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Coexpression cluster:C1353: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005256!7.50e-24!143;UBERON:0000914!2.08e-23!83;UBERON:0002329!2.08e-23!83;UBERON:0003077!2.08e-23!83;UBERON:0003059!2.08e-23!83;UBERON:0007282!2.08e-23!83;UBERON:0009618!2.08e-23!83;UBERON:0007285!2.08e-23!83;UBERON:0004290!1.72e-21!70;UBERON:0002049!2.04e-20!79;UBERON:0007798!2.04e-20!79;UBERON:0004872!2.29e-20!84;UBERON:0002385!2.44e-20!63;UBERON:0001015!2.44e-20!63;UBERON:0000383!2.44e-20!63;UBERON:0000486!3.31e-20!82;UBERON:0001134!3.45e-20!61;UBERON:0002036!3.45e-20!61;UBERON:0003082!3.45e-20!61;UBERON:0002100!3.52e-20!216;UBERON:0000475!2.47e-19!365;UBERON:0003914!2.45e-18!118;UBERON:0000055!1.06e-17!69;UBERON:0001009!1.99e-17!113;UBERON:0004535!4.91e-17!110;UBERON:0001981!4.92e-17!60;UBERON:0007500!4.92e-17!60;UBERON:0004537!4.92e-17!60;UBERON:0006965!4.92e-17!60;UBERON:0000481!2.01e-16!347;UBERON:0001637!6.41e-16!42;UBERON:0003509!6.41e-16!42;UBERON:0004572!6.41e-16!42;UBERON:0000490!2.50e-15!138;UBERON:0000119!8.30e-15!312;UBERON:0000483!2.09e-14!309;UBERON:0000468!2.51e-14!659;UBERON:0003104!4.04e-14!238;UBERON:0009142!4.04e-14!238;UBERON:0004573!4.72e-13!33;UBERON:0004571!4.72e-13!33;UBERON:0000477!4.78e-13!286;UBERON:0000467!3.24e-11!625;UBERON:0000480!4.02e-11!626;UBERON:0004111!4.31e-11!241;UBERON:0000926!2.81e-08!448;UBERON:0004120!2.81e-08!448;UBERON:0006603!2.81e-08!448;UBERON:0000025!3.02e-08!194;UBERON:0003102!3.18e-08!95;UBERON:0003103!6.23e-08!69;UBERON:0007100!2.28e-07!27;UBERON:0000922!2.84e-07!612;UBERON:0000947!3.01e-07!21;UBERON:0010191!3.01e-07!21;UBERON:0002050!4.21e-07!605;UBERON:0005423!4.21e-07!605;UBERON:0000948!4.21e-07!24;UBERON:0005498!4.21e-07!24;UBERON:0004140!4.21e-07!24;UBERON:0009881!4.21e-07!24;UBERON:0004141!4.21e-07!24;UBERON:0003084!4.21e-07!24;UBERON:0007005!4.21e-07!24;UBERON:0004139!4.21e-07!24;UBERON:0004291!4.21e-07!24;UBERON:0001135!4.51e-07!15;UBERON:0000923!5.73e-07!604;UBERON:0005291!5.73e-07!604;UBERON:0006598!5.73e-07!604;UBERON:0002532!5.73e-07!604
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}}
}}

Revision as of 17:11, 8 August 2012


Full id: C1353_Mesenchymal_Preadipocyte_basal_Adipocyte_Fibroblast_Smooth_leiomyoma



Phase1 CAGE Peaks

Hg19::chr11:844406..844448,+p4@TSPAN4
Hg19::chr19:42463447..42463513,-p1@RABAC1
Hg19::chr20:35169885..35169911,+p2@MYL9
Hg19::chr22:31503490..31503584,-p1@SELM
Hg19::chr22:43045336..43045416,-p1@CYB5R3
Hg19::chr22:43045417..43045424,-p6@CYB5R3


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
trunk mesenchyme7.50e-24143
somite2.08e-2383
paraxial mesoderm2.08e-2383
presomitic mesoderm2.08e-2383
presumptive segmental plate2.08e-2383
trunk paraxial mesoderm2.08e-2383
presumptive paraxial mesoderm2.08e-2383
dermomyotome1.72e-2170
vasculature2.04e-2079
vascular system2.04e-2079
splanchnic layer of lateral plate mesoderm2.29e-2084
muscle tissue2.44e-2063
musculature2.44e-2063
musculature of body2.44e-2063
multilaminar epithelium3.31e-2082
skeletal muscle tissue3.45e-2061
striated muscle tissue3.45e-2061
myotome3.45e-2061
trunk3.52e-20216
organism subdivision2.47e-19365
epithelial tube2.45e-18118
vessel1.06e-1769
circulatory system1.99e-17113
cardiovascular system4.91e-17110
blood vessel4.92e-1760
epithelial tube open at both ends4.92e-1760
blood vasculature4.92e-1760
vascular cord4.92e-1760
multi-tissue structure2.01e-16347
artery6.41e-1642
arterial blood vessel6.41e-1642
arterial system6.41e-1642
unilaminar epithelium2.50e-15138
cell layer8.30e-15312
epithelium2.09e-14309
multi-cellular organism2.51e-14659
mesenchyme4.04e-14238
entire embryonic mesenchyme4.04e-14238
systemic artery4.72e-1333
systemic arterial system4.72e-1333
anatomical cluster4.78e-13286
anatomical system3.24e-11625
anatomical group4.02e-11626
anatomical conduit4.31e-11241
mesoderm2.81e-08448
mesoderm-derived structure2.81e-08448
presumptive mesoderm2.81e-08448
tube3.02e-08194
surface structure3.18e-0895
compound organ6.23e-0869
primary circulatory organ2.28e-0727
embryo2.84e-07612
aorta3.01e-0721
aortic system3.01e-0721
embryonic structure4.21e-07605
developing anatomical structure4.21e-07605
heart4.21e-0724
primitive heart tube4.21e-0724
primary heart field4.21e-0724
anterior lateral plate mesoderm4.21e-0724
heart tube4.21e-0724
heart primordium4.21e-0724
cardiac mesoderm4.21e-0724
cardiogenic plate4.21e-0724
heart rudiment4.21e-0724
smooth muscle tissue4.51e-0715
germ layer5.73e-07604
embryonic tissue5.73e-07604
presumptive structure5.73e-07604
epiblast (generic)5.73e-07604


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

No analysis results for this cluster

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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