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Coexpression cluster:C2956: Difference between revisions

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|tf_chipseq_enrich=CHD2#1106;4:10.3440228341169:8.73193255208051e-05:0.00129428655096045!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.0099998199648886!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.01613521047212!ETS1#2113;4:9.72876092220234:0.000111595531741814:0.0015492390987084!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.00391133949755576!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186738642091839!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323582041238245!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0245244248547224!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00509428959343935!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0107152118521204!ZBTB33#10009;4:31.6647250299812:9.93721537730495e-07:4.21027519996086e-05
|tf_chipseq_enrich=CHD2#1106;4:10.3440228341169:8.73193255208051e-05:0.00129428655096045!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.0099998199648886!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.01613521047212!ETS1#2113;4:9.72876092220234:0.000111595531741814:0.0015492390987084!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.00391133949755576!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186738642091839!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323582041238245!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0245244248547224!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00509428959343935!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0107152118521204!ZBTB33#10009;4:31.6647250299812:9.93721537730495e-07:4.21027519996086e-05
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}}
}}

Revision as of 15:50, 26 November 2012


Full id: C2956_endometrial_nonsmall_cholangiocellular_liposarcoma_lymphangiectasia_medulloblastoma_melanoma



Phase1 CAGE Peaks

Hg19::chrX:151903196..151903211,-p1@MAGEA12
Hg19::chrX:151903207..151903234,+p1@CSAG1
Hg19::chrX:151903235..151903247,+p3@CSAG1
Hg19::chrX:151903253..151903273,+p2@CSAG1


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><br>uberon_data<br>disease_data<br>


Uber Anatomy
Ontology termp-valuen
neural tube3.28e-1856
neural rod3.28e-1856
future spinal cord3.28e-1856
neural keel3.28e-1856
brain3.43e-1868
future brain3.43e-1868
central nervous system5.59e-1881
nervous system3.55e-1789
regional part of nervous system6.34e-1753
regional part of brain6.34e-1753
larynx2.00e-159
brain grey matter2.15e-1434
gray matter2.15e-1434
telencephalon3.09e-1434
regional part of forebrain2.17e-1341
forebrain2.17e-1341
anterior neural tube2.17e-1341
future forebrain2.17e-1341
organ system subdivision7.90e-13223
regional part of telencephalon1.53e-1232
regional part of cerebral cortex1.55e-1222
cerebral hemisphere1.92e-1232
neocortex2.23e-1220
cerebral cortex4.09e-1225
pallium4.09e-1225
neural plate7.90e-1082
presumptive neural plate7.90e-1082
neurectoderm5.14e-0986
ecto-epithelium2.82e-08104
respiratory primordium3.18e-0838
endoderm of foregut3.18e-0838
pre-chordal neural plate3.54e-0761
adult organism8.54e-07114
Disease
Ontology termp-valuen
cancer5.83e-21235
disease of cellular proliferation7.79e-21239
cell type cancer5.17e-18143
carcinoma2.27e-12106
organ system cancer5.62e-09137


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
CHD2#1106410.34402283411698.73193255208051e-050.00129428655096045
E2F6#187645.017155731697390.00157802193473060.0099998199648886
ELF1#199744.258097958807540.003041525565781240.01613521047212
ETS1#211349.728760922202340.0001115955317418140.0015492390987084
GABPB1#255347.067683836182170.0004006876864423170.00391133949755576
HEY1#2346244.040111043105710.00375304636917980.0186738642091839
TAF1#687243.343046285745290.008005664898701650.0323582041238245
TBP#690843.706770687096390.005296377814784350.0245244248547224
USF1#739146.361499277207960.0006105011399140830.00509428959343935
YY1#752844.911170749853860.00171871838055440.0107152118521204
ZBTB33#10009431.66472502998129.93721537730495e-074.21027519996086e-05



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.