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Coexpression cluster:C3522: Difference between revisions

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|full_id=C3522_Fibroblast_Smooth_basal_mesenchymal_Meningeal_Ewing_Preadipocyte
|full_id=C3522_Fibroblast_Smooth_basal_mesenchymal_Meningeal_Ewing_Preadipocyte
|id=C3522
|id=C3522
|ontology_enrichment_celltype=CL:0000055!6.92e-52!180;CL:0000057!6.22e-39!75;CL:0000680!6.38e-25!57;CL:0000056!6.38e-25!57;CL:0000355!6.38e-25!57;CL:0000187!1.33e-24!54;CL:0000183!1.05e-23!59;CL:0000192!7.00e-22!42;CL:0000514!7.00e-22!42;CL:0000393!2.48e-20!60;CL:0000211!2.48e-20!60;CL:0000359!1.05e-17!32;CL:0002620!1.06e-16!23;CL:0000048!8.52e-15!430;CL:0000723!6.41e-14!436;CL:0000034!8.35e-13!444;CL:0000222!2.31e-12!119;CL:0002334!2.98e-09!12;CL:0002494!7.49e-09!16;CL:0002371!1.08e-07!591;CL:0000144!2.66e-07!625
|ontology_enrichment_celltype=CL:0000057!5.68e-38!76;CL:0000680!2.28e-24!58;CL:0000056!2.28e-24!58;CL:0000355!2.28e-24!58;CL:0000192!2.39e-24!43;CL:0000514!2.39e-24!43;CL:0000183!3.33e-24!59;CL:0000187!9.57e-24!55;CL:0000359!2.66e-22!32;CL:0002620!1.10e-20!23;CL:0000393!4.62e-20!61;CL:0000211!4.62e-20!61;CL:0000048!2.30e-16!427;CL:0000723!1.28e-15!433;CL:0000034!1.16e-14!441;CL:0000222!4.24e-14!121;CL:0000055!1.26e-11!106;CL:0002371!2.81e-09!588;CL:0002556!9.30e-08!6;CL:0002539!2.43e-07!10
|ontology_enrichment_disease=
|ontology_enrichment_disease=DOID:17!1.90e-07!5;DOID:450!1.90e-07!5;DOID:66!1.90e-07!5;DOID:423!1.90e-07!5;DOID:0080000!1.90e-07!5;DOID:11722!1.90e-07!5
|ontology_enrichment_uberon=UBERON:0004290!1.06e-24!70;UBERON:0000914!1.29e-24!83;UBERON:0002329!1.29e-24!83;UBERON:0003077!1.29e-24!83;UBERON:0003059!1.29e-24!83;UBERON:0007282!1.29e-24!83;UBERON:0009618!1.29e-24!83;UBERON:0007285!1.29e-24!83;UBERON:0001134!4.78e-22!61;UBERON:0002036!4.78e-22!61;UBERON:0003082!4.78e-22!61;UBERON:0002385!9.28e-21!63;UBERON:0001015!9.28e-21!63;UBERON:0000383!9.28e-21!63;UBERON:0000486!8.41e-20!82;UBERON:0000475!2.19e-18!365;UBERON:0005256!4.39e-16!143;UBERON:0000119!1.15e-12!312;UBERON:0001637!2.33e-12!42;UBERON:0003509!2.33e-12!42;UBERON:0004572!2.33e-12!42;UBERON:0002100!1.95e-11!216;UBERON:0000483!2.07e-11!309;UBERON:0004872!2.81e-11!84;UBERON:0004573!9.32e-11!33;UBERON:0004571!9.32e-11!33;UBERON:0002097!3.99e-10!40;UBERON:0000490!6.12e-10!138;UBERON:0002049!1.16e-09!79;UBERON:0007798!1.16e-09!79;UBERON:0004535!1.40e-09!110;UBERON:0002199!1.61e-09!45;UBERON:0002416!1.61e-09!45;UBERON:0001009!6.76e-09!113;UBERON:0000025!1.28e-08!194;UBERON:0003914!1.79e-08!118;UBERON:0001981!2.61e-08!60;UBERON:0007500!2.61e-08!60;UBERON:0004537!2.61e-08!60;UBERON:0006965!2.61e-08!60;UBERON:0000477!4.52e-08!286;UBERON:0000948!7.31e-08!24;UBERON:0005498!7.31e-08!24;UBERON:0004140!7.31e-08!24;UBERON:0009881!7.31e-08!24;UBERON:0004141!7.31e-08!24;UBERON:0003084!7.31e-08!24;UBERON:0007005!7.31e-08!24;UBERON:0004139!7.31e-08!24;UBERON:0004291!7.31e-08!24;UBERON:0000481!8.69e-08!347;UBERON:0000055!3.79e-07!69;UBERON:0003102!4.68e-07!95;UBERON:0004111!5.35e-07!241
|ontology_enrichment_uberon=UBERON:0002329!8.59e-25!71;UBERON:0003059!8.59e-25!71;UBERON:0007282!8.59e-25!71;UBERON:0004290!8.59e-25!71;UBERON:0009618!8.59e-25!71;UBERON:0003077!3.20e-24!72;UBERON:0007285!3.20e-24!72;UBERON:0007524!1.15e-23!73;UBERON:0007503!2.15e-22!78;UBERON:0001134!7.24e-22!62;UBERON:0002036!7.24e-22!62;UBERON:0003082!7.24e-22!62;UBERON:0002385!9.68e-21!64;UBERON:0001015!9.68e-21!64;UBERON:0000383!9.68e-21!64;UBERON:0000486!6.18e-20!83;UBERON:0005256!7.86e-18!122;UBERON:0001637!4.46e-15!42;UBERON:0003509!4.46e-15!42;UBERON:0004572!4.46e-15!42;UBERON:0000490!1.31e-12!148;UBERON:0004573!1.64e-12!33;UBERON:0004571!1.64e-12!33;UBERON:0002097!2.93e-12!41;UBERON:0004872!4.01e-11!83;UBERON:0002199!5.71e-11!46;UBERON:0002416!5.71e-11!46;UBERON:0003104!1.15e-10!160;UBERON:0009142!1.15e-10!160;UBERON:0002049!1.52e-10!78;UBERON:0007798!1.52e-10!78;UBERON:0002100!2.14e-10!199;UBERON:0000119!2.59e-10!309;UBERON:0007500!7.44e-10!59;UBERON:0001981!7.44e-10!59;UBERON:0004537!7.44e-10!59;UBERON:0006965!7.44e-10!59;UBERON:0004535!1.37e-09!109;UBERON:0000483!4.84e-09!306;UBERON:0001009!5.31e-09!112;UBERON:0003102!1.67e-08!99;UBERON:0003914!2.40e-08!117;UBERON:0001135!2.70e-08!15;UBERON:0000055!2.89e-08!68;UBERON:0000475!3.51e-08!264;UBERON:0001758!9.30e-08!6;UBERON:0003672!9.30e-08!6;UBERON:0004237!2.43e-07!10;UBERON:0004695!2.43e-07!10;UBERON:0002111!2.43e-07!10;UBERON:0004178!2.43e-07!10;UBERON:0000481!5.00e-07!342
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167256326255957
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167256326255957
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}}
}}

