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Coexpression cluster:C1145: Difference between revisions

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|tf_chipseq_enrich=BRCA1#672;3:8.65038456138161:0.00365929333120223:0.0184731697707574!CCNT2#905;6:5.43102992311083:9.35028339706757e-05:0.00135780623985865!E2F1#1869;7:4.90738921487932:1.45832274679793e-05:0.000346701045647232!E2F4#1874;7:12.6680603152844:1.90745058834676e-08:1.36633903975547e-06!E2F6#1876;7:5.01715573169739:1.24910426162553e-05:0.000308040613884082!EGR1#1958;6:4.27558208126583:0.000376213061986645:0.0037359813616833!ELF1#1997;5:3.04149854200538:0.00971956226937075:0.0365604669134094!GABPB1#2553;4:4.03867647781838:0.0098011349469615:0.0368434198152004!GATA1#2623;3:5.81156063305733:0.0111931160082029:0.0411256936774213!GTF2B#2959;3:13.6902128289961:0.000976196317024572:0.0070152733195988!HDAC2#3066;3:5.74955152998268:0.0115304170404053:0.0421691783199528!HEY1#23462;7:4.04011104310571:5.68979821988558e-05:0.000949563496782727!HMGN3#9324;5:5.84181980239328:0.000462918719129959:0.00426300750438354!HNF4A#3172;3:9.91383872698015:0.00247865482166154:0.0139213891325361!IRF1#3659;6:6.54614036019763:3.13027310449255e-05:0.000631734478763474!MAX#4149;5:4.60896822071937:0.00142433701403361:0.0091779573919457!MYC#4609;5:3.73020133686386:0.00382194422230669:0.0188692461299749!NFKB1#4790;5:3.9200453029956:0.00303658142448461:0.0161163495981171!NFYA#4800;4:10.528903257046:0.000265728718323708:0.00284436216183353!NFYB#4801;4:9.57702471630654:0.000383006171601648:0.00376017875126006!NRF1#4899;5:8.72162817693636:6.71450045004423e-05:0.00107324106596598!POLR2A#5430;7:2.14745317655807:0.00474763644761028:0.02232701742399!POU2F2#5452;4:5.20349946156716:0.00386671431017981:0.0190623448591394!PRDM1#639;2:37.6659873649888:0.001177328194587:0.00799837242662277!RFX5#5993;4:6.88452047268291:0.00135220703152858:0.00890267604903318!SIN3A#25942;7:5.40888472681514:7.3795239773719e-06:0.000211443101419134!SMARCB1#6598;4:10.4301233035185:0.000275586383300937:0.00293633608300006!SP1#6667;5:4.07027241295778:0.00254920612899158:0.014108236919387!SP2#6668;3:11.2086559259334:0.00174151533091611:0.0107165990835227!SREBF1#6720;3:20.1453640459236:0.000315801026139468:0.00323606194750587!SRF#6722;3:5.91307639807192:0.0106686813016745:0.0393900521959057!TAF1#6872;7:3.34304628574529:0.000214233631962245:0.0024646779344024!TAF7#6879;4:6.53318251709938:0.0016484941094751:0.0103106405736897!TBP#6908;7:3.70677068709639:0.000103967209750511:0.00145047173645921!YY1#7528;5:3.50797910703847:0.00507257067280898:0.0236126853493269
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}}
}}

Revision as of 14:42, 26 November 2012


Full id: C1145_Hodgkin_chronic_acute_Reticulocytes_lymphoma_diffuse_Hep2



Phase1 CAGE Peaks

Hg19::chr11:61560348..61560419,+p1@FEN1
Hg19::chr11:65029421..65029459,+p1@POLA2
Hg19::chr15:48624350..48624425,+p1@DUT
Hg19::chr20:5100567..5100581,-p2@PCNA
Hg19::chr20:5100591..5100611,-p1@PCNA
Hg19::chr6:31126291..31126399,+p1@TCF19
Hg19::chrX:48555110..48555164,+p1@SUV39H1


