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Coexpression cluster:C4714: Difference between revisions

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|full_id=C4714_Adipocyte_Osteoblast_Preadipocyte_Fibroblast_Mesenchymal_tenocyte_mesenchymal
|full_id=C4714_Adipocyte_Osteoblast_Preadipocyte_Fibroblast_Mesenchymal_tenocyte_mesenchymal
|id=C4714
|id=C4714
|ontology_enrichment_celltype=CL:0000055!1.74e-35!180;CL:0000057!3.63e-20!75;CL:0000183!9.58e-18!59;CL:0000680!1.26e-16!57;CL:0000056!1.26e-16!57;CL:0000355!1.26e-16!57;CL:0000187!1.13e-15!54;CL:0000393!1.61e-13!60;CL:0000211!1.61e-13!60;CL:0000222!3.61e-13!119;CL:0000192!4.86e-13!42;CL:0000514!4.86e-13!42;CL:0002371!1.56e-09!591;CL:0000359!1.90e-09!32;CL:0002334!2.03e-08!12;CL:0000144!1.47e-07!625;CL:0000048!2.41e-07!430;CL:0000548!3.21e-07!679;CL:0000004!3.21e-07!679;CL:0000255!3.21e-07!679;CL:0002620!3.74e-07!23;CL:0000012!9.33e-07!682
|ontology_enrichment_celltype=CL:0000057!1.74e-21!76;CL:0000183!9.16e-19!59;CL:0000680!1.08e-17!58;CL:0000056!1.08e-17!58;CL:0000355!1.08e-17!58;CL:0000187!9.53e-17!55;CL:0000055!6.82e-16!106;CL:0000393!1.32e-14!61;CL:0000211!1.32e-14!61;CL:0000222!3.04e-14!121;CL:0000192!1.36e-13!43;CL:0000514!1.36e-13!43;CL:0002371!4.34e-12!588;CL:0000048!4.01e-10!427;CL:0000723!2.25e-09!433;CL:0000359!2.37e-09!32;CL:0000034!1.00e-08!441;CL:0000548!1.43e-08!679;CL:0000255!1.43e-08!679;CL:0002334!2.21e-08!12;CL:0002620!1.90e-07!23
|ontology_enrichment_disease=DOID:2394!9.54e-07!14
|ontology_enrichment_disease=DOID:2394!8.42e-07!14
|ontology_enrichment_uberon=UBERON:0000914!5.95e-18!83;UBERON:0002329!5.95e-18!83;UBERON:0003077!5.95e-18!83;UBERON:0003059!5.95e-18!83;UBERON:0007282!5.95e-18!83;UBERON:0009618!5.95e-18!83;UBERON:0007285!5.95e-18!83;UBERON:0002049!1.41e-17!79;UBERON:0007798!1.41e-17!79;UBERON:0005256!2.55e-17!143;UBERON:0004290!3.53e-17!70;UBERON:0001134!7.51e-16!61;UBERON:0002036!7.51e-16!61;UBERON:0003082!7.51e-16!61;UBERON:0002385!1.52e-15!63;UBERON:0001015!1.52e-15!63;UBERON:0000383!1.52e-15!63;UBERON:0004872!1.49e-14!84;UBERON:0000055!4.00e-14!69;UBERON:0000486!5.44e-14!82;UBERON:0003914!5.62e-14!118;UBERON:0000475!1.35e-13!365;UBERON:0002100!2.12e-13!216;UBERON:0000490!1.14e-12!138;UBERON:0001009!3.97e-12!113;UBERON:0004535!4.65e-12!110;UBERON:0001981!1.73e-11!60;UBERON:0007500!1.73e-11!60;UBERON:0004537!1.73e-11!60;UBERON:0006965!1.73e-11!60;UBERON:0000468!2.74e-11!659;UBERON:0000119!1.40e-10!312;UBERON:0000483!4.54e-10!309;UBERON:0001637!4.03e-09!42;UBERON:0003509!4.03e-09!42;UBERON:0004572!4.03e-09!42;UBERON:0003102!5.84e-09!95;UBERON:0003104!6.49e-09!238;UBERON:0009142!6.49e-09!238;UBERON:0000477!7.26e-09!286;UBERON:0001013!1.33e-08!14;UBERON:0000481!1.71e-08!347;UBERON:0002199!2.67e-08!45;UBERON:0002416!2.67e-08!45;UBERON:0004111!8.35e-08!241;UBERON:0000480!9.73e-08!626;UBERON:0004573!1.19e-07!33;UBERON:0004571!1.19e-07!33;UBERON:0000467!1.35e-07!625
|ontology_enrichment_uberon=UBERON:0007503!1.03e-20!78;UBERON:0002329!1.80e-18!71;UBERON:0003059!1.80e-18!71;UBERON:0007282!1.80e-18!71;UBERON:0004290!1.80e-18!71;UBERON:0009618!1.80e-18!71;UBERON:0007524!1.99e-18!73;UBERON:0003077!3.08e-18!72;UBERON:0007285!3.08e-18!72;UBERON:0002049!2.24e-17!78;UBERON:0007798!2.24e-17!78;UBERON:0003104!3.11e-17!160;UBERON:0009142!3.11e-17!160;UBERON:0005256!6.16e-17!122;UBERON:0001134!7.85e-17!62;UBERON:0002036!7.85e-17!62;UBERON:0003082!7.85e-17!62;UBERON:0002385!1.99e-16!64;UBERON:0001015!1.99e-16!64;UBERON:0000383!1.99e-16!64;UBERON:0004872!3.35e-15!83;UBERON:0000486!5.56e-15!83;UBERON:0000490!6.48e-15!148;UBERON:0003914!1.25e-14!117;UBERON:0000475!4.63e-14!264;UBERON:0000055!6.42e-14!68;UBERON:0001009!2.24e-13!112;UBERON:0004535!2.68e-13!109;UBERON:0002100!2.58e-12!199;UBERON:0007500!2.72e-11!59;UBERON:0001981!2.72e-11!59;UBERON:0004537!2.72e-11!59;UBERON:0006965!2.72e-11!59;UBERON:0000119!3.24e-10!309;UBERON:0000483!1.25e-09!306;UBERON:0000468!1.54e-09!656;UBERON:0003102!3.78e-09!99;UBERON:0002199!5.79e-09!46;UBERON:0002416!5.79e-09!46;UBERON:0001637!6.82e-09!42;UBERON:0003509!6.82e-09!42;UBERON:0004572!6.82e-09!42;UBERON:0001013!7.81e-09!14;UBERON:0000926!1.49e-08!315;UBERON:0004120!1.49e-08!315;UBERON:0006603!1.49e-08!315;UBERON:0000481!6.37e-08!342;UBERON:0004573!1.44e-07!33;UBERON:0004571!1.44e-07!33;UBERON:0004111!6.45e-07!240;UBERON:0000480!6.92e-07!625;UBERON:0000477!7.19e-07!373;UBERON:0002097!8.89e-07!41;UBERON:0000467!9.16e-07!624
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281369008610205!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324408186980782!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322577658557042!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270876087911695!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140961886923789!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00243799098142813
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281369008610205!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324408186980782!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322577658557042!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270876087911695!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140961886923789!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00243799098142813
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}}
}}

