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Coexpression cluster:C714: Difference between revisions

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|ontology_enrichment_disease=DOID:2394!7.29e-07!14
|ontology_enrichment_disease=DOID:2394!7.29e-07!14
|ontology_enrichment_uberon=UBERON:0000914!7.15e-22!83;UBERON:0002329!7.15e-22!83;UBERON:0003077!7.15e-22!83;UBERON:0003059!7.15e-22!83;UBERON:0007282!7.15e-22!83;UBERON:0009618!7.15e-22!83;UBERON:0007285!7.15e-22!83;UBERON:0004290!4.16e-20!70;UBERON:0001134!2.12e-19!61;UBERON:0002036!2.12e-19!61;UBERON:0003082!2.12e-19!61;UBERON:0002385!2.29e-19!63;UBERON:0001015!2.29e-19!63;UBERON:0000383!2.29e-19!63;UBERON:0000486!4.01e-18!82;UBERON:0000475!6.27e-15!365;UBERON:0001637!4.35e-12!42;UBERON:0003509!4.35e-12!42;UBERON:0004572!4.35e-12!42;UBERON:0005256!7.85e-12!143;UBERON:0004573!1.12e-10!33;UBERON:0004571!1.12e-10!33;UBERON:0000481!2.36e-09!347;UBERON:0002049!2.68e-09!79;UBERON:0007798!2.68e-09!79;UBERON:0003102!9.28e-09!95;UBERON:0002100!1.60e-08!216;UBERON:0004872!2.59e-08!84;UBERON:0000119!3.23e-08!312;UBERON:0001981!6.39e-08!60;UBERON:0007500!6.39e-08!60;UBERON:0004537!6.39e-08!60;UBERON:0006965!6.39e-08!60;UBERON:0001135!1.03e-07!15;UBERON:0000483!1.04e-07!309;UBERON:0002199!2.27e-07!45;UBERON:0002416!2.27e-07!45;UBERON:0004237!2.64e-07!10;UBERON:0004695!2.64e-07!10;UBERON:0002111!2.64e-07!10;UBERON:0004178!2.64e-07!10;UBERON:0004535!3.41e-07!110;UBERON:0000055!9.40e-07!69
|ontology_enrichment_uberon=UBERON:0000914!7.15e-22!83;UBERON:0002329!7.15e-22!83;UBERON:0003077!7.15e-22!83;UBERON:0003059!7.15e-22!83;UBERON:0007282!7.15e-22!83;UBERON:0009618!7.15e-22!83;UBERON:0007285!7.15e-22!83;UBERON:0004290!4.16e-20!70;UBERON:0001134!2.12e-19!61;UBERON:0002036!2.12e-19!61;UBERON:0003082!2.12e-19!61;UBERON:0002385!2.29e-19!63;UBERON:0001015!2.29e-19!63;UBERON:0000383!2.29e-19!63;UBERON:0000486!4.01e-18!82;UBERON:0000475!6.27e-15!365;UBERON:0001637!4.35e-12!42;UBERON:0003509!4.35e-12!42;UBERON:0004572!4.35e-12!42;UBERON:0005256!7.85e-12!143;UBERON:0004573!1.12e-10!33;UBERON:0004571!1.12e-10!33;UBERON:0000481!2.36e-09!347;UBERON:0002049!2.68e-09!79;UBERON:0007798!2.68e-09!79;UBERON:0003102!9.28e-09!95;UBERON:0002100!1.60e-08!216;UBERON:0004872!2.59e-08!84;UBERON:0000119!3.23e-08!312;UBERON:0001981!6.39e-08!60;UBERON:0007500!6.39e-08!60;UBERON:0004537!6.39e-08!60;UBERON:0006965!6.39e-08!60;UBERON:0001135!1.03e-07!15;UBERON:0000483!1.04e-07!309;UBERON:0002199!2.27e-07!45;UBERON:0002416!2.27e-07!45;UBERON:0004237!2.64e-07!10;UBERON:0004695!2.64e-07!10;UBERON:0002111!2.64e-07!10;UBERON:0004178!2.64e-07!10;UBERON:0004535!3.41e-07!110;UBERON:0000055!9.40e-07!69
|tf_chipseq_enrich=CTCF#10664;12:5.36025637307503:1.77458566542848e-09:1.54704467705914e-07!NANOG#79923;3:7.31119462025316:0.00697119958520868:0.0294822884583766!TCF7L2#6934;6:5.38508828156867:0.000360576308593949:0.00360538335023872
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}}
}}

Revision as of 11:47, 5 September 2012


Full id: C714_Smooth_Fibroblast_Mesenchymal_mesenchymal_Myoblast_leiomyoma_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr6:130686664..130686693,+p7@TMEM200A
Hg19::chr6:130686698..130686732,+p8@TMEM200A
Hg19::chr6:130686856..130686885,+p11@TMEM200A
Hg19::chr6:130687103..130687170,+p1@TMEM200A
Hg19::chr6:130687172..130687179,+p10@TMEM200A
Hg19::chr6:130687198..130687218,+p3@TMEM200A
Hg19::chr6:130687449..130687474,+p5@TMEM200A
Hg19::chr6:130687521..130687535,+p6@TMEM200A
Hg19::chr6:130687547..130687569,+p2@TMEM200A
Hg19::chr6:130687570..130687594,+p4@TMEM200A
Hg19::chr6:130687599..130687610,+p9@TMEM200A
Hg19::chr6:130687612..130687617,+p13@TMEM200A


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
somite7.15e-2283
paraxial mesoderm7.15e-2283
presomitic mesoderm7.15e-2283
presumptive segmental plate7.15e-2283
trunk paraxial mesoderm7.15e-2283
presumptive paraxial mesoderm7.15e-2283
dermomyotome4.16e-2070
skeletal muscle tissue2.12e-1961
striated muscle tissue2.12e-1961
myotome2.12e-1961
muscle tissue2.29e-1963
musculature2.29e-1963
musculature of body2.29e-1963
multilaminar epithelium4.01e-1882
organism subdivision6.27e-15365
artery4.35e-1242
arterial blood vessel4.35e-1242
arterial system4.35e-1242
trunk mesenchyme7.85e-12143
systemic artery1.12e-1033
systemic arterial system1.12e-1033
multi-tissue structure2.36e-09347
vasculature2.68e-0979
vascular system2.68e-0979
surface structure9.28e-0995
trunk1.60e-08216
splanchnic layer of lateral plate mesoderm2.59e-0884
cell layer3.23e-08312
blood vessel6.39e-0860
epithelial tube open at both ends6.39e-0860
blood vasculature6.39e-0860
vascular cord6.39e-0860
smooth muscle tissue1.03e-0715
epithelium1.04e-07309
integument2.27e-0745
integumental system2.27e-0745
blood vessel smooth muscle2.64e-0710
arterial system smooth muscle2.64e-0710
artery smooth muscle tissue2.64e-0710
aorta smooth muscle tissue2.64e-0710
cardiovascular system3.41e-07110
vessel9.40e-0769
Disease
Ontology termp-valuen
ovarian cancer7.29e-0714


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#10664125.360256373075031.77458566542848e-091.54704467705914e-07
NANOG#7992337.311194620253160.006971199585208680.0294822884583766
TCF7L2#693465.385088281568670.0003605763085939490.00360538335023872



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.