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


p.valueFDRnGenesnPathwayName
0.0001805809699843390.01270086155556522100Pyrimidine metabolism (KEGG):00240
3.67416886898525e-081.16287444703383e-05336DNA replication (KEGG):03030
2.05925492603147e-050.00260701673635584234Base excision repair (KEGG):03410
8.58329659590162e-050.00679153343150715269G1 to S cell cycle control (Wikipathways):WP45
3.15809823992966e-050.00285582312267925242DNA Replication (Wikipathways):WP1806
0.0002067483186744810.01308716857209462107DNA Repair (Reactome):REACT_216
6.67157721853038e-060.001055777094832433200DNA Replication (Reactome):REACT_383
2.59719623007301e-050.002740042022727023315Cell Cycle, Mitotic (Reactome):REACT_152
3.75206069989847e-077.91684807678577e-05377Chromosome Maintenance (Reactome):REACT_22172
3.07978931231787e-081.16287444703383e-05334{PCNA,34} (Static Module):NA



Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


GO IDGO nameFDR corrected p-value
GO:0006260DNA replication3.23493187209283e-05
GO:0006259DNA metabolic process3.62539169331596e-05
GO:0005657replication fork0.00080180884438166
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00100012752440769
GO:0003887DNA-directed DNA polymerase activity0.00100012752440769
GO:0005634nucleus0.00100012752440769
GO:0044427chromosomal part0.00131180468070354
GO:0005694chromosome0.00175265536069073
GO:0000228nuclear chromosome0.00235908563354695
GO:0043283biopolymer metabolic process0.00235908563354695
GO:00171085'-flap endonuclease activity0.00235908563354695
GO:0043626PCNA complex0.00235908563354695
GO:0004170dUTP diphosphatase activity0.00235908563354695
GO:0030337DNA polymerase processivity factor activity0.00235908563354695
GO:0048015phosphoinositide-mediated signaling0.00264897946591783
GO:0043231intracellular membrane-bound organelle0.00300225166600379
GO:0043227membrane-bound organelle0.00300225166600379
GO:0047429nucleoside-triphosphate diphosphatase activity0.00300225166600379
GO:0048256flap endonuclease activity0.00300225166600379
GO:0006287base-excision repair, gap-filling0.00300225166600379
GO:0046974histone lysine N-methyltransferase activity (H3-K9 specific)0.00300225166600379
GO:0008309double-stranded DNA specific exodeoxyribonuclease activity0.00300225166600379
GO:0044428nuclear part0.00507998581710691
GO:0016779nucleotidyltransferase activity0.00507998581710691
GO:0005652nuclear lamina0.00507998581710691
GO:00084095'-3' exonuclease activity0.00507998581710691
GO:0032405MutLalpha complex binding0.00608285954516829
GO:0019932second-messenger-mediated signaling0.00608285954516829
GO:0043229intracellular organelle0.0063152511564931
GO:0043226organelle0.0063152511564931
GO:0009650UV protection0.00639000930182787
GO:0005663DNA replication factor C complex0.00684683280567824
GO:0005658alpha DNA polymerase:primase complex0.00684683280567824
GO:0043170macromolecule metabolic process0.00684683280567824
GO:0016895exodeoxyribonuclease activity, producing 5'-phosphomonoesters0.00686030240274865
GO:0000307cyclin-dependent protein kinase holoenzyme complex0.00686030240274865
GO:0032404mismatch repair complex binding0.00686030240274865
GO:0004529exodeoxyribonuclease activity0.00686030240274865
GO:0003677DNA binding0.00686030240274865
GO:0046080dUTP metabolic process0.0074267459690403
GO:0006281DNA repair0.0088115876286842
GO:0009200deoxyribonucleoside triphosphate metabolic process0.0100477932531831
GO:0009211pyrimidine deoxyribonucleoside triphosphate metabolic process0.0100477932531831
GO:0000287magnesium ion binding0.0100477932531831
GO:0006974response to DNA damage stimulus0.0100477932531831
GO:0009120deoxyribonucleoside metabolic process0.0100477932531831
GO:0043601nuclear replisome0.0100477932531831
GO:0030894replisome0.0100477932531831
GO:0046125pyrimidine deoxyribonucleoside metabolic process0.0100477932531831
GO:0044237cellular metabolic process0.0100477932531831
GO:0044238primary metabolic process0.0101510033057196
GO:0016888endodeoxyribonuclease activity, producing 5'-phosphomonoesters0.0101510033057196
GO:0043596nuclear replication fork0.0105811634345431
GO:0044424intracellular part0.0106570737760598
GO:0006213pyrimidine nucleoside metabolic process0.0113942924920784
GO:0006886intracellular protein transport0.0114259662429928
