI GP41 HIV_Collection.gmt.txt -2.4 0.04111 35.0 4.0 1.07
ION CHANNEL ACTIVITY GO_-_Molecular_Function.gmt.txt -2.7 0.04505 18.0 3.0 0.55
KEGG BIOSYNTHESIS OF UNSATURATED FATTY ACIDS Pathways_-_KEGGBioCarta.gmt.txt -3.8 0.01271 10.0 3.0 0.31
KEGG BUTANOATE METABOLISM Pathways_-_KEGGBioCarta.gmt.txt -3.9 0.01271 17.0 4.0 0.52
KEGG FATTY ACID METABOLISM Pathways_-_KEGGBioCarta.gmt.txt -2.7 0.0349 18.0 3.0 0.55
KEGG PEROXISOME Pathways_-_KEGGBioCarta.gmt.txt -3.4 0.02028 33.0 5.0 1.01
KEGG PPAR SIGNALING PATHWAY Pathways_-_KEGGBioCarta.gmt.txt -2.8 0.03261 17.0 3.0 0.52
Loss of Nlp from mitotic centrosomes Pathways_-_Reactome.gmt.txt -2.2 0.04176 38.0 4.0 1.17
Loss of proteins required for interphase microtubule organizationfrom the centrosome Pathways_-_Reactome.gmt.txt -2.2 0.04176 38.0 4.0 1.17
MITOCHONDRIAL ENVELOPE GO_-_Cellular_Component.gmt.txt -3.5 0.01045 58.0 7.0 1.78
MITOCHONDRIAL INNER MEMBRANE GO_-_Cellular_Component.gmt.txt -2.9 0.0251 40.0 5.0 1.23
MITOCHONDRIAL MEMBRANE GO_-_Cellular_Component.gmt.txt -3.8 0.00641 52.0 7.0 1.59
MITOCHONDRIAL MEMBRANE PART GO_-_Cellular_Component.gmt.txt -3.0 0.02106 38.0 5.0 1.17
MITOCHONDRIAL PART GO_-_Cellular_Component.gmt.txt -2.9 0.02592 87.0 8.0 2.67
MITOCHONDRION GO_-_Cellular_Component.gmt.txt -3.2 0.01679 208.0 15.0 6.38
NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 Pathways_-_Reactome.gmt.txt -4.6 0.00318 7.0 3.0 0.21
NUCLEOBASENUCLEOSIDE AND NUCLEOTIDE METABOLIC PROCESS GO_-_Biological_Process.gmt.txt -3.3 0.03669 23.0 4.0 0.71
Negative regulators of RIG-I/MDA5 signaling Pathways_-_Reactome.gmt.txt -2.2 0.04176 24.0 3.0 0.74
ORGANELLE ENVELOPE GO_-_Cellular_Component.gmt.txt -3.1 0.01889 98.0 9.0 3.0
ORGANELLE INNER MEMBRANE GO_-_Cellular_Component.gmt.txt -2.6 0.03799 45.0 5.0 1.38
ORGANELLE MEMBRANE GO_-_Cellular_Component.gmt.txt -2.7 0.03413 168.0 12.0 5.15
RAS GTPASE ACTIVATOR ACTIVITY GO_-_Molecular_Function.gmt.txt -3.3 0.03238 13.0 3.0 0.4
RESPONSE TO CHEMICAL STIMULUS GO_-_Biological_Process.gmt.txt -3.0 0.04495 84.0 8.0 2.58
RESPONSE TO OXIDATIVE STRESS GO_-_Biological_Process.gmt.txt -3.6 0.02851 20.0 4.0 0.61
SMALL GTPASE BINDING GO_-_Molecular_Function.gmt.txt -2.7 0.04505 18.0 3.0 0.55
SUBSTRATE SPECIFIC CHANNEL ACTIVITY GO_-_Molecular_Function.gmt.txt -2.7 0.04505 18.0 3.0 0.55
TRAF6 mediated NF-kB activation Pathways_-_Reactome.gmt.txt -3.5 0.00951 12.0 3.0 0.37
