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Coexpression cluster:C4330: Difference between revisions

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|full_id=C4330_leiomyoma_Smooth_Fibroblast_Preadipocyte_Mesenchymal_mesenchymal_Adipocyte
|full_id=C4330_leiomyoma_Smooth_Fibroblast_Preadipocyte_Mesenchymal_mesenchymal_Adipocyte
|id=C4330
|id=C4330
|ontology_enrichment_celltype=CL:0000393!4.81e-21!60;CL:0000211!4.81e-21!60;CL:0000055!5.26e-20!180;CL:0000680!9.09e-19!57;CL:0000056!9.09e-19!57;CL:0000355!9.09e-19!57;CL:0000187!4.08e-18!54;CL:0000192!1.39e-17!42;CL:0000514!1.39e-17!42;CL:0000183!7.02e-17!59;CL:0000359!1.27e-14!32;CL:0000222!2.40e-10!119;CL:0002321!8.98e-09!248;CL:0000220!2.10e-08!246;CL:0002539!7.49e-08!10
|ontology_enrichment_celltype=CL:0000393!2.65e-23!61;CL:0000211!2.65e-23!61;CL:0000680!2.14e-20!58;CL:0000056!2.14e-20!58;CL:0000355!2.14e-20!58;CL:0000187!2.07e-19!55;CL:0000192!2.63e-19!43;CL:0000514!2.63e-19!43;CL:0000055!9.54e-19!106;CL:0000183!6.19e-18!59;CL:0000359!4.87e-17!32;CL:0002539!5.45e-10!10;CL:0000222!5.39e-09!121;CL:0002321!3.90e-08!250;CL:0000047!1.93e-07!8
|ontology_enrichment_disease=DOID:2394!7.00e-08!14
|ontology_enrichment_disease=DOID:2394!3.89e-10!14
|ontology_enrichment_uberon=UBERON:0004290!6.03e-21!70;UBERON:0000914!6.94e-20!83;UBERON:0002329!6.94e-20!83;UBERON:0003077!6.94e-20!83;UBERON:0003059!6.94e-20!83;UBERON:0007282!6.94e-20!83;UBERON:0009618!6.94e-20!83;UBERON:0007285!6.94e-20!83;UBERON:0000486!2.16e-17!82;UBERON:0001134!1.77e-16!61;UBERON:0002036!1.77e-16!61;UBERON:0003082!1.77e-16!61;UBERON:0001637!7.04e-16!42;UBERON:0003509!7.04e-16!42;UBERON:0004572!7.04e-16!42;UBERON:0002385!3.16e-15!63;UBERON:0001015!3.16e-15!63;UBERON:0000383!3.16e-15!63;UBERON:0004573!2.93e-13!33;UBERON:0004571!2.93e-13!33;UBERON:0005256!1.20e-11!143;UBERON:0001981!1.23e-10!60;UBERON:0007500!1.23e-10!60;UBERON:0004537!1.23e-10!60;UBERON:0006965!1.23e-10!60;UBERON:0004872!9.03e-10!84;UBERON:0002100!1.05e-08!216;UBERON:0000475!2.39e-08!365;UBERON:0000055!3.63e-08!69;UBERON:0000490!6.03e-08!138;UBERON:0004237!7.49e-08!10;UBERON:0004695!7.49e-08!10;UBERON:0002111!7.49e-08!10;UBERON:0004178!7.49e-08!10;UBERON:0000922!8.23e-08!612;UBERON:0002049!1.29e-07!79;UBERON:0007798!1.29e-07!79;UBERON:0000468!2.38e-07!659;UBERON:0002050!7.21e-07!605;UBERON:0005423!7.21e-07!605
|ontology_enrichment_uberon=UBERON:0003077!6.01e-24!72;UBERON:0007285!6.01e-24!72;UBERON:0002329!1.28e-23!71;UBERON:0003059!1.28e-23!71;UBERON:0007282!1.28e-23!71;UBERON:0004290!1.28e-23!71;UBERON:0009618!1.28e-23!71;UBERON:0007524!2.46e-23!73;UBERON:0007503!1.06e-19!78;UBERON:0000486!4.17e-19!83;UBERON:0001637!4.30e-18!42;UBERON:0003509!4.30e-18!42;UBERON:0004572!4.30e-18!42;UBERON:0001134!5.28e-18!62;UBERON:0002036!5.28e-18!62;UBERON:0003082!5.28e-18!62;UBERON:0002385!6.23e-17!64;UBERON:0001015!6.23e-17!64;UBERON:0000383!6.23e-17!64;UBERON:0005256!1.34e-14!122;UBERON:0004573!5.59e-14!33;UBERON:0004571!5.59e-14!33;UBERON:0007500!9.29e-12!59;UBERON:0001981!9.29e-12!59;UBERON:0004537!9.29e-12!59;UBERON:0006965!9.29e-12!59;UBERON:0000490!3.10e-11!148;UBERON:0004872!3.53e-10!83;UBERON:0004237!5.45e-10!10;UBERON:0004695!5.45e-10!10;UBERON:0002111!5.45e-10!10;UBERON:0004178!5.45e-10!10;UBERON:0003104!9.00e-09!160;UBERON:0009142!9.00e-09!160;UBERON:0001135!9.04e-09!15;UBERON:0000055!1.26e-08!68;UBERON:0002100!2.02e-08!199;UBERON:0000926!2.89e-08!315;UBERON:0004120!2.89e-08!315;UBERON:0006603!2.89e-08!315;UBERON:0002067!1.37e-07!9;UBERON:0004016!1.37e-07!9;UBERON:0010083!1.37e-07!9;UBERON:0002049!4.40e-07!78;UBERON:0007798!4.40e-07!78
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326735754734825!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323494432600741!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457743291803405
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326735754734825!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323494432600741!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457743291803405
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}}
}}