Revision as of 15:10, 19 October 2012


Full id: C3522_Fibroblast_Smooth_basal_mesenchymal_Meningeal_Ewing_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr15:80842610..80842647,-p@chr15:80842610..80842647
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Hg19::chr15:80842672..80842689,-p@chr15:80842672..80842689
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Hg19::chr15:80842696..80842711,-p@chr15:80842696..80842711
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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
somite8.59e-2571
presomitic mesoderm8.59e-2571
presumptive segmental plate8.59e-2571
dermomyotome8.59e-2571
trunk paraxial mesoderm8.59e-2571
paraxial mesoderm3.20e-2472
presumptive paraxial mesoderm3.20e-2472
dense mesenchyme tissue1.15e-2373
epithelial vesicle2.15e-2278
skeletal muscle tissue7.24e-2262
striated muscle tissue7.24e-2262
myotome7.24e-2262
muscle tissue9.68e-2164
musculature9.68e-2164
musculature of body9.68e-2164
multilaminar epithelium6.18e-2083
trunk mesenchyme7.86e-18122
artery4.46e-1542
arterial blood vessel4.46e-1542
arterial system4.46e-1542
unilaminar epithelium1.31e-12148
systemic artery1.64e-1233
systemic arterial system1.64e-1233
skin of body2.93e-1241
splanchnic layer of lateral plate mesoderm4.01e-1183
integument5.71e-1146
integumental system5.71e-1146
mesenchyme1.15e-10160
entire embryonic mesenchyme1.15e-10160
vasculature1.52e-1078
vascular system1.52e-1078
trunk2.14e-10199
cell layer2.59e-10309
epithelial tube open at both ends7.44e-1059
blood vessel7.44e-1059
blood vasculature7.44e-1059
vascular cord7.44e-1059
cardiovascular system1.37e-09109
epithelium4.84e-09306
circulatory system5.31e-09112
surface structure1.67e-0899
epithelial tube2.40e-08117
smooth muscle tissue2.70e-0815
vessel2.89e-0868
organism subdivision3.51e-08264
periodontium9.30e-086
dentition9.30e-086
blood vessel smooth muscle2.43e-0710
arterial system smooth muscle2.43e-0710
artery smooth muscle tissue2.43e-0710
aorta smooth muscle tissue2.43e-0710
multi-tissue structure5.00e-07342
Disease
Ontology termp-valuen
musculoskeletal system disease1.90e-075
myotonic disease1.90e-075
muscle tissue disease1.90e-075
myopathy1.90e-075
muscular disease1.90e-075
myotonic dystrophy1.90e-075


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
EP300#203336.77394172622320.003216880500103790.0167256326255957



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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