PEACHi
Cluster oo- is enriched in the following gene classes
GeneSet DB Hit Count
Pathways_-_KEGGBioCarta.gmt.txt 4
Pathways_-_Reactome.gmt.txt 40
TarBase_6beta.gmt.txt 2
GO_-_Biological_Process.gmt.txt 6
Chromosomal_Bands.gmt.txt 2
TFmiRNA_Targets.gmt.txt 13
GO_-_Molecular_Function.gmt.txt 2
GeneSet Name GeneSet DB log(P) Qvalue Observed in Background Observed in Cluster Expected in Cluster
ACTGCAG,MIR-17-3P TFmiRNA_Targets.gmt.txt -3.6 0.04593 48.0 5.0 0.91
AGTCTTA,MIR-499 TFmiRNA_Targets.gmt.txt -4.8 0.0115 29.0 5.0 0.55
APC/C-mediated degradation of cell cycle proteins Pathways_-_Reactome.gmt.txt -2.5 0.03156 53.0 4.0 1.01
BIOCARTA CELLCYCLE PATHWAY Pathways_-_KEGGBioCarta.gmt.txt -3.7 0.01426 16.0 3.0 0.3
CCACACA,MIR-147 TFmiRNA_Targets.gmt.txt -3.4 0.04965 33.0 4.0 0.63
CDK-mediated phosphorylation and removal of Cdc6 Pathways_-_Reactome.gmt.txt -2.4 0.03389 34.0 3.0 0.65
CELL CELL ADHESION GO_-_Biological_Process.gmt.txt -3.6 0.02851 17.0 3.0 0.32
Cell Cycle Pathways_-_Reactome.gmt.txt -2.4 0.03396 260.0 11.0 4.95
Cell Cycle Checkpoints Pathways_-_Reactome.gmt.txt -3.9 0.00576 79.0 7.0 1.5
Chromosome Maintenance Pathways_-_Reactome.gmt.txt -2.2 0.04432 62.0 4.0 1.18
Cyclin A:Cdk2-associated events at S phase entry Pathways_-_Reactome.gmt.txt -2.8 0.01967 45.0 4.0 0.86
Cyclin E associated events during G1/S transition Pathways_-_Reactome.gmt.txt -2.8 0.01967 45.0 4.0 0.86
DNA Replication Pre-Initiation Pathways_-_Reactome.gmt.txt -2.4 0.03515 57.0 4.0 1.08
Deposition of New CENPA-containing Nucleosomes at the Centromere Pathways_-_Reactome.gmt.txt -3.2 0.01298 22.0 3.0 0.42
Destabilization of mRNA by AUF1 (hnRNP D0) Pathways_-_Reactome.gmt.txt -2.2 0.04386 39.0 3.0 0.74
G1/S DNA Damage Checkpoints Pathways_-_Reactome.gmt.txt -2.9 0.0181 43.0 4.0 0.82
G1/S Transition Pathways_-_Reactome.gmt.txt -3.1 0.01299 79.0 6.0 1.5
G2/M Checkpoints Pathways_-_Reactome.gmt.txt -3.6 0.00878 31.0 4.0 0.59
GTGCCAT,MIR-183 TFmiRNA_Targets.gmt.txt -3.7 0.03976 84.0 7.0 1.6
GTTTGTT,MIR-495 TFmiRNA_Targets.gmt.txt -5.0 0.01046 94.0 9.0 1.79
Gene Expression Pathways_-_Reactome.gmt.txt -2.7 0.02291 484.0 18.0 9.21
KEGG NUCLEOTIDE EXCISION REPAIR Pathways_-_KEGGBioCarta.gmt.txt -2.4 0.04745 34.0 3.0 0.65
KEGG P53 SIGNALING PATHWAY Pathways_-_KEGGBioCarta.gmt.txt -4.1 0.01271 39.0 5.0 0.74
KEGG PROGESTERONE MEDIATED OOCYTE MATURATION Pathways_-_KEGGBioCarta.gmt.txt -2.9 0.02854 42.0 4.0 0.8
M/G1 Transition Pathways_-_Reactome.gmt.txt -2.4 0.03515 57.0 4.0 1.08
Meiosis Pathways_-_Reactome.gmt.txt -3.4 0.01001 34.0 4.0 0.65
