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Coexpression cluster:C1421: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007524!3.41e-22!73;UBERON:0003077!1.36e-21!72;UBERON:0007285!1.36e-21!72;UBERON:0002329!1.39e-21!71;UBERON:0003059!1.39e-21!71;UBERON:0007282!1.39e-21!71;UBERON:0004290!1.39e-21!71;UBERON:0009618!1.39e-21!71;UBERON:0007503!2.80e-21!78;UBERON:0001134!1.28e-18!62;UBERON:0002036!1.28e-18!62;UBERON:0003082!1.28e-18!62;UBERON:0003104!2.87e-18!160;UBERON:0009142!2.87e-18!160;UBERON:0002385!5.57e-18!64;UBERON:0001015!5.57e-18!64;UBERON:0000383!5.57e-18!64;UBERON:0005256!1.55e-17!122;UBERON:0000486!2.99e-17!83;UBERON:0000475!2.19e-13!264;UBERON:0002199!3.94e-11!46;UBERON:0002416!3.94e-11!46;UBERON:0002100!4.04e-11!199;UBERON:0000481!4.70e-11!342;UBERON:0003102!7.48e-11!99;UBERON:0000490!2.34e-09!148;UBERON:0002097!5.13e-09!41;UBERON:0000468!9.12e-09!656;UBERON:0004923!9.36e-09!66;UBERON:0000479!1.21e-08!773;UBERON:0001013!2.26e-07!14;UBERON:0000926!6.74e-07!315;UBERON:0004120!6.74e-07!315;UBERON:0006603!6.74e-07!315
|ontology_enrichment_uberon=UBERON:0007524!3.41e-22!73;UBERON:0003077!1.36e-21!72;UBERON:0007285!1.36e-21!72;UBERON:0002329!1.39e-21!71;UBERON:0003059!1.39e-21!71;UBERON:0007282!1.39e-21!71;UBERON:0004290!1.39e-21!71;UBERON:0009618!1.39e-21!71;UBERON:0007503!2.80e-21!78;UBERON:0001134!1.28e-18!62;UBERON:0002036!1.28e-18!62;UBERON:0003082!1.28e-18!62;UBERON:0003104!2.87e-18!160;UBERON:0009142!2.87e-18!160;UBERON:0002385!5.57e-18!64;UBERON:0001015!5.57e-18!64;UBERON:0000383!5.57e-18!64;UBERON:0005256!1.55e-17!122;UBERON:0000486!2.99e-17!83;UBERON:0000475!2.19e-13!264;UBERON:0002199!3.94e-11!46;UBERON:0002416!3.94e-11!46;UBERON:0002100!4.04e-11!199;UBERON:0000481!4.70e-11!342;UBERON:0003102!7.48e-11!99;UBERON:0000490!2.34e-09!148;UBERON:0002097!5.13e-09!41;UBERON:0000468!9.12e-09!656;UBERON:0004923!9.36e-09!66;UBERON:0000479!1.21e-08!773;UBERON:0001013!2.26e-07!14;UBERON:0000926!6.74e-07!315;UBERON:0004120!6.74e-07!315;UBERON:0006603!6.74e-07!315
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}}
}}

Revision as of 14:52, 26 November 2012


Full id: C1421_Mesenchymal_Preadipocyte_Fibroblast_tenocyte_Adipocyte_Osteoblast_Nucleus



Phase1 CAGE Peaks

Hg19::chr16:4431722..4431771,+p@chr16:4431722..4431771
+
Hg19::chr19:14049136..14049171,-p2@PODNL1
Hg19::chr19:14049184..14049242,-p1@PODNL1
Hg19::chr1:1290954..1290971,-p8@MXRA8
Hg19::chr1:1293904..1293949,-p1@MXRA8
Hg19::chr21:47517478..47517529,+p9@COL6A2


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:0005578proteinaceous extracellular matrix0.0118525173614682
GO:0044421extracellular region part0.0274556468016525
GO:0030198extracellular matrix organization and biogenesis0.0351588482143845
GO:0043062extracellular structure organization and biogenesis0.041676742962934
GO:0030674protein binding, bridging0.041676742962934
GO:0005201extracellular matrix structural constituent0.0467083833212877
GO:0006817phosphate transport0.0467083833212877



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
dense mesenchyme tissue3.41e-2273
paraxial mesoderm1.36e-2172
presumptive paraxial mesoderm1.36e-2172
somite1.39e-2171
presomitic mesoderm1.39e-2171
presumptive segmental plate1.39e-2171
dermomyotome1.39e-2171
trunk paraxial mesoderm1.39e-2171
epithelial vesicle2.80e-2178
skeletal muscle tissue1.28e-1862
striated muscle tissue1.28e-1862
myotome1.28e-1862
mesenchyme2.87e-18160
entire embryonic mesenchyme2.87e-18160
muscle tissue5.57e-1864
musculature5.57e-1864
musculature of body5.57e-1864
trunk mesenchyme1.55e-17122
multilaminar epithelium2.99e-1783
organism subdivision2.19e-13264
integument3.94e-1146
integumental system3.94e-1146
trunk4.04e-11199
multi-tissue structure4.70e-11342
surface structure7.48e-1199
unilaminar epithelium2.34e-09148
skin of body5.13e-0941
multi-cellular organism9.12e-09656
organ component layer9.36e-0966
tissue1.21e-08773
adipose tissue2.26e-0714
mesoderm6.74e-07315
mesoderm-derived structure6.74e-07315
presumptive mesoderm6.74e-07315


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)

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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.