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Coexpression cluster:C4124: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!2.57e-14!365;UBERON:0002385!1.64e-12!63;UBERON:0001015!1.64e-12!63;UBERON:0000383!1.64e-12!63;UBERON:0001134!2.29e-12!61;UBERON:0002036!2.29e-12!61;UBERON:0003082!2.29e-12!61;UBERON:0001637!1.23e-11!42;UBERON:0003509!1.23e-11!42;UBERON:0004572!1.23e-11!42;UBERON:0000914!2.24e-11!83;UBERON:0002329!2.24e-11!83;UBERON:0003077!2.24e-11!83;UBERON:0003059!2.24e-11!83;UBERON:0007282!2.24e-11!83;UBERON:0009618!2.24e-11!83;UBERON:0007285!2.24e-11!83;UBERON:0004290!4.58e-11!70;UBERON:0000025!7.35e-11!194;UBERON:0005256!3.31e-10!143;UBERON:0004573!4.93e-10!33;UBERON:0004571!4.93e-10!33;UBERON:0004872!9.92e-10!84;UBERON:0002100!1.17e-09!216;UBERON:0000486!2.69e-09!82;UBERON:0003914!4.67e-09!118;UBERON:0000481!1.42e-08!347;UBERON:0004111!4.24e-08!241;UBERON:0001981!7.98e-08!60;UBERON:0007500!7.98e-08!60;UBERON:0004537!7.98e-08!60;UBERON:0006965!7.98e-08!60;UBERON:0000483!8.43e-08!309;UBERON:0000119!1.92e-07!312;UBERON:0001135!2.05e-07!15;UBERON:0000490!2.09e-07!138;UBERON:0000477!2.25e-07!286;UBERON:0003688!2.46e-07!6;UBERON:0002358!2.46e-07!6;UBERON:0003684!2.46e-07!6;UBERON:0001178!2.46e-07!6;UBERON:0000948!5.48e-07!24;UBERON:0005498!5.48e-07!24;UBERON:0004140!5.48e-07!24;UBERON:0009881!5.48e-07!24;UBERON:0004141!5.48e-07!24;UBERON:0003084!5.48e-07!24;UBERON:0007005!5.48e-07!24;UBERON:0004139!5.48e-07!24;UBERON:0004291!5.48e-07!24;UBERON:0004457!9.18e-07!12;UBERON:0000042!9.18e-07!12
|ontology_enrichment_uberon=UBERON:0000475!2.57e-14!365;UBERON:0002385!1.64e-12!63;UBERON:0001015!1.64e-12!63;UBERON:0000383!1.64e-12!63;UBERON:0001134!2.29e-12!61;UBERON:0002036!2.29e-12!61;UBERON:0003082!2.29e-12!61;UBERON:0001637!1.23e-11!42;UBERON:0003509!1.23e-11!42;UBERON:0004572!1.23e-11!42;UBERON:0000914!2.24e-11!83;UBERON:0002329!2.24e-11!83;UBERON:0003077!2.24e-11!83;UBERON:0003059!2.24e-11!83;UBERON:0007282!2.24e-11!83;UBERON:0009618!2.24e-11!83;UBERON:0007285!2.24e-11!83;UBERON:0004290!4.58e-11!70;UBERON:0000025!7.35e-11!194;UBERON:0005256!3.31e-10!143;UBERON:0004573!4.93e-10!33;UBERON:0004571!4.93e-10!33;UBERON:0004872!9.92e-10!84;UBERON:0002100!1.17e-09!216;UBERON:0000486!2.69e-09!82;UBERON:0003914!4.67e-09!118;UBERON:0000481!1.42e-08!347;UBERON:0004111!4.24e-08!241;UBERON:0001981!7.98e-08!60;UBERON:0007500!7.98e-08!60;UBERON:0004537!7.98e-08!60;UBERON:0006965!7.98e-08!60;UBERON:0000483!8.43e-08!309;UBERON:0000119!1.92e-07!312;UBERON:0001135!2.05e-07!15;UBERON:0000490!2.09e-07!138;UBERON:0000477!2.25e-07!286;UBERON:0003688!2.46e-07!6;UBERON:0002358!2.46e-07!6;UBERON:0003684!2.46e-07!6;UBERON:0001178!2.46e-07!6;UBERON:0000948!5.48e-07!24;UBERON:0005498!5.48e-07!24;UBERON:0004140!5.48e-07!24;UBERON:0009881!5.48e-07!24;UBERON:0004141!5.48e-07!24;UBERON:0003084!5.48e-07!24;UBERON:0007005!5.48e-07!24;UBERON:0004139!5.48e-07!24;UBERON:0004291!5.48e-07!24;UBERON:0004457!9.18e-07!12;UBERON:0000042!9.18e-07!12
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115437053842048!HNF4A#3172;2:15.4215269086358:0.00544421048668661:0.0246793653812693!HNF4G#3174;2:19.1689483509645:0.00354398661128422:0.0179762223261735!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457664105682275
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}}
}}

Revision as of 12:57, 5 September 2012


Full id: C4124_Adipocyte_Preadipocyte_Fibroblast_Ewing_basal_Smooth_neurofibroma



Phase1 CAGE Peaks

Hg19::chr2:13056054..13056074,-p@chr2:13056054..13056074
-
Hg19::chr8:22446481..22446512,+p6@PDLIM2
Hg19::chr8:22446541..22446558,+p7@PDLIM2


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
organism subdivision2.57e-14365
muscle tissue1.64e-1263
musculature1.64e-1263
musculature of body1.64e-1263
skeletal muscle tissue2.29e-1261
striated muscle tissue2.29e-1261
myotome2.29e-1261
artery1.23e-1142
arterial blood vessel1.23e-1142
arterial system1.23e-1142
somite2.24e-1183
paraxial mesoderm2.24e-1183
presomitic mesoderm2.24e-1183
presumptive segmental plate2.24e-1183
trunk paraxial mesoderm2.24e-1183
presumptive paraxial mesoderm2.24e-1183
dermomyotome4.58e-1170
tube7.35e-11194
trunk mesenchyme3.31e-10143
systemic artery4.93e-1033
systemic arterial system4.93e-1033
splanchnic layer of lateral plate mesoderm9.92e-1084
trunk1.17e-09216
multilaminar epithelium2.69e-0982
epithelial tube4.67e-09118
multi-tissue structure1.42e-08347
anatomical conduit4.24e-08241
blood vessel7.98e-0860
epithelial tube open at both ends7.98e-0860
blood vasculature7.98e-0860
vascular cord7.98e-0860
epithelium8.43e-08309
cell layer1.92e-07312
smooth muscle tissue2.05e-0715
unilaminar epithelium2.09e-07138
anatomical cluster2.25e-07286
omentum2.46e-076
peritoneum2.46e-076
abdominal cavity2.46e-076
visceral peritoneum2.46e-076
heart5.48e-0724
primitive heart tube5.48e-0724
primary heart field5.48e-0724
anterior lateral plate mesoderm5.48e-0724
heart tube5.48e-0724
heart primordium5.48e-0724
cardiac mesoderm5.48e-0724
cardiogenic plate5.48e-0724
heart rudiment5.48e-0724
cavity lining9.18e-0712
serous membrane9.18e-0712


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
CEBPB#105137.971147625824820.001974187055288560.0115437053842048
HNF4A#3172215.42152690863580.005444210486686610.0246793653812693
HNF4G#3174219.16894835096450.003543986611284220.0179762223261735
SMC3#9126210.02995522995520.0126656379767470.0457664105682275



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.