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Coexpression cluster:C2956: Difference between revisions

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|ontology_enrichment_disease=DOID:14566!2.31e-18!239;DOID:162!4.80e-18!235;DOID:0050687!6.91e-16!143;DOID:305!1.67e-11!106;DOID:0050686!3.45e-07!137
|ontology_enrichment_disease=DOID:14566!2.31e-18!239;DOID:162!4.80e-18!235;DOID:0050687!6.91e-16!143;DOID:305!1.67e-11!106;DOID:0050686!3.45e-07!137
|ontology_enrichment_uberon=UBERON:0001017!3.71e-22!82;UBERON:0005743!2.21e-21!86;UBERON:0000955!2.74e-21!69;UBERON:0006238!2.74e-21!69;UBERON:0000073!7.49e-21!94;UBERON:0001016!7.49e-21!94;UBERON:0001049!3.74e-20!57;UBERON:0005068!3.74e-20!57;UBERON:0006241!3.74e-20!57;UBERON:0007135!3.74e-20!57;UBERON:0002616!9.07e-18!59;UBERON:0002780!1.17e-17!41;UBERON:0001890!1.17e-17!41;UBERON:0006240!1.17e-17!41;UBERON:0003080!4.96e-17!42;UBERON:0002020!1.20e-16!34;UBERON:0003528!1.20e-16!34;UBERON:0001893!1.47e-16!34;UBERON:0002791!9.20e-16!33;UBERON:0001869!5.04e-15!32;UBERON:0003075!1.86e-13!86;UBERON:0007284!1.86e-13!86;UBERON:0002346!2.47e-12!90;UBERON:0001737!2.61e-12!9;UBERON:0001950!4.52e-12!20;UBERON:0002619!5.24e-12!22;UBERON:0000956!2.35e-11!25;UBERON:0000203!2.35e-11!25;UBERON:0003056!8.82e-11!61;UBERON:0007023!4.18e-09!115;UBERON:0000033!5.53e-09!123;UBERON:0004121!1.59e-08!169;UBERON:0000153!1.68e-08!129;UBERON:0007811!1.68e-08!129;UBERON:0008947!3.31e-08!38;UBERON:0003258!3.31e-08!38;UBERON:0000924!5.17e-08!173;UBERON:0006601!5.17e-08!173;UBERON:0002308!6.05e-07!9;UBERON:0000125!6.05e-07!9
|ontology_enrichment_uberon=UBERON:0001017!3.71e-22!82;UBERON:0005743!2.21e-21!86;UBERON:0000955!2.74e-21!69;UBERON:0006238!2.74e-21!69;UBERON:0000073!7.49e-21!94;UBERON:0001016!7.49e-21!94;UBERON:0001049!3.74e-20!57;UBERON:0005068!3.74e-20!57;UBERON:0006241!3.74e-20!57;UBERON:0007135!3.74e-20!57;UBERON:0002616!9.07e-18!59;UBERON:0002780!1.17e-17!41;UBERON:0001890!1.17e-17!41;UBERON:0006240!1.17e-17!41;UBERON:0003080!4.96e-17!42;UBERON:0002020!1.20e-16!34;UBERON:0003528!1.20e-16!34;UBERON:0001893!1.47e-16!34;UBERON:0002791!9.20e-16!33;UBERON:0001869!5.04e-15!32;UBERON:0003075!1.86e-13!86;UBERON:0007284!1.86e-13!86;UBERON:0002346!2.47e-12!90;UBERON:0001737!2.61e-12!9;UBERON:0001950!4.52e-12!20;UBERON:0002619!5.24e-12!22;UBERON:0000956!2.35e-11!25;UBERON:0000203!2.35e-11!25;UBERON:0003056!8.82e-11!61;UBERON:0007023!4.18e-09!115;UBERON:0000033!5.53e-09!123;UBERON:0004121!1.59e-08!169;UBERON:0000153!1.68e-08!129;UBERON:0007811!1.68e-08!129;UBERON:0008947!3.31e-08!38;UBERON:0003258!3.31e-08!38;UBERON:0000924!5.17e-08!173;UBERON:0006601!5.17e-08!173;UBERON:0002308!6.05e-07!9;UBERON:0000125!6.05e-07!9
|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 13:44, 5 September 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
central nervous system3.71e-2282
brain2.74e-2169
future brain2.74e-2169
regional part of nervous system7.49e-2194
nervous system7.49e-2194
neural tube3.74e-2057
neural rod3.74e-2057
future spinal cord3.74e-2057
neural keel3.74e-2057
regional part of brain9.07e-1859
regional part of forebrain1.17e-1741
forebrain1.17e-1741
future forebrain1.17e-1741
anterior neural tube4.96e-1742
gray matter1.20e-1634
brain grey matter1.20e-1634
telencephalon1.47e-1634
regional part of telencephalon9.20e-1633
cerebral hemisphere5.04e-1532
neural plate1.86e-1386
presumptive neural plate1.86e-1386
neurectoderm2.47e-1290
larynx2.61e-129
neocortex4.52e-1220
regional part of cerebral cortex5.24e-1222
cerebral cortex2.35e-1125
pallium2.35e-1125
pre-chordal neural plate8.82e-1161
adult organism4.18e-09115
head5.53e-09123
ectoderm-derived structure1.59e-08169
anterior region of body1.68e-08129
craniocervical region1.68e-08129
respiratory primordium3.31e-0838
endoderm of foregut3.31e-0838
ectoderm5.17e-08173
presumptive ectoderm5.17e-08173
nucleus of brain6.05e-079
neural nucleus6.05e-079
Disease
Ontology termp-valuen
disease of cellular proliferation2.31e-18239
cancer4.80e-18235
cell type cancer6.91e-16143
carcinoma1.67e-11106
organ system cancer3.45e-07137


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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C2956&oldid=2132549"