chr11q13 Chromosomal_Bands.gmt.txt -2.1 0.0412 94.0 7.0 2.88
chr12q24 Chromosomal_Bands.gmt.txt -2.3 0.03202 70.0 6.0 2.15
chr14q24 Chromosomal_Bands.gmt.txt -2.6 0.02486 32.0 4.0 0.98
chr17q11 Chromosomal_Bands.gmt.txt -2.1 0.0385 40.0 4.0 1.23
chr1p36 Chromosomal_Bands.gmt.txt -2.5 0.02637 118.0 9.0 3.62
hsa-mir-30 targets TarBase_6beta.gmt.txt -3.3 0.01925 46.0 6.0 1.41
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
ENSG00000165029 ABCA1 --o
ENSG00000160179 ABCG1 --o
ENSG00000224908 AC002407.1 --o
ENSG00000196656 AC004057.1 --o
ENSG00000245793 AC013418.3 --o
ENSG00000234513 AC073072.7 --o
ENSG00000225026 AC091492.2 --o
ENSG00000145050 AC092037.1 --o
ENSG00000229503 AC092155.1 --o
ENSG00000214401 AC217773.1 --o
ENSG00000122971 ACADS --o
ENSG00000110881 ACCN2 --o
ENSG00000184227 ACOT1 --o
ENSG00000119673 ACOT2 --o
ENSG00000116863 ADPRHL2 --o
ENSG00000133612 AGAP3 --o
ENSG00000177674 AGTRAP --o
ENSG00000146416 AIG1 --o
ENSG00000246609 AL135999.2 --o
ENSG00000073331 ALPK1 --o
ENSG00000144504 ANKMY1 --o
ENSG00000196372 ASB13 --o
ENSG00000215915 ATAD3C --o
ENSG00000168010 ATG16L2 --o
ENSG00000175711 B3GNTL1 --o
ENSG00000161267 BDH1 --o
ENSG00000185963 BICD2 --o
ENSG00000136717 BIN1 --o
ENSG00000064726 BTBD1 --o
ENSG00000166167 BTRC --o
ENSG00000119650 C14orf179 --o
ENSG00000173436 C1orf151 --o
ENSG00000143303 C1orf66 --o
ENSG00000164096 C4orf3 --o
ENSG00000243449 C4orf48 --o
ENSG00000188186 C7orf59 --o
ENSG00000149679 CABLES2 --o
ENSG00000012822 CALCOCO1 --o
ENSG00000108509 CAMTA2 --o
ENSG00000100307 CBX7 --o
ENSG00000121289 CCDC123 --o
ENSG00000183978 CCDC56 --o
ENSG00000104983 CCDC61 --o
ENSG00000155111 CDK19 --o
ENSG00000111328 CDK2AP1 --o
ENSG00000177830 CHID1 --o
ENSG00000198791 CNOT7 --o
ENSG00000103051 COG4 --o
ENSG00000204248 COL11A2 --o
ENSG00000110090 CPT1A --o
ENSG00000163703 CRELD1 --o
ENSG00000058453 CROCC --o
ENSG00000101439 CST3 --o
ENSG00000231084 CTA-253N17.1 --o
ENSG00000040531 CTNS --o
ENSG00000164733 CTSB --o
ENSG00000107874 CUEDC2 --o
ENSG00000175203 DCTN2 --o
ENSG00000242612 DECR2 --o
ENSG00000182108 DEXI --o
ENSG00000183628 DGCR6 --o
ENSG00000128185 DGCR6L --o
ENSG00000149091 DGKZ --o
ENSG00000106976 DNM1 --o
ENSG00000149927 DOC2A --o
ENSG00000088986 DYNLL1 --o
ENSG00000254137 ENSG00000254137 --o
ENSG00000177106 EPS8L2 --o
ENSG00000182473 EXOC7 --o