Meiotic Recombination Pathways_-_Reactome.gmt.txt -4.9 0.00318 17.0 4.0 0.32
Mitotic G1-G1/S phases Pathways_-_Reactome.gmt.txt -3.4 0.01001 95.0 7.0 1.81
NEGATIVE REGULATION OF BIOLOGICAL PROCESS GO_-_Biological_Process.gmt.txt -3.4 0.03264 290.0 14.0 5.52
NEGATIVE REGULATION OF CELLULAR PROCESS GO_-_Biological_Process.gmt.txt -3.6 0.02851 281.0 14.0 5.35
NEGATIVE REGULATION OF CELL PROLIFERATION GO_-_Biological_Process.gmt.txt -3.3 0.03669 54.0 5.0 1.03
Nucleosome assembly Pathways_-_Reactome.gmt.txt -3.2 0.01298 22.0 3.0 0.42
Orc1 removal from chromatin Pathways_-_Reactome.gmt.txt -2.6 0.02439 49.0 4.0 0.93
Processing of Capped Intron-Containing Pre-mRNA Pathways_-_Reactome.gmt.txt -2.7 0.02407 95.0 6.0 1.81
REGULATION OF CELL PROLIFERATION GO_-_Biological_Process.gmt.txt -3.3 0.03669 98.0 7.0 1.86
REGULATION OF DNA METABOLIC PROCESS GO_-_Biological_Process.gmt.txt -3.2 0.03669 21.0 3.0 0.4
RNA Polymerase I Chain Elongation Pathways_-_Reactome.gmt.txt -4.5 0.00318 20.0 4.0 0.38
RNA Polymerase I Promoter Clearance Pathways_-_Reactome.gmt.txt -4.1 0.00528 24.0 4.0 0.46
RNA Polymerase I Transcription Pathways_-_Reactome.gmt.txt -4.0 0.00574 25.0 4.0 0.48
Regulation of APC/C activators between G1/S and early anaphase Pathways_-_Reactome.gmt.txt -2.6 0.02439 49.0 4.0 0.93
Regulation of DNA replication Pathways_-_Reactome.gmt.txt -2.6 0.02804 51.0 4.0 0.97
Regulation of mRNA Stability by Proteins that Bind AU-rich Elements Pathways_-_Reactome.gmt.txt -2.2 0.04432 62.0 4.0 1.18
Regulation of mitotic cell cycle Pathways_-_Reactome.gmt.txt -2.5 0.03156 53.0 4.0 1.01
Removal of licensing factors from origins Pathways_-_Reactome.gmt.txt -2.6 0.02439 49.0 4.0 0.93
S Phase Pathways_-_Reactome.gmt.txt -2.4 0.035 81.0 5.0 1.54
SCF(Skp2)-mediated degradation of p27/p21 Pathways_-_Reactome.gmt.txt -3.0 0.01417 40.0 4.0 0.76
SINGLE STRANDED DNA BINDING GO_-_Molecular_Function.gmt.txt -4.1 0.01435 24.0 4.0 0.46
STRUCTURE SPECIFIC DNA BINDING GO_-_Molecular_Function.gmt.txt -3.3 0.03238 35.0 4.0 0.67
Switching of origins to a post-replicative state Pathways_-_Reactome.gmt.txt -2.6 0.02439 49.0 4.0 0.93
Synthesis of DNA Pathways_-_Reactome.gmt.txt -2.7 0.02439 71.0 5.0 1.35
TGGAAA V$NFAT Q4 01 TFmiRNA_Targets.gmt.txt -4.8 0.0115 523.0 24.0 9.95
TTANWNANTGGM UNKNOWN TFmiRNA_Targets.gmt.txt -3.7 0.03976 16.0 3.0 0.3
Telomere Maintenance Pathways_-_Reactome.gmt.txt -2.3 0.03659 36.0 3.0 0.68
Transcription Pathways_-_Reactome.gmt.txt -2.6 0.02804 99.0 6.0 1.88
V$ATF6 01 TFmiRNA_Targets.gmt.txt -3.4 0.04965 51.0 5.0 0.97
V$CDX2 Q5 TFmiRNA_Targets.gmt.txt -3.4 0.04965 51.0 5.0 0.97
