PEACHi
GeneSet DNA Repair (Pathways_-_Reactome.gmt.txt) is enriched in the following clusters
Cluster log(P) Qvalue Observed in Background Observed in Cluster Expected in Cluster
DownRegulated -2.6 0.03668 64.0 48.0 37.79
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
ENSG00000100823 APEX1 NonAssociatedWithProgression
ENSG00000149311 ATM NonAssociatedWithProgression
ENSG00000175054 ATR NonAssociatedWithProgression
ENSG00000012048 BRCA1 NonAssociatedWithProgression
ENSG00000134480 CCNH -o-
ENSG00000152669 CCNO -+o
ENSG00000134058 CDK7 o+o
ENSG00000167986 DDB1 o--a
ENSG00000134574 DDB2 o--a
ENSG00000104884 ERCC2 ---
ENSG00000163161 ERCC3 o-o
ENSG00000175595 ERCC4 o-o
ENSG00000134899 ERCC5 NonAssociatedWithProgression
ENSG00000049167 ERCC8 -+o
ENSG00000187741 FANCA -o-
ENSG00000158169 FANCC o-o
ENSG00000144554 FANCD2 oo+
ENSG00000112039 FANCE -oo
ENSG00000183161 FANCF NonAssociatedWithProgression
ENSG00000140525 FANCI o--b
ENSG00000115392 FANCL NonAssociatedWithProgression
ENSG00000168496 FEN1 NonAssociatedWithProgression
ENSG00000110768 GTF2H1 o++b
ENSG00000145736 GTF2H2 o++b
ENSG00000111358 GTF2H3 NonAssociatedWithProgression
ENSG00000188486 H2AFX ---
ENSG00000105486 LIG1 o--a
ENSG00000005156 LIG3 NonAssociatedWithProgression
ENSG00000174405 LIG4 -+o
ENSG00000116670 MAD2L2 o--a
ENSG00000129071 MBD4 o+o
ENSG00000137337 MDC1 o-o
ENSG00000103152 MPG o--a
ENSG00000132781 MUTYH o--a
ENSG00000104320 NBN NonAssociatedWithProgression
ENSG00000065057 NTHL1 --o
ENSG00000114026 OGG1 o--a
ENSG00000083093 PALB2 o-o
ENSG00000132646 PCNA -o-
ENSG00000070501 POLB o+-
ENSG00000062822 POLD1 o--a
ENSG00000106628 POLD2 o--b
ENSG00000077514 POLD3 o+o
ENSG00000175482 POLD4 --o
ENSG00000177084 POLE o--b
ENSG00000100479 POLE2 -o-
ENSG00000181222 POLR2A ---
ENSG00000047315 POLR2B +oo
ENSG00000102978 POLR2C NonAssociatedWithProgression
ENSG00000144231 POLR2D o--b
ENSG00000100142 POLR2F NonAssociatedWithProgression
ENSG00000168002 POLR2G NonAssociatedWithProgression
ENSG00000163882 POLR2H o-o
ENSG00000105258 POLR2I --o
ENSG00000005075 POLR2J ---
ENSG00000177700 POLR2L o-o
ENSG00000253729 PRKDC o--b
ENSG00000119318 RAD23B oo-
ENSG00000113522 RAD50 NonAssociatedWithProgression
ENSG00000051180 RAD51 NonAssociatedWithProgression
ENSG00000135945 REV1 ---
ENSG00000035928 RFC1 o--b
ENSG00000049541 RFC2 o--b
ENSG00000133119 RFC3 -oo
ENSG00000163918 RFC4 o--a
ENSG00000111445 RFC5 -oo
ENSG00000117748 RPA2 oo-
ENSG00000106399 RPA3 o++b
ENSG00000143947 RPS27A o+o
ENSG00000123415 SMUG1 NonAssociatedWithProgression
ENSG00000187735 TCEA1 NonAssociatedWithProgression
ENSG00000139372 TDG NonAssociatedWithProgression
ENSG00000042088 TDP1 o--a
ENSG00000067369 TP53BP1 o+o
ENSG00000221983 UBA52 o--a
ENSG00000170315 UBB ---
ENSG00000162607 USP1 o--b
ENSG00000136936 XPA o++b
ENSG00000154767 XPC o--b
ENSG00000073050 XRCC1 ---
ENSG00000152422 XRCC4 o++a
ENSG00000079246 XRCC5 -o-
ENSG00000196419 XRCC6 o--b