ENSG00000178896 EXOSC4 --o
ENSG00000131187 F12 --o
ENSG00000123427 FAM119B --o
ENSG00000172366 FAM195A --o
ENSG00000165716 FAM69B --o
ENSG00000037637 FBXO42 --o
ENSG00000172500 FIBP --o
ENSG00000214253 FIS1 --o
ENSG00000134285 FKBP11 --o
ENSG00000137312 FLOT1 --o
ENSG00000184481 FOXO4 --o
ENSG00000068438 FTSJ1 --o
ENSG00000115271 GCA --o
ENSG00000102886 GDPD3 --o
ENSG00000122694 GLIPR2 --o
ENSG00000089639 GMIP --o
ENSG00000144591 GMPPA --o
ENSG00000114353 GNAI2 --o
ENSG00000178719 GRINA --o
ENSG00000068400 GRIPAP1 --o
ENSG00000225071 GS1-184P14.2 --o
ENSG00000125812 GZF1 --o
ENSG00000138796 HADH --o
ENSG00000114735 HEMK1 --o
ENSG00000169660 HEXDC --o
ENSG00000117305 HMGCL --o
ENSG00000115756 HPCAL1 --o
ENSG00000073009 IKBKG --o
ENSG00000224882 IKBKGP1 --o
ENSG00000240682 ISY1 --o
ENSG00000100605 ITPK1 --o
ENSG00000168135 KCNJ4 --o
ENSG00000100379 KCTD17 --o
ENSG00000135314 KHDC1 --o
ENSG00000226950 KIAA0114 --o
ENSG00000196976 LAGE3 --o
ENSG00000205629 LCMT1 --o
ENSG00000204392 LSM2 --o
ENSG00000169641 LUZP1 --o
ENSG00000214113 LYRM4 --o
ENSG00000088888 MAVS --o
ENSG00000146701 MDH2 --o
ENSG00000146263 MMS22L --o
ENSG00000115204 MPV17 --o
ENSG00000182180 MRPS16 --o
ENSG00000090263 MRPS33 --o
ENSG00000242114 MTFP1 --o
ENSG00000150456 N6AMT2 --o
ENSG00000188554 NBR1 --o
ENSG00000072864 NDE1 --o
ENSG00000101079 NDRG3 --o
ENSG00000136521 NDUFB5 --o
ENSG00000158864 NDUFS2 --o
ENSG00000167792 NDUFV1 --o
ENSG00000169599 NFU1 --o
ENSG00000103202 NME4 --o
ENSG00000140939 NOL3 --o
ENSG00000154146 NRGN --o
ENSG00000178425 NT5DC1 --o
ENSG00000065057 NTHL1 --o
ENSG00000104805 NUCB1 --o
ENSG00000165609 NUDT5 --o
ENSG00000108256 NUFIP2 --o
ENSG00000102898 NUTF2 --o
ENSG00000107960 OBFC1 --o
ENSG00000167770 OTUB1 --o
ENSG00000135124 P2RX4 --o
ENSG00000230457 PA2G4P4 --o
ENSG00000102981 PARD6A --o
ENSG00000162735 PEX19 --o
ENSG00000152556 PFKM --o
ENSG00000079739 PGM1 --o
ENSG00000040633 PHF23 --o
ENSG00000197563 PIGN --o
ENSG00000083444 PLOD1 --o
ENSG00000004399 PLXND1 --o
ENSG00000127838 PNKD --o
ENSG00000175482 POLD4 --o
ENSG00000105258 POLR2I --o
ENSG00000111110 PPM1H --o
ENSG00000149923 PPP4C --o
ENSG00000117450 PRDX1 --o
ENSG00000167815 PRDX2 --o
ENSG00000180228 PRKRA --o
ENSG00000224940 PRRT4 --o
ENSG00000187024 PTRH1 --o
ENSG00000017797 RALBP1 --o
ENSG00000111344 RASAL1 --o
ENSG00000136653 RASSF5 --o
ENSG00000163933 RFT1 --o
