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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1700_heart_adipose_mature_breast_left_smooth_vagina
|full_id=C1700_heart_adipose_mature_breast_left_smooth_vagina
|gostat_on_coexpression_clusters=GO:0051014!actin filament severing!0.0340117855475839!2934$GO:0005737!cytoplasm!0.0340117855475839!6867;2934;23263;84708$GO:0051693!actin filament capping!0.0340117855475839!2934$GO:0051016!barbed-end actin filament capping!0.0340117855475839!2934$GO:0030835!negative regulation of actin filament depolymerization!0.0340117855475839!2934$GO:0030834!regulation of actin filament depolymerization!0.0340117855475839!2934$GO:0030042!actin filament depolymerization!0.0340117855475839!2934$GO:0030041!actin filament polymerization!0.036177181378452!2934$GO:0008064!regulation of actin polymerization and/or depolymerization!0.036177181378452!2934$GO:0051261!protein depolymerization!0.036177181378452!2934$GO:0030832!regulation of actin filament length!0.036177181378452!2934$GO:0032535!regulation of cellular component size!0.036177181378452!2934$GO:0032956!regulation of actin cytoskeleton organization and biogenesis!0.036177181378452!2934$GO:0051129!negative regulation of cellular component organization and biogenesis!0.036177181378452!2934$GO:0051493!regulation of cytoskeleton organization and biogenesis!0.036177181378452!2934$GO:0033043!regulation of organelle organization and biogenesis!0.036177181378452!2934$GO:0008154!actin polymerization and/or depolymerization!0.0370810211729326!2934
|gostat_on_coexpression_clusters=GO:0051014!actin filament severing!0.0340117855475839!2934$GO:0005737!cytoplasm!0.0340117855475839!6867;2934;23263;84708$GO:0051693!actin filament capping!0.0340117855475839!2934$GO:0051016!barbed-end actin filament capping!0.0340117855475839!2934$GO:0030835!negative regulation of actin filament depolymerization!0.0340117855475839!2934$GO:0030834!regulation of actin filament depolymerization!0.0340117855475839!2934$GO:0030042!actin filament depolymerization!0.0340117855475839!2934$GO:0030041!actin filament polymerization!0.036177181378452!2934$GO:0008064!regulation of actin polymerization and/or depolymerization!0.036177181378452!2934$GO:0051261!protein depolymerization!0.036177181378452!2934$GO:0030832!regulation of actin filament length!0.036177181378452!2934$GO:0032535!regulation of cellular component size!0.036177181378452!2934$GO:0032956!regulation of actin cytoskeleton organization and biogenesis!0.036177181378452!2934$GO:0051129!negative regulation of cellular component organization and biogenesis!0.036177181378452!2934$GO:0051493!regulation of cytoskeleton organization and biogenesis!0.036177181378452!2934$GO:0033043!regulation of organelle organization and biogenesis!0.036177181378452!2934$GO:0008154!actin polymerization and/or depolymerization!0.0370810211729326!2934

Revision as of 14:18, 12 September 2012


Full id: C1700_heart_adipose_mature_breast_left_smooth_vagina



Phase1 CAGE Peaks

Hg19::chr13:113633620..113633695,+p2@MCF2L
Hg19::chr1:112903200..112903261,-p1@ENST00000427290
Hg19::chr4:54518619..54518649,-p5@LNX1
Hg19::chr8:38586068..38586128,+p3@TACC1
Hg19::chr9:124062100..124062115,+p2@GSN


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


GO IDGO nameFDR corrected p-value
GO:0051014actin filament severing0.0340117855475839
GO:0005737cytoplasm0.0340117855475839
GO:0051693actin filament capping0.0340117855475839
GO:0051016barbed-end actin filament capping0.0340117855475839
GO:0030835negative regulation of actin filament depolymerization0.0340117855475839
GO:0030834regulation of actin filament depolymerization0.0340117855475839
GO:0030042actin filament depolymerization0.0340117855475839
GO:0030041actin filament polymerization0.036177181378452
GO:0008064regulation of actin polymerization and/or depolymerization0.036177181378452
GO:0051261protein depolymerization0.036177181378452
GO:0030832regulation of actin filament length0.036177181378452
GO:0032535regulation of cellular component size0.036177181378452
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.036177181378452
GO:0051129negative regulation of cellular component organization and biogenesis0.036177181378452
GO:0051493regulation of cytoskeleton organization and biogenesis0.036177181378452
GO:0033043regulation of organelle organization and biogenesis0.036177181378452
GO:0008154actin polymerization and/or depolymerization0.0370810211729326



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>


Cell Type
Ontology termp-valuen
fat cell2.81e-0715
Uber Anatomy
Ontology termp-valuen
adult organism2.75e-44115
anatomical conduit3.21e-23241
anatomical cluster8.75e-22286
neural tube1.65e-2157
neural rod1.65e-2157
future spinal cord1.65e-2157
neural keel1.65e-2157
regional part of brain6.41e-2059
multi-cellular organism1.03e-19659
organism subdivision3.13e-18365
tube4.35e-18194
neural plate5.23e-1886
presumptive neural plate5.23e-1886
multi-tissue structure1.35e-17347
anterior neural tube6.54e-1742
regional part of forebrain2.92e-1641
forebrain2.92e-1641
future forebrain2.92e-1641
neurectoderm4.10e-1690
anatomical system5.13e-16625
brain1.04e-1569
future brain1.04e-1569
anatomical group1.14e-15626
organ3.75e-15511
cell layer1.25e-14312
epithelium1.50e-14309
anterior region of body3.60e-14129
craniocervical region3.60e-14129
head7.27e-14123
central nervous system1.12e-1382
gray matter2.44e-1334
brain grey matter2.44e-1334
telencephalon3.03e-1334
regional part of telencephalon7.19e-1333
cerebral hemisphere2.89e-1232
pre-chordal neural plate4.13e-1261
embryo1.14e-11612
organ part1.19e-11219
regional part of nervous system1.81e-1194
nervous system1.81e-1194
embryonic structure3.17e-11605
developing anatomical structure3.17e-11605
germ layer6.64e-11604
embryonic tissue6.64e-11604
presumptive structure6.64e-11604
epiblast (generic)6.64e-11604
ectoderm-derived structure4.86e-10169
regional part of cerebral cortex9.21e-1022
cerebral cortex3.31e-0925
pallium3.31e-0925
ectoderm3.39e-09173
presumptive ectoderm3.39e-09173
neocortex7.28e-0920
compound organ1.11e-0769


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.