PEACHi
Cluster +-o is enriched in the following gene classes
GeneSet DB Hit Count
Pathways_-_KEGGBioCarta.gmt.txt 3
Pathways_-_Reactome.gmt.txt 10
GO_-_Biological_Process.gmt.txt 3
HIV_Collection.gmt.txt 1
Chromosomal_Bands.gmt.txt 3
TFmiRNA_Targets.gmt.txt 7
GeneSet Name GeneSet DB log(P) Qvalue Observed in Background Observed in Cluster Expected in Cluster
AATGTGA,MIR-23A,MIR-23B TFmiRNA_Targets.gmt.txt -5.5 0.01038 163.0 17.0 5.1
Amino acid and oligopeptide SLC transporters Pathways_-_Reactome.gmt.txt -3.9 0.00597 17.0 4.0 0.53
Amino acid transport across the plasma membrane Pathways_-_Reactome.gmt.txt -4.2 0.00492 15.0 4.0 0.47
BIOCARTA ALK PATHWAY Pathways_-_KEGGBioCarta.gmt.txt -3.3 0.02172 13.0 3.0 0.41
BIOCARTA VEGF PATHWAY Pathways_-_KEGGBioCarta.gmt.txt -2.8 0.03296 17.0 3.0 0.53
CD28 co-stimulation Pathways_-_Reactome.gmt.txt -2.4 0.03515 22.0 3.0 0.69
CHROMATIN ASSEMBLY GO_-_Biological_Process.gmt.txt -4.0 0.01958 9.0 3.0 0.28
CHROMATIN ASSEMBLY OR DISASSEMBLY GO_-_Biological_Process.gmt.txt -2.9 0.04823 16.0 3.0 0.5
DNA PACKAGING GO_-_Biological_Process.gmt.txt -3.8 0.02583 18.0 4.0 0.56
HIV human PPI TAT HIV_Collection.gmt.txt -4.0 0.01349 16.0 4.0 0.5
KEGG ANTIGEN PROCESSING AND PRESENTATION Pathways_-_KEGGBioCarta.gmt.txt -2.4 0.04745 21.0 3.0 0.66
Post-Elongation Processing of Intron-Containing pre-mRNA Pathways_-_Reactome.gmt.txt -2.2 0.0434 24.0 3.0 0.75
Signaling by EGFR Pathways_-_Reactome.gmt.txt -2.5 0.03073 62.0 6.0 1.94
Signaling by EGFR in Cancer Pathways_-_Reactome.gmt.txt -2.5 0.03236 63.0 6.0 1.97
TATTATA,MIR-374 TFmiRNA_Targets.gmt.txt -3.5 0.04864 102.0 10.0 3.19
TGAATGT,MIR-181A,MIR-181B,MIR-181C,MIR-181D TFmiRNA_Targets.gmt.txt -5.1 0.01046 208.0 19.0 6.51
Transport of Mature Transcript to Cytoplasm Pathways_-_Reactome.gmt.txt -2.2 0.04638 39.0 4.0 1.22
Transport of Mature mRNA derived from an Intron-Containing Transcript Pathways_-_Reactome.gmt.txt -2.2 0.04394 38.0 4.0 1.19
Transport of inorganic cations/anions and amino acids/oligopeptides Pathways_-_Reactome.gmt.txt -2.5 0.02931 32.0 4.0 1.0
V$CEBPB 01 TFmiRNA_Targets.gmt.txt -3.6 0.04443 83.0 9.0 2.6
V$CEBP 01 TFmiRNA_Targets.gmt.txt -3.5 0.04965 71.0 8.0 2.22
V$GATA6 01 TFmiRNA_Targets.gmt.txt -3.7 0.03976 52.0 7.0 1.63
V$USF C TFmiRNA_Targets.gmt.txt -4.1 0.02246 102.0 11.0 3.19
chr12q21 Chromosomal_Bands.gmt.txt -3.4 0.0089 12.0 3.0 0.38
