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Coexpression cluster:C1026: Difference between revisions

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|tf_chipseq_enrich=BRCA1#672;5:12.6151441520149:1.47177326411908e-05:0.000349421522917327!CEBPB#1051;5:4.98196726614051:0.00125052377879302:0.0084059633734546!CHD2#1106;6:7.75801712558764:1.92157406469162e-05:0.000434294035365349!E2F1#1869;8:4.90738921487932:2.97124777369457e-06:0.000101476176009446!E2F4#1874;8:12.6680603152844:1.5050509647149e-09:1.33434650003277e-07!E2F6#1876;7:4.39001126523521:8.25033297218753e-05:0.00123997197479104!ELF1#1997;7:3.7258357139566:0.000250341272551272:0.00269846136484491!ELK4#2005;5:10.1473010365425:4.23608403932528e-05:0.000758334557735847!ETS1#2113;7:8.51266580692704:8.8174082362229e-07:3.82267039760433e-05!FOS#2353;6:6.7484664816708:4.31702653902356e-05:0.000770052834686731!GABPB1#2553;6:5.30076287713663:0.00017345294309267:0.00211133472303676!HEY1#23462;8:4.04011104310571:1.4081650274634e-05:0.00033902108645286!IRF1#3659;7:6.68251828436841:4.6709523292352e-06:0.000145057862121022!IRF3#3661;5:29.363720132181:2.31300241196823e-07:1.22003868133106e-05!MAX#4149;6:4.83941663175534:0.000291750431370536:0.00309718675563198!MXI1#4601;7:8.71637517516439:7.48926294096089e-07:3.31428445886023e-05!NFYA#4800;6:13.8191855248729:6.49659712753933e-07:2.94614896831559e-05!NFYB#4801;6:12.5698449401523:1.13616741401493e-06:4.66065155350768e-05!PAX5#5079;5:4.16847845698614:0.00284750870610728:0.0154360511656358!POLR2A#5430;8:2.14745317655807:0.00221072578897191:0.0127167873250957!POU2F2#5452;4:4.55306202887126:0.00706247384683113:0.0294591303654124!RFX5#5993;5:7.52994426699694:0.00017791725685856:0.00215863155077267!SIN3A#25942;8:5.40888472681514:1.36410592556506e-06:5.35183541548044e-05!SMARCB1#6598;3:6.84476841793403:0.00747369013463395:0.0308223315420563!SP1#6667;8:5.6983813781409:8.98832477855329e-07:3.86309321624414e-05!SREBF1#6720;3:17.6271935401831:0.000497260515006821:0.00439554726422322!TAF1#6872;8:3.34304628574529:6.40776711117462e-05:0.00104337510028682!TAF7#6879;8:11.4330694049239:3.41987905000906e-09:2.81678823425785e-07!TBP#6908;8:3.70677068709639:2.80450451364125e-05:0.000592075291894437!TFAP2C#7022;6:8.10692145739517:1.48721435420767e-05:0.000352606537886709
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}}
}}

Revision as of 14:38, 26 November 2012


Full id: C1026_Fibroblast_mesothelioma_Chondrocyte_epidermoid_Reticulocytes_clear_myxofibrosarcoma



Phase1 CAGE Peaks

Hg19::chr13:60738003..60738103,-p1@DIAPH3
Hg19::chr15:66797627..66797684,+p1@ZWILCH
Hg19::chr15:69706643..69706710,+p1@KIF23
Hg19::chr15:69706713..69706724,+p4@KIF23
Hg19::chr15:69706740..69706754,+p2@KIF23
Hg19::chr16:46655208..46655316,-p1@SHCBP1
Hg19::chr5:137514834..137514865,+p2@KIF20A
Hg19::chr7:36429461..36429486,+p1@ANLN


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
6.67157721853038e-060.004223108379329733200DNA Replication (Reactome):REACT_383
2.59719623007301e-050.008220126068181063315Cell Cycle, Mitotic (Reactome):REACT_152