V$CREB Q2 01 TFmiRNA_Targets.gmt.txt -3.7 0.03976 64.0 6.0 1.22
V$CREB Q4 TFmiRNA_Targets.gmt.txt -3.9 0.03441 80.0 7.0 1.52
V$OCT1 06 TFmiRNA_Targets.gmt.txt -4.3 0.01708 52.0 6.0 0.99
V$YY1 01 TFmiRNA_Targets.gmt.txt -3.4 0.04965 93.0 7.0 1.77
chr1q42 Chromosomal_Bands.gmt.txt -2.4 0.028 35.0 3.0 0.67
chr2p21 Chromosomal_Bands.gmt.txt -3.8 0.00573 15.0 3.0 0.29
hsa-miR-130b-3p targets TarBase_6beta.gmt.txt -3.6 0.01523 112.0 8.0 2.13
hsa-miR-19b-3p targets TarBase_6beta.gmt.txt -2.9 0.04171 113.0 7.0 2.15
mRNA Processing Pathways_-_Reactome.gmt.txt -2.4 0.03389 105.0 6.0 2.0
mRNA Splicing Pathways_-_Reactome.gmt.txt -2.6 0.02716 73.0 5.0 1.39
mRNA Splicing - Major Pathway Pathways_-_Reactome.gmt.txt -2.6 0.02716 73.0 5.0 1.39
p53-Dependent G1 DNA Damage Response Pathways_-_Reactome.gmt.txt -3.0 0.01417 40.0 4.0 0.76
p53-Dependent G1/S DNA damage checkpoint Pathways_-_Reactome.gmt.txt -3.0 0.01417 40.0 4.0 0.76
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
ENSG00000200488 7SK.30 oo-
ENSG00000201428 7SK.58 oo-
ENSG00000205047 AC010536.1 oo-
ENSG00000249622 AC116351.4 oo-
ENSG00000006831 ADIPOR2 oo-
ENSG00000130706 ADRM1 oo-
ENSG00000173744 AGFG1 oo-
ENSG00000135334 AKIRIN2 oo-
ENSG00000176020 AMIGO3 oo-
ENSG00000118454 ANKRD13C oo-
ENSG00000143401 ANP32E oo-
ENSG00000241994 AP000812.1 oo-
ENSG00000198826 ARHGAP11A oo-
ENSG00000104728 ARHGEF10 oo-
ENSG00000017260 ATP2C1 oo-
ENSG00000135390 ATP5G2 oo-
ENSG00000009954 BAZ1B oo-
ENSG00000157764 BRAF oo-
ENSG00000141867 BRD4 oo-
ENSG00000215699 BX511012.1 oo-
ENSG00000236686 BZW1P1 oo-
ENSG00000198406 BZW1P2 oo-
ENSG00000128891 C15orf57 oo-
ENSG00000167747 C19orf48 oo-
ENSG00000000460 C1orf112 oo-
ENSG00000010072 C1orf124 oo-
ENSG00000179021 C3orf38 oo-
ENSG00000196366 C9orf163 oo-
ENSG00000134057 CCNB1 oo-
ENSG00000157456 CCNB2 oo-
ENSG00000135535 CD164 oo-
ENSG00000123374 CDK2 oo-
ENSG00000124762 CDKN1A oo-
ENSG00000153044 CENPH oo-
ENSG00000155508 CNOT8 oo-
ENSG00000139842 CUL4A oo-
ENSG00000119004 CYP20A1 oo-
ENSG00000215301 DDX3X oo-
ENSG00000108406 DHX40 oo-
ENSG00000231607 DLEU2 oo-
ENSG00000116652 DLEU2L oo-
ENSG00000169016 E2F6 oo-
ENSG00000167658 EEF2 oo-
ENSG00000104131 EIF3J oo-
ENSG00000143924 EML4 oo-
ENSG00000143420 ENSA oo-
ENSG00000135999 EPC2 oo-
ENSG00000139146 FAM60A oo-
ENSG00000178974 FBXO34 oo-
ENSG00000114861 FOXP1 oo-
ENSG00000167996 FTH1 oo-
ENSG00000223361 FTH1P10 oo-
ENSG00000145990 GFOD1 oo-
ENSG00000005955 GGNBP2 oo-
ENSG00000165474 GJB2 oo-
ENSG00000106070 GRB10 oo-
ENSG00000147099 HDAC8 oo-
ENSG00000137259 HIST1H2AB oo-
ENSG00000197459 HIST1H2BH oo-