ENSG00000131378 RFTN1 --o
ENSG00000107185 RGP1 --o
ENSG00000155366 RHOC --o
ENSG00000139725 RHOF --o
ENSG00000177181 RIMKLA --o
ENSG00000159753 RLTPR --o
ENSG00000164068 RNF123 --o
ENSG00000181481 RNF135 --o
ENSG00000067836 ROGDI --o
ENSG00000125995 ROMO1 --o
ENSG00000220848 RP1-12G14.3 --o
ENSG00000234354 RP11-151A6.3 --o
ENSG00000223416 RP11-393I23.2 --o
ENSG00000226457 RP11-430L17.1 --o
ENSG00000244558 RP11-445H22.4 --o
ENSG00000241081 RP11-488C13.1 --o
ENSG00000248348 RP11-546N22.5 --o
ENSG00000213178 RP11-641D5.1 --o
ENSG00000233778 RP11-777J24.1 --o
ENSG00000249590 RP4-539M6.19 --o
ENSG00000213653 RP4-581F12.2 --o
ENSG00000212829 RPS26P3 --o
ENSG00000204652 RPS26P8 --o
ENSG00000117676 RPS6KA1 --o
ENSG00000130347 RTN4IP1 --o
ENSG00000176783 RUFY1 --o
ENSG00000163785 RYK --o
ENSG00000145284 SCD5 --o
ENSG00000162572 SCNN1D --o
ENSG00000136193 SCRN1 --o
ENSG00000157020 SEC13 --o
ENSG00000100003 SEC14L2 --o
ENSG00000129158 SERGEF --o
ENSG00000120742 SERP1 --o
ENSG00000149257 SERPINH1 --o
ENSG00000164466 SFXN1 --o
ENSG00000100092 SH3BP1 --o
ENSG00000197417 SHPK --o
ENSG00000164403 SHROOM1 --o
ENSG00000068903 SIRT2 --o
ENSG00000124523 SIRT5 --o
ENSG00000126903 SLC10A3 --o
ENSG00000130304 SLC27A1 --o
ENSG00000133065 SLC41A1 --o
ENSG00000139613 SMARCC2 --o
ENSG00000199293 SNORA21 --o
ENSG00000205302 SNX2 --o
ENSG00000090487 SPG21 --o
ENSG00000126091 ST3GAL3 --o
ENSG00000109689 STIM2 --o
ENSG00000115694 STK25 --o
ENSG00000197457 STMN3 --o
ENSG00000169689 STRA13 --o
ENSG00000165209 STRBP --o
ENSG00000197226 TBC1D9B --o
ENSG00000126351 THRA --o
ENSG00000126768 TIMM17B --o
ENSG00000150779 TIMM8B --o
ENSG00000171914 TLN2 --o
ENSG00000170348 TMED10 --o
ENSG00000105518 TMEM205 --o
ENSG00000125247 TMTC4 --o
ENSG00000186815 TPCN1 --o
ENSG00000163870 TPRA1 --o
ENSG00000167632 TRAPPC9 --o
ENSG00000124496 TRERF1 --o
ENSG00000173113 TRMT112 --o
ENSG00000067445 TRO --o
ENSG00000131462 TUBG1 --o
ENSG00000184470 TXNRD2 --o
ENSG00000134882 UBAC2 --o
ENSG00000131508 UBE2D2 --o
ENSG00000138629 UBL7 --o
ENSG00000109103 UNC119 --o
ENSG00000126088 UROD --o
ENSG00000168899 VAMP5 --o
ENSG00000213585 VDAC1 --o
ENSG00000100568 VTI1B --o
ENSG00000167992 VWCE --o
ENSG00000015532 XYLT2 --o
ENSG00000179627 ZBTB42 --o
ENSG00000155329 ZCCHC10 --o
ENSG00000158552 ZFAND2B --o
ENSG00000147130 ZMYM3 --o
hsa-let-7f-1* hsa-let-7f-1* --o
hsa-miR-26a hsa-miR-26a --o