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Coexpression cluster:C4871: Difference between revisions

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|full_id=C4871_Mesenchymal_astrocytoma_tubular_melanoma_Prostate_MCF7_mesenchymal
|full_id=C4871_Mesenchymal_astrocytoma_tubular_melanoma_Prostate_MCF7_mesenchymal
|id=C4871
|id=C4871
|ontology_enrichment_celltype=CL:0002319!2.26e-07!25;CL:0000133!2.57e-07!59;CL:0000128!4.05e-07!7;CL:0000126!4.05e-07!7;CL:0000127!4.05e-07!7;CL:0002453!4.05e-07!7
|ontology_enrichment_celltype=CL:0002319!3.69e-09!25;CL:0000128!3.09e-08!7;CL:0000126!3.09e-08!7;CL:0000127!3.09e-08!7;CL:0002453!3.09e-08!7;CL:0000133!5.48e-08!59
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005743!1.61e-32!86;UBERON:0000073!5.30e-30!94;UBERON:0001016!5.30e-30!94;UBERON:0001017!3.55e-29!82;UBERON:0002346!1.55e-26!90;UBERON:0003075!1.23e-24!86;UBERON:0007284!1.23e-24!86;UBERON:0000955!1.62e-23!69;UBERON:0006238!1.62e-23!69;UBERON:0002616!9.87e-23!59;UBERON:0001049!1.58e-22!57;UBERON:0005068!1.58e-22!57;UBERON:0006241!1.58e-22!57;UBERON:0007135!1.58e-22!57;UBERON:0003056!2.30e-22!61;UBERON:0000924!5.17e-22!173;UBERON:0006601!5.17e-22!173;UBERON:0004121!2.11e-20!169;UBERON:0003080!1.04e-17!42;UBERON:0002780!3.72e-17!41;UBERON:0001890!3.72e-17!41;UBERON:0006240!3.72e-17!41;UBERON:0000033!4.66e-17!123;UBERON:0001869!1.08e-16!32;UBERON:0002020!1.71e-16!34;UBERON:0003528!1.71e-16!34;UBERON:0000153!2.61e-16!129;UBERON:0007811!2.61e-16!129;UBERON:0001893!4.44e-16!34;UBERON:0002791!1.09e-15!33;UBERON:0000956!4.44e-12!25;UBERON:0000203!4.44e-12!25;UBERON:0007625!2.35e-11!11;UBERON:0000475!1.54e-10!365;UBERON:0002619!7.40e-10!22;UBERON:0001950!2.31e-08!20
|ontology_enrichment_uberon=UBERON:0001017!2.19e-24!81;UBERON:0001016!6.83e-22!89;UBERON:0002346!6.89e-21!86;UBERON:0003075!3.59e-20!82;UBERON:0007284!3.59e-20!82;UBERON:0004121!6.13e-19!171;UBERON:0000924!6.13e-19!171;UBERON:0006601!6.13e-19!171;UBERON:0000955!2.58e-18!68;UBERON:0006238!2.58e-18!68;UBERON:0003056!9.37e-18!61;UBERON:0010371!3.90e-17!104;UBERON:0001049!4.37e-16!56;UBERON:0005068!4.37e-16!56;UBERON:0006241!4.37e-16!56;UBERON:0007135!4.37e-16!56;UBERON:0001869!8.89e-15!32;UBERON:0003528!7.57e-14!34;UBERON:0002020!7.57e-14!34;UBERON:0007625!7.89e-14!11;UBERON:0000073!1.26e-13!53;UBERON:0002616!1.26e-13!53;UBERON:0001893!1.45e-13!34;UBERON:0002791!2.13e-13!32;UBERON:0000956!2.08e-11!25;UBERON:0000203!2.08e-11!25;UBERON:0010314!2.36e-11!132;UBERON:0002780!2.72e-11!41;UBERON:0001890!2.72e-11!41;UBERON:0003080!2.72e-11!41;UBERON:0006240!2.72e-11!41;UBERON:0002619!1.66e-08!22;UBERON:0006876!6.77e-08!11;UBERON:0000349!9.01e-08!5;UBERON:0000019!9.04e-08!20;UBERON:0000047!9.04e-08!20;UBERON:0010312!9.04e-08!20;UBERON:0004088!9.04e-08!20;UBERON:0010230!9.04e-08!20;UBERON:0003072!9.04e-08!20;UBERON:0004128!9.04e-08!20;UBERON:0003071!9.04e-08!20;UBERON:0011216!1.15e-07!223;UBERON:0000970!2.91e-07!21;UBERON:0002104!2.91e-07!21;UBERON:0000488!4.90e-07!4;UBERON:0001456!8.38e-07!22
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281848521842935!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0328350493712966!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00244251634318527!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00446722831352223!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157849459144527!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00669846162429557!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0110322558007266
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281848521842935!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0328350493712966!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00244251634318527!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00446722831352223!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157849459144527!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00669846162429557!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0110322558007266
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}}
}}