Revision as of 16:11, 19 October 2012


Full id: C4714_Adipocyte_Osteoblast_Preadipocyte_Fibroblast_Mesenchymal_tenocyte_mesenchymal



Phase1 CAGE Peaks

Hg19::chr8:104383700..104383709,+p4@CTHRC1
Hg19::chr8:104383728..104383756,+p2@CTHRC1
Hg19::chr8:104383759..104383821,+p1@CTHRC1


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
epithelial vesicle1.03e-2078
somite1.80e-1871
presomitic mesoderm1.80e-1871
presumptive segmental plate1.80e-1871
dermomyotome1.80e-1871
trunk paraxial mesoderm1.80e-1871
dense mesenchyme tissue1.99e-1873
paraxial mesoderm3.08e-1872
presumptive paraxial mesoderm3.08e-1872
vasculature2.24e-1778
vascular system2.24e-1778
mesenchyme3.11e-17160
entire embryonic mesenchyme3.11e-17160
trunk mesenchyme6.16e-17122
skeletal muscle tissue7.85e-1762
striated muscle tissue7.85e-1762
myotome7.85e-1762
muscle tissue1.99e-1664
musculature1.99e-1664
musculature of body1.99e-1664
splanchnic layer of lateral plate mesoderm3.35e-1583
multilaminar epithelium5.56e-1583
unilaminar epithelium6.48e-15148
epithelial tube1.25e-14117
organism subdivision4.63e-14264
vessel6.42e-1468
circulatory system2.24e-13112
cardiovascular system2.68e-13109
trunk2.58e-12199
epithelial tube open at both ends2.72e-1159
blood vessel2.72e-1159
blood vasculature2.72e-1159
vascular cord2.72e-1159
cell layer3.24e-10309
epithelium1.25e-09306
multi-cellular organism1.54e-09656
surface structure3.78e-0999
integument5.79e-0946
integumental system5.79e-0946
artery6.82e-0942
arterial blood vessel6.82e-0942
arterial system6.82e-0942
adipose tissue7.81e-0914
mesoderm1.49e-08315
mesoderm-derived structure1.49e-08315
presumptive mesoderm1.49e-08315
multi-tissue structure6.37e-08342
systemic artery1.44e-0733
systemic arterial system1.44e-0733
anatomical conduit6.45e-07240
anatomical group6.92e-07625
anatomical cluster7.19e-07373
skin of body8.89e-0741
anatomical system9.16e-07624
Disease
Ontology termp-valuen
ovarian cancer8.42e-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#1066435.360256373075030.0064925092527670.0281369008610205
E2F6#187635.017155731697390.00791769806886330.0324408186980782
EGR1#195834.988179094810140.008056488137383440.0322577658557042
NFKB1#479035.488063424193840.006049381815655430.0270876087911695
ZBTB7A#5134137.35190930787590.002516255860282270.0140961886923789
ZEB1#6935316.88843201754390.0002075486917327580.00243799098142813



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C4714&oldid=2251076"