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:0007010cytoskeleton organization and biogenesis0.000253758630431385
GO:0006996organelle organization and biogenesis0.00299768850949541
GO:0003777microtubule motor activity0.00364784772441998
GO:0000921septin ring assembly0.00364784772441998
GO:0000022mitotic spindle elongation0.00364784772441998
GO:0032185septin cytoskeleton organization and biogenesis0.00364784772441998
GO:0051231spindle elongation0.00364784772441998
GO:0031106septin ring organization0.00364784772441998
GO:0005826contractile ring0.00364784772441998
GO:0044430cytoskeletal part0.00364784772441998
GO:0007018microtubule-based movement0.00364784772441998
GO:0005875microtubule associated complex0.00364784772441998
GO:0030705cytoskeleton-dependent intracellular transport0.00398926605803164
GO:0032153cell division site0.00404014110159463
GO:0032155cell division site part0.00404014110159463
GO:0043232intracellular non-membrane-bound organelle0.00404014110159463
GO:0043228non-membrane-bound organelle0.00404014110159463
GO:0007067mitosis0.00404014110159463
GO:0000087M phase of mitotic cell cycle0.00404014110159463
GO:0051301cell division0.00404014110159463
GO:0016043cellular component organization and biogenesis0.00541511559004266
GO:0005874microtubule0.00541511559004266
GO:0000279M phase0.0054585510817247
GO:0007017microtubule-based process0.00547302045029384
GO:0005856cytoskeleton0.00547302045029384
GO:0000278mitotic cell cycle0.00547302045029384
GO:0022403cell cycle phase0.00673190003874274
GO:0007052mitotic spindle organization and biogenesis0.00734938574349256
GO:0007096regulation of exit from mitosis0.00810540212515731
GO:0010458exit from mitosis0.00810540212515731
GO:0003779actin binding0.00821972114767682
GO:0044446intracellular organelle part0.00857158797561516
GO:0044422organelle part0.00857158797561516
GO:0042169SH2 domain binding0.00986760624313977
GO:0015630microtubule cytoskeleton0.00986760624313977
GO:0007051spindle organization and biogenesis0.00986760624313977
GO:0008092cytoskeletal protein binding0.0128918198713952
GO:0022402cell cycle process0.013414253511694
GO:0005871kinesin complex0.013414253511694
GO:0000776kinetochore0.0144770113713652
GO:0017048Rho GTPase binding0.0145784508666697
GO:0000910cytokinesis0.0151185788309958
GO:0044448cell cortex part0.0195287248205947
GO:0007049cell cycle0.020608139162833
GO:0046907intracellular transport0.0231279426470676
GO:0043234protein complex0.0231279426470676
GO:0005938cell cortex0.025374928519782
GO:0007088regulation of mitosis0.0260052133793836
GO:0043623cellular protein complex assembly0.0262310674601063
GO:0000775chromosome, pericentric region0.0279232946214486
GO:0017016Ras GTPase binding0.0279232946214486
GO:0005819spindle0.0279232946214486
GO:0051649establishment of cellular localization0.0287133850572141
GO:0031267small GTPase binding0.0290343433953052
GO:0051641cellular localization0.0290343433953052
GO:0051020GTPase binding0.0321997196792408
GO:0000226microtubule cytoskeleton organization and biogenesis0.0332532401154693
GO:0019904protein domain specific binding0.0406149369245473
GO:0032991macromolecular complex0.0410585754456491



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 cell4.91e-25679
eukaryotic cell4.91e-25679
epithelial cell1.04e-18253
native cell2.18e-14722
embryonic cell6.08e-11250
squamous epithelial cell2.08e-0763
fibroblast2.23e-0776
Uber Anatomy
Ontology termp-valuen
larynx4.53e-079
Disease
Ontology termp-valuen
cancer7.10e-48235
disease of cellular proliferation3.08e-47239
cell type cancer2.52e-26143
carcinoma2.87e-20106
organ system cancer2.64e-19137
hematologic cancer2.78e-1051
immune system cancer2.78e-1051
leukemia2.09e-0739


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#672512.61514415201491.47177326411908e-050.000349421522917327
CEBPB#105154.981967266140510.001250523778793020.0084059633734546
CHD2#110667.758017125587641.92157406469162e-050.000434294035365349
E2F1#186984.907389214879322.97124777369457e-060.000101476176009446
E2F4#1874812.66806031528441.5050509647149e-091.33434650003277e-07
E2F6#187674.390011265235218.25033297218753e-050.00123997197479104
ELF1#199773.72583571395660.0002503412725512720.00269846136484491
ELK4#2005510.14730103654254.23608403932528e-050.000758334557735847
ETS1#211378.512665806927048.8174082362229e-073.82267039760433e-05
FOS#235366.74846648167084.31702653902356e-050.000770052834686731
GABPB1#255365.300762877136630.000173452943092670.00211133472303676
HEY1#2346284.040111043105711.4081650274634e-050.00033902108645286
IRF1#365976.682518284368414.6709523292352e-060.000145057862121022
IRF3#3661529.3637201321812.31300241196823e-071.22003868133106e-05
MAX#414964.839416631755340.0002917504313705360.00309718675563198
MXI1#460178.716375175164397.48926294096089e-073.31428445886023e-05
NFYA#4800613.81918552487296.49659712753933e-072.94614896831559e-05
NFYB#4801612.56984494015231.13616741401493e-064.66065155350768e-05
PAX5#507954.168478456986140.002847508706107280.0154360511656358
POLR2A#543082.147453176558070.002210725788971910.0127167873250957
POU2F2#545244.553062028871260.007062473846831130.0294591303654124
RFX5#599357.529944266996940.000177917256858560.00215863155077267
SIN3A#2594285.408884726815141.36410592556506e-065.35183541548044e-05
SMARCB1#659836.844768417934030.007473690134633950.0308223315420563
SP1#666785.69838137814098.98832477855329e-073.86309321624414e-05
SREBF1#6720317.62719354018310.0004972605150068210.00439554726422322
TAF1#687283.343046285745296.40776711117462e-050.00104337510028682
TAF7#6879811.43306940492393.41987905000906e-092.81678823425785e-07
TBP#690883.706770687096392.80450451364125e-050.000592075291894437
TFAP2C#702268.106921457395171.48721435420767e-050.000352606537886709



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.