GO:0009719response to endogenous stimulus0.0114259662429928
GO:0009219pyrimidine deoxyribonucleotide metabolic process0.0118930548377811
GO:0016796exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters0.0118930548377811
GO:0004523ribonuclease H activity0.0118930548377811
GO:0000060protein import into nucleus, translocation0.0118930548377811
GO:0018024histone-lysine N-methyltransferase activity0.0139067156443542
GO:0016278lysine N-methyltransferase activity0.0139067156443542
GO:0016279protein-lysine N-methyltransferase activity0.0139067156443542
GO:0006275regulation of DNA replication0.0141988607925667
GO:0000781chromosome, telomeric region0.0150233136872658
GO:0000794condensed nuclear chromosome0.0150233136872658
GO:0009262deoxyribonucleotide metabolic process0.0150233136872658
GO:0004520endodeoxyribonuclease activity0.0152820594469177
GO:0009411response to UV0.0155333432796311
GO:0005515protein binding0.0157953884552327
GO:0042054histone methyltransferase activity0.0157953884552327
GO:0006284base-excision repair0.0157953884552327
GO:0006302double-strand break repair0.0160259561931682
GO:0008283cell proliferation0.016940445835313
GO:0016891endoribonuclease activity, producing 5'-phosphomonoesters0.0173199076507755
GO:0005622intracellular0.0173199076507755
GO:0008276protein methyltransferase activity0.0198242929997908
GO:0051052regulation of DNA metabolic process0.0198242929997908
GO:0003684damaged DNA binding0.0198242929997908
GO:0008170N-methyltransferase activity0.0198242929997908
GO:0009147pyrimidine nucleoside triphosphate metabolic process0.0198242929997908
GO:0004536deoxyribonuclease activity0.0198242929997908
GO:0015031protein transport0.0198951299519024
GO:0000793condensed chromosome0.0198951299519024
GO:0009116nucleoside metabolic process0.0198951299519024
GO:0016893endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters0.0207964623323496
GO:0046907intracellular transport0.0212665692053063
GO:0045184establishment of protein localization0.0213738883507893
GO:0043232intracellular non-membrane-bound organelle0.0213738883507893
GO:0043228non-membrane-bound organelle0.0213738883507893
GO:0008104protein localization0.0225955583078951
GO:0044454nuclear chromosome part0.0236785144343018
GO:0006220pyrimidine nucleotide metabolic process0.0241223676371893
GO:0033036macromolecule localization0.0241693364343283
GO:0004527exonuclease activity0.024387293458585
GO:0004521endoribonuclease activity0.024387293458585
GO:0003676nucleic acid binding0.0256838301287325
GO:0016740transferase activity0.0263206029691129
GO:0009416response to light stimulus0.0263206029691129
GO:0016043cellular component organization and biogenesis0.0263206029691129
GO:0051649establishment of cellular localization0.0263206029691129
GO:0051641cellular localization0.0271406759701018
GO:0008757S-adenosylmethionine-dependent methyltransferase activity0.0271406759701018
GO:0006606protein import into nucleus0.029831475488504
GO:0051170nuclear import0.029831475488504
GO:0046872metal ion binding0.029831475488504
GO:0004540ribonuclease activity0.029831475488504
GO:0006950response to stress0.029831475488504
GO:0009314response to radiation0.029831475488504
GO:0032403protein complex binding0.029831475488504
GO:0046982protein heterodimerization activity0.0305734825634199
GO:0043167ion binding0.0305734825634199
GO:0003690double-stranded DNA binding0.0310435675766427
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0328864569882111
GO:0003682chromatin binding0.033308670484058
GO:0017038protein import0.034133394260944
GO:0031323regulation of cellular metabolic process0.0375000074527852
GO:0030145manganese ion binding0.0400260820590306
GO:0009141nucleoside triphosphate metabolic process0.0400260820590306
GO:0004519endonuclease activity0.0406235751363442
GO:0044446intracellular organelle part0.0406235751363442
GO:0006913nucleocytoplasmic transport0.0406235751363442
GO:0044422organelle part0.0406235751363442
GO:0051169nuclear transport0.0406235751363442
GO:0019222regulation of metabolic process0.0406235751363442
GO:0043566structure-specific DNA binding0.0408711770132874
GO:0006261DNA-dependent DNA replication0.0417374929281751
GO:0009628response to abiotic stimulus0.0417374929281751
GO:0005635nuclear envelope0.0485919622754928