Revision as of 16:19, 19 October 2012


Full id: C4871_Mesenchymal_astrocytoma_tubular_melanoma_Prostate_MCF7_mesenchymal



Phase1 CAGE Peaks

Hg19::chrX:37765302..37765334,+p1@ENST00000449263
Hg19::chrX:37765335..37765354,+p5@ENST00000449263
Hg19::chrX:37765364..37765390,+p3@ENST00000449263


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><br>

Cell Type
Ontology termp-valuen
neural cell3.69e-0925
oligodendrocyte3.09e-087
macroglial cell3.09e-087
astrocyte3.09e-087
oligodendrocyte precursor cell3.09e-087
neurectodermal cell5.48e-0859
Uber Anatomy
Ontology termp-valuen
central nervous system2.19e-2481
nervous system6.83e-2289
neurectoderm6.89e-2186
neural plate3.59e-2082
presumptive neural plate3.59e-2082
ectoderm-derived structure6.13e-19171
ectoderm6.13e-19171
presumptive ectoderm6.13e-19171
brain2.58e-1868
future brain2.58e-1868
pre-chordal neural plate9.37e-1861
ecto-epithelium3.90e-17104
neural tube4.37e-1656
neural rod4.37e-1656
future spinal cord4.37e-1656
neural keel4.37e-1656
cerebral hemisphere8.89e-1532
brain grey matter7.57e-1434
gray matter7.57e-1434
pigment epithelium of eye7.89e-1411
regional part of nervous system1.26e-1353
regional part of brain1.26e-1353
telencephalon1.45e-1334
regional part of telencephalon2.13e-1332
cerebral cortex2.08e-1125
pallium2.08e-1125
structure with developmental contribution from neural crest2.36e-11132
regional part of forebrain2.72e-1141
forebrain2.72e-1141
anterior neural tube2.72e-1141
future forebrain2.72e-1141
regional part of cerebral cortex1.66e-0822
vasculature of organ6.77e-0811
limbic system9.01e-085
camera-type eye9.04e-0820
simple eye9.04e-0820
immature eye9.04e-0820
ocular region9.04e-0820
eyeball of camera-type eye9.04e-0820
optic cup9.04e-0820
optic vesicle9.04e-0820
eye primordium9.04e-0820
organ system subdivision1.15e-07223
eye2.91e-0721
visual system2.91e-0721
atypical epithelium4.90e-074
face8.38e-0722


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#1066435.360256373075030.0064925092527670.0281848521842935
E2F1#186934.907389214879320.008460985347239390.0328350493712966
FOSL2#2355316.93020060456170.0002060162053171620.00244251634318527
JUN#3725312.51282919233630.0005103313992726250.00446722831352223
JUND#372736.994663941871030.002921845042734990.0157849459144527
RAD21#5885310.35503389545630.0009004912073565420.00669846162429557
ZNF263#1012738.221841637010680.001799043925565870.0110322558007266



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:C4871&oldid=2251249"