ENSG00000149948 HMGA2 oo-
ENSG00000112972 HMGCS1 oo-
ENSG00000122566 HNRNPA2B1 oo-
ENSG00000138668 HNRNPD oo-
ENSG00000152795 HNRPDL oo-
ENSG00000177508 IRX3 oo-
ENSG00000176595 KBTBD11 oo-
ENSG00000170852 KBTBD2 oo-
ENSG00000120071 KIAA1267 oo-
ENSG00000131437 KIF3A oo-
ENSG00000169926 KLF13 oo-
ENSG00000118263 KLF7 oo-
ENSG00000189308 LIN54 oo-
ENSG00000143669 LYST oo-
ENSG00000120254 MTHFD1L oo-
ENSG00000179820 MYADM oo-
ENSG00000204899 MZT1 oo-
ENSG00000173848 NET1 oo-
ENSG00000163273 NPPC oo-
ENSG00000163002 NUP35 oo-
ENSG00000165494 PCF11 oo-
ENSG00000150593 PDCD4 oo-
ENSG00000180957 PITPNB oo-
ENSG00000181690 PLAG1 oo-
ENSG00000141682 PMAIP1 oo-
ENSG00000100941 PNN oo-
ENSG00000186866 POFUT2 oo-
ENSG00000125630 POLR1B oo-
ENSG00000197746 PSAP oo-
ENSG00000126067 PSMB2 oo-
ENSG00000197170 PSMD12 oo-
ENSG00000060749 QSER1 oo-
ENSG00000119318 RAD23B oo-
ENSG00000091009 RBM27 oo-
ENSG00000147274 RBMX oo-
ENSG00000124784 RIOK1 oo-
ENSG00000202538 RNU4-2 oo-
ENSG00000235492 RP11-16L9.4 oo-
ENSG00000223482 RP11-322M19.1 oo-
ENSG00000117748 RPA2 oo-
ENSG00000155876 RRAGA oo-
ENSG00000137876 RSL24D1 oo-
ENSG00000163191 S100A11 oo-
ENSG00000137575 SDCBP oo-
ENSG00000140612 SEC11A oo-
ENSG00000112701 SENP6 oo-
ENSG00000132824 SERINC3 oo-
ENSG00000134294 SLC38A2 oo-
ENSG00000247092 SNHG10 oo-
ENSG00000238649 SNORD42A oo-
ENSG00000089006 SNX5 oo-
ENSG00000171150 SOCS5 oo-
ENSG00000008294 SPAG9 oo-
ENSG00000115306 SPTBN1 oo-
ENSG00000188529 SRSF10 oo-
ENSG00000161547 SRSF2 oo-
ENSG00000115750 TAF1B oo-
ENSG00000125676 THOC2 oo-
ENSG00000083312 TNPO1 oo-
ENSG00000143514 TP53BP2 oo-
ENSG00000143549 TPM3 oo-
ENSG00000133112 TPT1 oo-
ENSG00000136527 TRA2B oo-
ENSG00000204599 TRIM39 oo-
ENSG00000140830 TXNL4B oo-
ENSG00000244687 UBE2V1 oo-
ENSG00000140455 USP3 oo-
ENSG00000148516 ZEB1 oo-
ENSG00000173276 ZNF295 oo-
ENSG00000083828 ZNF586 oo-
hsa-let-7i hsa-let-7i oo-
hsa-miR-106b hsa-miR-106b oo-
hsa-miR-130b hsa-miR-130b oo-
hsa-miR-142-3p hsa-miR-142-3p oo-
hsa-miR-18a hsa-miR-18a oo-
hsa-miR-19b hsa-miR-19b oo-
hsa-miR-19b-1* hsa-miR-19b-1* oo-
hsa-miR-19b-2* hsa-miR-19b-2* oo-
hsa-miR-20a* hsa-miR-20a* oo-
hsa-miR-23a hsa-miR-23a oo-
hsa-miR-26a-2* hsa-miR-26a-2* oo-
hsa-miR-30b hsa-miR-30b oo-
hsa-miR-30e hsa-miR-30e oo-
hsa-miR-33b hsa-miR-33b oo-
hsa-miR-3613-5p hsa-miR-3613-5p oo-
hsa-miR-374a hsa-miR-374a oo-
hsa-miR-378d hsa-miR-378d oo-
hsa-miR-3913-3p hsa-miR-3913-3p oo-
hsa-miR-548d-3p hsa-miR-548d-3p oo-
hsa-miR-548z hsa-miR-548z oo-
hsa-miR-570 hsa-miR-570 oo-
hsa-miR-590-5p hsa-miR-590-5p oo-
hsa-miR-624 hsa-miR-624 oo-