PEACHi
GeneSet DNA_METABOLIC_PROCESS (GO_-_Biological_Process.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 0.03669 140.0 33.0 19.34
DownRegulated -3.4 0.01171 140.0 101.0 82.68
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
ENSG00000097007 ABL1 o--a
ENSG00000102977 ACD o+-
ENSG00000156709 AIFM1 NonAssociatedWithProgression
ENSG00000100823 APEX1 NonAssociatedWithProgression
ENSG00000137074 APTX NonAssociatedWithProgression
ENSG00000111875 ASF1A NonAssociatedWithProgression
ENSG00000171681 ATF7IP ---
ENSG00000149311 ATM NonAssociatedWithProgression
ENSG00000175054 ATR NonAssociatedWithProgression
ENSG00000085224 ATRX -oo
ENSG00000066427 ATXN3 NonAssociatedWithProgression
ENSG00000197299 BLM ---
ENSG00000012048 BRCA1 NonAssociatedWithProgression
ENSG00000159388 BTG2 o-o
ENSG00000115355 CCDC88A +o+
ENSG00000152669 CCNO -+o
ENSG00000094804 CDC6 NonAssociatedWithProgression
ENSG00000123374 CDK2 oo-
ENSG00000111328 CDK2AP1 --o
ENSG00000149554 CHEK1 o+o
ENSG00000141551 CSNK1D o--a
ENSG00000213923 CSNK1E o--b
ENSG00000172115 CYCS o--b
ENSG00000006634 DBF4 ---
ENSG00000167986 DDB1 o--a
ENSG00000134574 DDB2 o--a
ENSG00000160049 DFFA NonAssociatedWithProgression
ENSG00000130826 DKC1 o--b
ENSG00000178028 DMAP1 o--a
ENSG00000105612 DNASE2 NonAssociatedWithProgression
ENSG00000130816 DNMT1 o-o
ENSG00000119772 DNMT3A o-o
ENSG00000128951 DUT o--a
ENSG00000104884 ERCC2 ---
ENSG00000163161 ERCC3 o-o
ENSG00000175595 ERCC4 o-o
ENSG00000134899 ERCC5 NonAssociatedWithProgression
ENSG00000049167 ERCC8 -+o
ENSG00000174371 EXO1 o++b
ENSG00000187741 FANCA -o-
ENSG00000158169 FANCC o-o
ENSG00000168496 FEN1 NonAssociatedWithProgression
ENSG00000170345 FOS NonAssociatedWithProgression
ENSG00000116717 GADD45A o+o
ENSG00000167491 GATAD2A o--a
ENSG00000112312 GMNN NonAssociatedWithProgression
ENSG00000110768 GTF2H1 o++b
ENSG00000107937 GTPBP4 o--b
ENSG00000119969 HELLS +o+
ENSG00000189403 HMGB1 o--b
ENSG00000164104 HMGB2 o--b
ENSG00000136273 HUS1 o+o
ENSG00000132740 IGHMBP2 ---
ENSG00000113520 IL4 NonAssociatedWithProgression
ENSG00000168685 IL7R o++b
ENSG00000174943 KCTD13 o--a
ENSG00000151657 KIN o+o
ENSG00000114030 KPNA1 NonAssociatedWithProgression
ENSG00000182481 KPNA2 o--a
ENSG00000105486 LIG1 o--a
ENSG00000005156 LIG3 NonAssociatedWithProgression
ENSG00000174405 LIG4 -+o
ENSG00000073111 MCM2 o--a
ENSG00000160294 MCM3AP NonAssociatedWithProgression
ENSG00000100297 MCM5 o--b
ENSG00000166508 MCM7 o--b
ENSG00000076242 MLH1 o--b
ENSG00000155229 MMS19 o--b
ENSG00000103152 MPG o--a
ENSG00000095002 MSH2 +oo
ENSG00000204410 MSH5 NonAssociatedWithProgression
ENSG00000116062 MSH6 o--a
ENSG00000132781 MUTYH o--a
ENSG00000136504 MYST2 NonAssociatedWithProgression
ENSG00000159593 NAE1 o+o
ENSG00000187109 NAP1L1 +-o
ENSG00000132780 NASP o--a
ENSG00000104320 NBN NonAssociatedWithProgression
ENSG00000186575 NF2 o--b
ENSG00000187736 NHEJ1 o-o
ENSG00000198000 NOL8 -oo
ENSG00000065057 NTHL1 --o
ENSG00000110713 NUP98 o--a
ENSG00000114026 OGG1 o--a
ENSG00000143799 PARP1 o--b
ENSG00000041880 PARP3 o++a
ENSG00000100151 PICK1 ---
ENSG00000140451 PIF1 ---
ENSG00000064933 PMS1 -+o