chr20p13 Chromosomal_Bands.gmt.txt -3.0 0.01685 26.0 4.0 0.81
chr3q26 Chromosomal_Bands.gmt.txt -2.7 0.02168 18.0 3.0 0.56
mRNA 3'-end processing Pathways_-_Reactome.gmt.txt -2.2 0.0434 24.0 3.0 0.75
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
ENSG00000103591 AAGAB +-o
ENSG00000227403 AC009299.3 +-o
ENSG00000251290 AC020661.1 +-o
ENSG00000172965 AC068491.1 +-o
ENSG00000230002 AC074008.4 +-o
ENSG00000214311 AC083906.1 +-o
ENSG00000212694 AC084018.1 +-o
ENSG00000230008 AC092139.2 +-o
ENSG00000239788 AC092610.8 +-o
ENSG00000237940 AC093642.3 +-o
ENSG00000179818 AC136007.2 +-o
ENSG00000114739 ACVR2B +-o
ENSG00000151694 ADAM17 +-o
ENSG00000170425 ADORA2B +-o
ENSG00000172493 AFF1 +-o
ENSG00000228364 AL662791.3 +-o
ENSG00000231074 AL662795.2 +-o
ENSG00000109107 ALDOC +-o
ENSG00000154856 APCDD1 +-o
ENSG00000162772 ATF3 +-o
ENSG00000070961 ATP2B1 +-o
ENSG00000087586 AURKA +-o
ENSG00000103126 AXIN1 +-o
ENSG00000112182 BACH2 +-o
ENSG00000172530 BANP +-o
ENSG00000060982 BCAT1 +-o
ENSG00000113916 BCL6 +-o
ENSG00000104081 BMF +-o
ENSG00000138756 BMP2K +-o
ENSG00000125378 BMP4 +-o
ENSG00000150776 C11orf57 +-o
ENSG00000110696 C11orf58 +-o
ENSG00000166002 C11orf75 +-o
ENSG00000174718 C12orf35 +-o
ENSG00000102445 C13orf18 +-o
ENSG00000095932 C19orf77 +-o
ENSG00000152495 CAMK4 +-o
ENSG00000130559 CAMSAP1 +-o
ENSG00000064012 CASP8 +-o
ENSG00000090061 CCNK +-o
ENSG00000223773 CD99P1 +-o
ENSG00000172216 CEBPB +-o
ENSG00000003402 CFLAR +-o
ENSG00000100888 CHD8 +-o
ENSG00000169684 CHRNA5 +-o
ENSG00000122966 CIT +-o
ENSG00000122705 CLTA +-o
ENSG00000113300 CNOT6 +-o
ENSG00000121058 COIL +-o
ENSG00000110442 COMMD9 +-o
ENSG00000131055 COX4I2 +-o
ENSG00000245694 CRNDE +-o
ENSG00000062485 CS +-o
ENSG00000242602 CTD-2339M3.1 +-o
ENSG00000175826 CTDNEP1 +-o
ENSG00000175197 DDIT3 +-o
ENSG00000204311 DFNB59 +-o
ENSG00000109606 DHX15 +-o
ENSG00000135829 DHX9 +-o
ENSG00000172869 DMXL1 +-o
ENSG00000138166 DUSP5 +-o
ENSG00000122882 ECD +-o
ENSG00000173812 EIF1 +-o
ENSG00000104408 EIF3E +-o
ENSG00000118402 ELOVL4 +-o
ENSG00000085832 EPS15 +-o
ENSG00000244405 ETV5 +-o
ENSG00000126860 EVI2A +-o
ENSG00000174839 FAM116A +-o
ENSG00000141699 FAM134C +-o
ENSG00000127452 FBXL12 +-o
ENSG00000119402 FBXW2 +-o
ENSG00000132436 FIGNL1 +-o
ENSG00000162769 FLVCR1 +-o
ENSG00000075420 FNDC3B +-o
ENSG00000125740 FOSB +-o
