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Coexpression cluster:C3183: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0005172!vascular endothelial growth factor receptor binding!0.00388555280819498!7423$GO:0008201!heparin binding!0.0222339966246713!7423$GO:0005539!glycosaminoglycan binding!0.0222339966246713!7423$GO:0030247!polysaccharide binding!0.0222339966246713!7423$GO:0001871!pattern binding!0.0222339966246713!7423$GO:0001558!regulation of cell growth!0.0222339966246713!7423$GO:0016049!cell growth!0.0222339966246713!7423$GO:0040008!regulation of growth!0.0222339966246713!7423$GO:0008361!regulation of cell size!0.0222339966246713!7423$GO:0008284!positive regulation of cell proliferation!0.0223419286471212!7423$GO:0008083!growth factor activity!0.0223419286471212!7423$GO:0005125!cytokine activity!0.0250941952195926!7423$GO:0042127!regulation of cell proliferation!0.0290202225362063!7423$GO:0030246!carbohydrate binding!0.0290202225362063!7423$GO:0032989!cellular structure morphogenesis!0.0290202225362063!7423$GO:0000902!cell morphogenesis!0.0290202225362063!7423$GO:0008283!cell proliferation!0.0425696594427245!7423$GO:0065008!regulation of biological quality!0.046891557753444!7423$GO:0048522!positive regulation of cellular process!0.046891557753444!7423$GO:0005102!receptor binding!0.046891557753444!7423$GO:0009653!anatomical structure morphogenesis!0.046891557753444!7423$GO:0048518!positive regulation of biological process!0.046891557753444!7423
|gostat_on_coexpression_clusters=GO:0005172!vascular endothelial growth factor receptor binding!0.00388555280819498!7423$GO:0008201!heparin binding!0.0222339966246713!7423$GO:0005539!glycosaminoglycan binding!0.0222339966246713!7423$GO:0030247!polysaccharide binding!0.0222339966246713!7423$GO:0001871!pattern binding!0.0222339966246713!7423$GO:0001558!regulation of cell growth!0.0222339966246713!7423$GO:0016049!cell growth!0.0222339966246713!7423$GO:0040008!regulation of growth!0.0222339966246713!7423$GO:0008361!regulation of cell size!0.0222339966246713!7423$GO:0008284!positive regulation of cell proliferation!0.0223419286471212!7423$GO:0008083!growth factor activity!0.0223419286471212!7423$GO:0005125!cytokine activity!0.0250941952195926!7423$GO:0042127!regulation of cell proliferation!0.0290202225362063!7423$GO:0030246!carbohydrate binding!0.0290202225362063!7423$GO:0032989!cellular structure morphogenesis!0.0290202225362063!7423$GO:0000902!cell morphogenesis!0.0290202225362063!7423$GO:0008283!cell proliferation!0.0425696594427245!7423$GO:0065008!regulation of biological quality!0.046891557753444!7423$GO:0048522!positive regulation of cellular process!0.046891557753444!7423$GO:0005102!receptor binding!0.046891557753444!7423$GO:0009653!anatomical structure morphogenesis!0.046891557753444!7423$GO:0048518!positive regulation of biological process!0.046891557753444!7423
|id=C3183
|id=C3183
|ontology_enrichment_celltype=CL:0000136!2.57e-08!15;CL:0000325!4.87e-07!39
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004872!1.69e-07!84
|ontology_enrichment_uberon=UBERON:0000926!1.43e-07!315;UBERON:0004120!1.43e-07!315;UBERON:0006603!1.43e-07!315
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}}
}}

Revision as of 14:52, 19 October 2012


Full id: C3183_Osteoblast_breast_Mesenchymal_Melanocyte_Fibroblast_left_Adipocyte



Phase1 CAGE Peaks

Hg19::chr11:64003292..64003325,+p@chr11:64003292..64003325
+
Hg19::chr11:64004888..64004909,+p3@VEGFB
Hg19::chr17:7154873..7154884,-p6@CTDNEP1


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:0005172vascular endothelial growth factor receptor binding0.00388555280819498
GO:0008201heparin binding0.0222339966246713
GO:0005539glycosaminoglycan binding0.0222339966246713
GO:0030247polysaccharide binding0.0222339966246713
GO:0001871pattern binding0.0222339966246713
GO:0001558regulation of cell growth0.0222339966246713
GO:0016049cell growth0.0222339966246713
GO:0040008regulation of growth0.0222339966246713
GO:0008361regulation of cell size0.0222339966246713
GO:0008284positive regulation of cell proliferation0.0223419286471212
GO:0008083growth factor activity0.0223419286471212
GO:0005125cytokine activity0.0250941952195926
GO:0042127regulation of cell proliferation0.0290202225362063
GO:0030246carbohydrate binding0.0290202225362063
GO:0032989cellular structure morphogenesis0.0290202225362063
GO:0000902cell morphogenesis0.0290202225362063
GO:0008283cell proliferation0.0425696594427245
GO:0065008regulation of biological quality0.046891557753444
GO:0048522positive regulation of cellular process0.046891557753444
GO:0005102receptor binding0.046891557753444
GO:0009653anatomical structure morphogenesis0.046891557753444
GO:0048518positive regulation of biological process0.046891557753444



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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
mesoderm1.43e-07315
mesoderm-derived structure1.43e-07315
presumptive mesoderm1.43e-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)

{{{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.