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Coexpression cluster:C2455: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!9.54e-17!115;UBERON:0001049!6.18e-13!57;UBERON:0005068!6.18e-13!57;UBERON:0006241!6.18e-13!57;UBERON:0007135!6.18e-13!57;UBERON:0001017!4.01e-12!82;UBERON:0005743!5.54e-12!86;UBERON:0002616!1.68e-11!59;UBERON:0003075!3.42e-11!86;UBERON:0007284!3.42e-11!86;UBERON:0000477!5.66e-11!286;UBERON:0002346!9.37e-11!90;UBERON:0000073!9.43e-11!94;UBERON:0001016!9.43e-11!94;UBERON:0001986!1.15e-10!18;UBERON:0004638!1.15e-10!18;UBERON:0004852!1.15e-10!18;UBERON:0000955!3.04e-10!69;UBERON:0006238!3.04e-10!69;UBERON:0000033!2.18e-09!123;UBERON:0000153!2.28e-09!129;UBERON:0007811!2.28e-09!129;UBERON:0006914!1.09e-08!25;UBERON:0004111!1.41e-08!241;UBERON:0004121!2.33e-08!169;UBERON:0003080!2.41e-08!42;UBERON:0000924!3.37e-08!173;UBERON:0006601!3.37e-08!173;UBERON:0002780!6.04e-08!41;UBERON:0001890!6.04e-08!41;UBERON:0006240!6.04e-08!41;UBERON:0000487!6.21e-08!22;UBERON:0000468!7.13e-08!659;UBERON:0003056!2.31e-07!61;UBERON:0002049!3.14e-07!79;UBERON:0007798!3.14e-07!79
|ontology_enrichment_uberon=UBERON:0007023!9.54e-17!115;UBERON:0001049!6.18e-13!57;UBERON:0005068!6.18e-13!57;UBERON:0006241!6.18e-13!57;UBERON:0007135!6.18e-13!57;UBERON:0001017!4.01e-12!82;UBERON:0005743!5.54e-12!86;UBERON:0002616!1.68e-11!59;UBERON:0003075!3.42e-11!86;UBERON:0007284!3.42e-11!86;UBERON:0000477!5.66e-11!286;UBERON:0002346!9.37e-11!90;UBERON:0000073!9.43e-11!94;UBERON:0001016!9.43e-11!94;UBERON:0001986!1.15e-10!18;UBERON:0004638!1.15e-10!18;UBERON:0004852!1.15e-10!18;UBERON:0000955!3.04e-10!69;UBERON:0006238!3.04e-10!69;UBERON:0000033!2.18e-09!123;UBERON:0000153!2.28e-09!129;UBERON:0007811!2.28e-09!129;UBERON:0006914!1.09e-08!25;UBERON:0004111!1.41e-08!241;UBERON:0004121!2.33e-08!169;UBERON:0003080!2.41e-08!42;UBERON:0000924!3.37e-08!173;UBERON:0006601!3.37e-08!173;UBERON:0002780!6.04e-08!41;UBERON:0001890!6.04e-08!41;UBERON:0006240!6.04e-08!41;UBERON:0000487!6.21e-08!22;UBERON:0000468!7.13e-08!659;UBERON:0003056!2.31e-07!61;UBERON:0002049!3.14e-07!79;UBERON:0007798!3.14e-07!79
|tf_chipseq_enrich=CCNT2#905;3:4.75215118272197:0.0138620699668949:0.0487208724641606!EP300#2033;3:5.0804562946674:0.0114429840539824:0.0418919591844456!GATA2#2624;3:9.5586988001655:0.00181815161835744:0.0108985787103043!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0386889172293298!NANOG#79923;3:21.9335838607595:0.000155753581638277:0.00196505778119353!RAD21#5885;3:7.76627542159225:0.003341119385872:0.0172667211411295!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342410232980589!ZNF263#10127;3:6.16638122775801:0.00653981434797598:0.02797393801967
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}}
}}

Revision as of 11:39, 5 September 2012


Full id: C2455_cerebellum_Endothelial_acute_Mast_CD34_skeletal_throat



Phase1 CAGE Peaks

Hg19::chr18:22642711..22642717,-p@chr18:22642711..22642717
-
Hg19::chr18:22931979..22931992,-p3@ZNF521
Hg19::chr18:22932004..22932021,-p2@ZNF521
Hg19::chr18:22932080..22932170,-p1@ZNF521


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>

Uber Anatomy
Ontology termp-valuen
adult organism9.54e-17115
neural tube6.18e-1357
neural rod6.18e-1357
future spinal cord6.18e-1357
neural keel6.18e-1357
central nervous system4.01e-1282
regional part of brain1.68e-1159
neural plate3.42e-1186
presumptive neural plate3.42e-1186
anatomical cluster5.66e-11286
neurectoderm9.37e-1190
regional part of nervous system9.43e-1194
nervous system9.43e-1194
endothelium1.15e-1018
blood vessel endothelium1.15e-1018
cardiovascular system endothelium1.15e-1018
brain3.04e-1069
future brain3.04e-1069
head2.18e-09123
anterior region of body2.28e-09129
craniocervical region2.28e-09129
squamous epithelium1.09e-0825
anatomical conduit1.41e-08241
ectoderm-derived structure2.33e-08169
anterior neural tube2.41e-0842
ectoderm3.37e-08173
presumptive ectoderm3.37e-08173
regional part of forebrain6.04e-0841
forebrain6.04e-0841
future forebrain6.04e-0841
simple squamous epithelium6.21e-0822
multi-cellular organism7.13e-08659
pre-chordal neural plate2.31e-0761
vasculature3.14e-0779
vascular system3.14e-0779


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
CCNT2#90534.752151182721970.01386206996689490.0487208724641606
EP300#203335.08045629466740.01144298405398240.0418919591844456
GATA2#262439.55869880016550.001818151618357440.0108985787103043
JUND#372735.245997956403270.01043432751748420.0386889172293298
NANOG#79923321.93358386075950.0001557535816382770.00196505778119353
RAD21#588537.766275421592250.0033411193858720.0172667211411295
ZBTB7A#5134135.513931980906920.009038352821081090.0342410232980589
ZNF263#1012736.166381227758010.006539814347975980.02797393801967



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.

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