ENSG00000122512 PMS2 NonAssociatedWithProgression
ENSG00000101868 POLA1 NonAssociatedWithProgression
ENSG00000070501 POLB o+-
ENSG00000062822 POLD1 o--a
ENSG00000106628 POLD2 o--b
ENSG00000175482 POLD4 --o
ENSG00000177084 POLE o--b
ENSG00000100479 POLE2 -o-
ENSG00000148229 POLE3 o--a
ENSG00000140521 POLG o--b
ENSG00000136480 POLG2 NonAssociatedWithProgression
ENSG00000101751 POLI o+-
ENSG00000122008 POLK +o+
ENSG00000051341 POLQ +o+
ENSG00000128513 POT1 o++b
ENSG00000131238 PPT1 +-o
ENSG00000198056 PRIM1 ---
ENSG00000146143 PRIM2 o-+
ENSG00000110958 PTGES3 o--b
ENSG00000159335 PTMS o--a
ENSG00000185129 PURA ---
ENSG00000113456 RAD1 NonAssociatedWithProgression
ENSG00000152942 RAD17 o--a
ENSG00000164754 RAD21 o--b
ENSG00000179262 RAD23A NonAssociatedWithProgression
ENSG00000119318 RAD23B oo-
ENSG00000113522 RAD50 NonAssociatedWithProgression
ENSG00000051180 RAD51 NonAssociatedWithProgression
ENSG00000108384 RAD51C o+-
ENSG00000182185 RAD51L1 ---
ENSG00000185379 RAD51L3 o--b
ENSG00000197275 RAD54B NonAssociatedWithProgression
ENSG00000085999 RAD54L NonAssociatedWithProgression
ENSG00000172613 RAD9A o--b
ENSG00000166349 RAG1 ---
ENSG00000132341 RAN o--b
ENSG00000101773 RBBP8 NonAssociatedWithProgression
ENSG00000153250 RBMS1 o++b
ENSG00000004700 RECQL NonAssociatedWithProgression
ENSG00000160957 RECQL4 o--b
ENSG00000108469 RECQL5 NonAssociatedWithProgression
ENSG00000214022 REPIN1 o--a
ENSG00000135945 REV1 ---
ENSG00000009413 REV3L o-o
ENSG00000035928 RFC1 o--b
ENSG00000133119 RFC3 -oo
ENSG00000163918 RFC4 o--a
ENSG00000104889 RNASEH2A o--b
ENSG00000117748 RPA2 oo-
ENSG00000106399 RPA3 o++b
ENSG00000129197 RPAIN o+o
ENSG00000183207 RUVBL2 o--a
ENSG00000163191 S100A11 oo-
ENSG00000119335 SET o--b
ENSG00000170364 SETMAR NonAssociatedWithProgression
ENSG00000107290 SETX o+o
ENSG00000163104 SMARCAD1 o+o
ENSG00000138375 SMARCAL1 -+o
ENSG00000099956 SMARCB1 ---
ENSG00000072501 SMC1A o--a
ENSG00000070366 SMG6 ---
ENSG00000123415 SMUG1 NonAssociatedWithProgression
ENSG00000142168 SOD1 NonAssociatedWithProgression
ENSG00000116030 SUMO1 NonAssociatedWithProgression
ENSG00000156502 SUPV3L1 o--a
ENSG00000154144 TBRG1 o--b
ENSG00000139372 TDG NonAssociatedWithProgression
ENSG00000129566 TEP1 +o+
ENSG00000132604 TERF2 o--a
ENSG00000166848 TERF2IP o--b
ENSG00000108064 TFAM NonAssociatedWithProgression
ENSG00000105329 TGFB1 o--a
ENSG00000092330 TINF2 o--b
ENSG00000075131 TIPIN NonAssociatedWithProgression
ENSG00000198586 TLK1 NonAssociatedWithProgression
ENSG00000131747 TOP2A o--b
ENSG00000141510 TP53 o--a
ENSG00000211460 TSN NonAssociatedWithProgression
ENSG00000184205 TSPYL2 o--b
ENSG00000077721 UBE2A -o-
ENSG00000119048 UBE2B o+-
ENSG00000177889 UBE2N o--a
ENSG00000244687 UBE2V1 oo-
ENSG00000169139 UBE2V2 o++b
ENSG00000005007 UPF1 o--b
ENSG00000198382 UVRAG o++a
ENSG00000165280 VCP o+-
ENSG00000124535 WRNIP1 o--b
ENSG00000154767 XPC o--b
ENSG00000196584 XRCC2 ---
ENSG00000126215 XRCC3 NonAssociatedWithProgression
ENSG00000152422 XRCC4 o++a
ENSG00000079246 XRCC5 -o-
ENSG00000196419 XRCC6 o--b
ENSG00000166896 XRCC6BP1 o++a
ENSG00000088930 XRN2 NonAssociatedWithProgression