ENSG00000164916 FOXK1 +-o
ENSG00000137166 FOXP4 +-o
ENSG00000104064 GABPB1 +-o
ENSG00000106105 GARS +-o
ENSG00000160844 GATS +-o
ENSG00000114480 GBE1 +-o
ENSG00000197045 GMFB +-o
ENSG00000105220 GPI +-o
ENSG00000142751 GPN2 +-o
ENSG00000148358 GPR107 +-o
ENSG00000112406 HECA +-o
ENSG00000138646 HERC5 +-o
ENSG00000197409 HIST1H3D +-o
ENSG00000124529 HIST1H4B +-o
ENSG00000127124 HIVEP3 +-o
ENSG00000206503 HLA-A +-o
ENSG00000204592 HLA-E +-o
ENSG00000169045 HNRNPH1 +-o
ENSG00000096746 HNRNPH3 +-o
ENSG00000067064 IDI1 +-o
ENSG00000197081 IGF2R +-o
ENSG00000185811 IKZF1 +-o
ENSG00000211459 J01415.23 +-o
ENSG00000168301 KCTD6 +-o
ENSG00000100441 KHNYN +-o
ENSG00000067082 KLF6 +-o
ENSG00000167748 KLK1 +-o
ENSG00000138709 LARP1B +-o
ENSG00000134333 LDHA +-o
ENSG00000188636 LDOC1L +-o
ENSG00000174106 LEMD3 +-o
ENSG00000100600 LGMN +-o
ENSG00000213171 LINGO4 +-o
ENSG00000139636 LMBR1L +-o
ENSG00000105216 LSM14A +-o
ENSG00000071054 MAP4K4 +-o
ENSG00000165406 MARCH8 +-o
ENSG00000155130 MARCKS +-o
ENSG00000133030 MPRIP +-o
ENSG00000198899 MT-ATP6 +-o
ENSG00000143033 MTF2 +-o
ENSG00000065911 MTHFD2 +-o
ENSG00000185499 MUC1 +-o
ENSG00000119950 MXI1 +-o
ENSG00000083168 MYST3 +-o
ENSG00000187109 NAP1L1 +-o
ENSG00000109805 NCAPG +-o
ENSG00000222041 NCRNA00152 +-o
ENSG00000177410 NCRNA00275 +-o
ENSG00000131507 NDFIP1 +-o
ENSG00000245532 NEAT1 +-o
ENSG00000183691 NOG +-o
ENSG00000147383 NSDHL +-o
ENSG00000139496 NUPL1 +-o
ENSG00000125779 PANK2 +-o
ENSG00000137817 PARP6 +-o
ENSG00000121892 PDS5A +-o
ENSG00000132326 PER2 +-o
ENSG00000127980 PEX1 +-o
ENSG00000056487 PHF21B +-o
ENSG00000121879 PIK3CA +-o
ENSG00000168734 PKIG +-o
ENSG00000127564 PKMYT1 +-o
ENSG00000126003 PLAGL2 +-o
ENSG00000163803 PLB1 +-o
ENSG00000115896 PLCL1 +-o
ENSG00000120278 PLEKHG1 +-o
ENSG00000213639 PPP1CB +-o
ENSG00000158615 PPP1R15B +-o
ENSG00000131238 PPT1 +-o
ENSG00000198901 PRC1 +-o
ENSG00000141956 PRDM15 +-o
ENSG00000135069 PSAT1 +-o
ENSG00000156471 PTDSS1 +-o
ENSG00000167461 RAB8A +-o
ENSG00000070950 RAD18 +-o
ENSG00000179837 RBM15B +-o
ENSG00000131795 RBM8A +-o
ENSG00000135870 RC3H1 +-o
ENSG00000144468 RHBDD1 +-o
ENSG00000005486 RHBDD2 +-o
ENSG00000143878 RHOB +-o
ENSG00000131263 RLIM +-o
ENSG00000022840 RNF10 +-o
ENSG00000206737 RNU1-5 +-o
ENSG00000230526 RP11-472G21.2 +-o
ENSG00000230018 RP11-481H12.1 +-o
ENSG00000250135 RP4-622L5.2 +-o