Revision as of 15:52, 19 October 2012


Full id: C4330_leiomyoma_Smooth_Fibroblast_Preadipocyte_Mesenchymal_mesenchymal_Adipocyte



Phase1 CAGE Peaks

Hg19::chr3:45266600..45266635,-p2@TMEM158
Hg19::chr3:45266648..45266677,-p3@TMEM158
Hg19::chr3:45267139..45267195,-p1@ENST00000325090


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
paraxial mesoderm6.01e-2472
presumptive paraxial mesoderm6.01e-2472
somite1.28e-2371
presomitic mesoderm1.28e-2371
presumptive segmental plate1.28e-2371
dermomyotome1.28e-2371
trunk paraxial mesoderm1.28e-2371
dense mesenchyme tissue2.46e-2373
epithelial vesicle1.06e-1978
multilaminar epithelium4.17e-1983
artery4.30e-1842
arterial blood vessel4.30e-1842
arterial system4.30e-1842
skeletal muscle tissue5.28e-1862
striated muscle tissue5.28e-1862
myotome5.28e-1862
muscle tissue6.23e-1764
musculature6.23e-1764
musculature of body6.23e-1764
trunk mesenchyme1.34e-14122
systemic artery5.59e-1433
systemic arterial system5.59e-1433
epithelial tube open at both ends9.29e-1259
blood vessel9.29e-1259
blood vasculature9.29e-1259
vascular cord9.29e-1259
unilaminar epithelium3.10e-11148
splanchnic layer of lateral plate mesoderm3.53e-1083
blood vessel smooth muscle5.45e-1010
arterial system smooth muscle5.45e-1010
artery smooth muscle tissue5.45e-1010
aorta smooth muscle tissue5.45e-1010
mesenchyme9.00e-09160
entire embryonic mesenchyme9.00e-09160
smooth muscle tissue9.04e-0915
vessel1.26e-0868
trunk2.02e-08199
mesoderm2.89e-08315
mesoderm-derived structure2.89e-08315
presumptive mesoderm2.89e-08315
dermis1.37e-079
dermatome1.37e-079
future dermis1.37e-079
vasculature4.40e-0778
vascular system4.40e-0778
Disease
Ontology termp-valuen
ovarian cancer3.89e-1014


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
E2F1#186934.907389214879320.008460985347239390.0326735754734825
E2F6#187635.017155731697390.00791769806886330.0323494432600741
SMC3#9126210.02995522995520.0126656379767470.0457743291803405



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.