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Coexpression cluster:C3973: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279709254124962!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00171929344348622!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.032567605818757!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322585811271754!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320953450022959!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00664591910148469!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00309336835228226!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190479579918148!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00421993484773737!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140359582220808!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109525123020795
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279709254124962!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00171929344348622!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.032567605818757!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322585811271754!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320953450022959!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00664591910148469!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00309336835228226!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190479579918148!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00421993484773737!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140359582220808!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109525123020795
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}}
}}

Revision as of 16:28, 26 November 2012


Full id: C3973_bronchogenic_chorionic_hepatoblastoma_small_testicular_rectum_adenocarcinoma



Phase1 CAGE Peaks

Hg19::chr1:3371210..3371219,+p9@ARHGEF16
Hg19::chr1:3371222..3371243,+p1@ARHGEF16
Hg19::chr1:3371261..3371278,+p4@ARHGEF16


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


No results for this coexpression

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


No GOStat results

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>


Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.23e-21160
endoderm2.23e-21160
presumptive endoderm2.23e-21160
digestive system3.17e-19145
digestive tract3.17e-19145
primitive gut3.17e-19145
subdivision of digestive tract1.28e-18118
trunk region element5.78e-13101
respiratory primordium1.79e-1238
endoderm of foregut1.79e-1238
respiratory tract1.79e-1254
foregut1.80e-1287
respiratory system1.06e-1174
segment of respiratory tract3.04e-1147
urinary system structure1.33e-0947
renal system3.25e-0948
subdivision of trunk4.31e-09112
gastrointestinal system5.25e-0925
organ system subdivision9.42e-09223
immaterial anatomical entity1.15e-08117
larynx1.16e-089
organ part1.34e-08218
endo-epithelium3.16e-0882
anatomical space3.28e-0895
cavitated compound organ5.17e-0831
organ segment6.92e-0898
kidney1.02e-0726
kidney mesenchyme1.02e-0726
upper urinary tract1.02e-0726
kidney rudiment1.02e-0726
kidney field1.02e-0726
organ1.25e-07503
nephron tubule epithelium1.70e-0710
abdomen element4.05e-0754
abdominal segment element4.05e-0754
respiratory tract epithelium6.60e-0719
lung epithelium6.60e-0719
Disease
Ontology termp-valuen
carcinoma2.84e-41106
cell type cancer1.56e-29143
cancer2.25e-16235
disease of cellular proliferation8.09e-16239
squamous cell carcinoma1.03e-0914
adenocarcinoma3.98e-0825


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
CTCF#1066435.360256373075030.0064925092527670.0279709254124962
CTCFL#140690319.74647435897440.0001298372005551160.00171929344348622
E2F1#186934.907389214879320.008460985347239390.032567605818757
E2F6#187635.017155731697390.00791769806886330.0322585811271754
EGR1#195834.988179094810140.008056488137383440.0320953450022959
RAD21#5885310.35503389545630.0009004912073565420.00664591910148469
SMC3#9126315.04493284493280.0002935825420371870.00309336835228226
USF1#739136.361499277207960.00388404057290560.0190479579918148
USF2#7392312.99219738506960.0004558979393427810.00421993484773737
ZBTB7A#5134137.35190930787590.002516255860282270.0140359582220808
ZNF263#1012738.221841637010680.001799043925565870.0109525123020795



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.