ENSG00000225828 RP4-811H24.6 +-o
ENSG00000088899 RP5-1187M17.10 +-o
ENSG00000116251 RPL22 +-o
ENSG00000141425 RPRD1A +-o
ENSG00000215695 RSC1A1 +-o
ENSG00000048649 RSF1 +-o
ENSG00000163993 S100P +-o
ENSG00000130254 SAFB2 +-o
ENSG00000052802 SC4MOL +-o
ENSG00000099194 SCD +-o
ENSG00000130766 SESN2 +-o
ENSG00000116560 SFPQ +-o
ENSG00000118515 SGK1 +-o
ENSG00000096717 SIRT1 +-o
ENSG00000182628 SKA2 +-o
ENSG00000109171 SLAIN2 +-o
ENSG00000089057 SLC23A2 +-o
ENSG00000144741 SLC25A26 +-o
ENSG00000164933 SLC25A32 +-o
ENSG00000111371 SLC38A1 +-o
ENSG00000168003 SLC3A2 +-o
ENSG00000072041 SLC6A15 +-o
ENSG00000139514 SLC7A1 +-o
ENSG00000103061 SLC7A6OS +-o
ENSG00000163877 SNIP1 +-o
ENSG00000187678 SPRY4 +-o
ENSG00000162032 SPSB3 +-o
ENSG00000112081 SRSF3 +-o
ENSG00000124193 SRSF6 +-o
ENSG00000111450 STX2 +-o
ENSG00000113387 SUB1 +-o
ENSG00000135801 TAF5L +-o
ENSG00000101849 TBL1X +-o
ENSG00000100109 TFIP11 +-o
ENSG00000136114 THSD1 +-o
ENSG00000166881 TMEM194A +-o
ENSG00000204178 TMEM57 +-o
ENSG00000090905 TNRC6A +-o
ENSG00000173726 TOMM20 +-o
ENSG00000198846 TOX +-o
ENSG00000124191 TOX2 +-o
ENSG00000211772 TRBC2 +-o
ENSG00000101255 TRIB3 +-o
ENSG00000234127 TRIM26 +-o
ENSG00000104228 TRIM35 +-o
ENSG00000146063 TRIM41 +-o
ENSG00000135451 TROAP +-o
ENSG00000100991 TRPC4AP +-o
ENSG00000157514 TSC22D3 +-o
ENSG00000198860 TSEN15 +-o
ENSG00000189241 TSPYL1 +-o
ENSG00000011295 TTC19 +-o
ENSG00000114383 TUSC2 +-o
ENSG00000207501 U1.93 +-o
ENSG00000132388 UBE2G1 +-o
ENSG00000226632 UBE2V1P1 +-o
ENSG00000140740 UQCRC2 +-o
ENSG00000124486 USP9X +-o
ENSG00000112715 VEGFA +-o
ENSG00000185596 WASH1 +-o
ENSG00000146556 WASH2P +-o
ENSG00000198373 WWP2 +-o
ENSG00000163872 YEATS2 +-o
ENSG00000176105 YES1 +-o
ENSG00000128245 YWHAH +-o
ENSG00000185670 ZBTB3 +-o
ENSG00000105939 ZC3HAV1 +-o
ENSG00000186660 ZFP91 +-o
ENSG00000043355 ZIC2 +-o
ENSG00000172667 ZMAT3 +-o
ENSG00000147118 ZNF182 +-o
ENSG00000130856 ZNF236 +-o
ENSG00000130684 ZNF337 +-o
ENSG00000081386 ZNF510 +-o
ENSG00000164048 ZNF589 +-o
ENSG00000185730 ZNF696 +-o
ENSG00000204514 ZNF814 +-o
hsa-let-7a* hsa-let-7a* +-o
hsa-miR-1255b hsa-miR-1255b +-o
hsa-miR-2964a-5p hsa-miR-2964a-5p +-o
hsa-miR-301a hsa-miR-301a +-o
hsa-miR-301b hsa-miR-301b +-o
hsa-miR-330-3p hsa-miR-330-3p +-o
hsa-miR-4649-3p hsa-miR-4649-3p +-o
hsa-miR-4676-3p hsa-miR-4676-3p +-o
hsa-miR-548a-5p hsa-miR-548a-5p +-o