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>


Cell Type
Ontology termp-valuen
animal cell6.15e-22679
eukaryotic cell6.15e-22679
epithelial cell1.36e-17253
native cell2.19e-16722
embryonic cell2.06e-09250
migratory neural crest cell8.97e-0841
Uber Anatomy
Ontology termp-valuen
larynx1.62e-079
Disease
Ontology termp-valuen
cancer1.75e-36235
disease of cellular proliferation9.23e-36239
hematologic cancer1.38e-1951
immune system cancer1.38e-1951
organ system cancer5.10e-19137
leukemia2.18e-1539
cell type cancer4.47e-15143
carcinoma6.17e-14106
myeloid leukemia2.58e-1131


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BRCA1#67238.650384561381610.003659293331202230.0184731697707574
CCNT2#90565.431029923110839.35028339706757e-050.00135780623985865
E2F1#186974.907389214879321.45832274679793e-050.000346701045647232
E2F4#1874712.66806031528441.90745058834676e-081.36633903975547e-06
E2F6#187675.017155731697391.24910426162553e-050.000308040613884082
EGR1#195864.275582081265830.0003762130619866450.0037359813616833
ELF1#199753.041498542005380.009719562269370750.0365604669134094
GABPB1#255344.038676477818380.00980113494696150.0368434198152004
GATA1#262335.811560633057330.01119311600820290.0411256936774213
GTF2B#2959313.69021282899610.0009761963170245720.0070152733195988
HDAC2#306635.749551529982680.01153041704040530.0421691783199528
HEY1#2346274.040111043105715.68979821988558e-050.000949563496782727
HMGN3#932455.841819802393280.0004629187191299590.00426300750438354
HNF4A#317239.913838726980150.002478654821661540.0139213891325361
IRF1#365966.546140360197633.13027310449255e-050.000631734478763474
MAX#414954.608968220719370.001424337014033610.0091779573919457
MYC#460953.730201336863860.003821944222306690.0188692461299749
NFKB1#479053.92004530299560.003036581424484610.0161163495981171
NFYA#4800410.5289032570460.0002657287183237080.00284436216183353
NFYB#480149.577024716306540.0003830061716016480.00376017875126006
NRF1#489958.721628176936366.71450045004423e-050.00107324106596598
POLR2A#543072.147453176558070.004747636447610280.02232701742399
POU2F2#545245.203499461567160.003866714310179810.0190623448591394
PRDM1#639237.66598736498880.0011773281945870.00799837242662277
RFX5#599346.884520472682910.001352207031528580.00890267604903318
SIN3A#2594275.408884726815147.3795239773719e-060.000211443101419134
SMARCB1#6598410.43012330351850.0002755863833009370.00293633608300006
SP1#666754.070272412957780.002549206128991580.014108236919387
SP2#6668311.20865592593340.001741515330916110.0107165990835227
SREBF1#6720320.14536404592360.0003158010261394680.00323606194750587
SRF#672235.913076398071920.01066868130167450.0393900521959057
TAF1#687273.343046285745290.0002142336319622450.0024646779344024
TAF7#687946.533182517099380.00164849410947510.0103106405736897
TBP#690873.706770687096390.0001039672097505110.00145047173645921
YY1#752853.507979107038470.005072570672808980.0236126853493269



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.