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Coexpression cluster:C4323: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0017015!regulation of transforming growth factor beta receptor signaling pathway!0.021247165877831!$GO:0007179!transforming growth factor beta receptor signaling pathway!0.027944037936819!$GO:0007178!transmembrane receptor protein serine/threonine kinase signaling pathway!0.0283057811010493!
|gostat_on_coexpression_clusters=GO:0017015!regulation of transforming growth factor beta receptor signaling pathway!0.021247165877831!$GO:0007179!transforming growth factor beta receptor signaling pathway!0.027944037936819!$GO:0007178!transmembrane receptor protein serine/threonine kinase signaling pathway!0.0283057811010493!
|id=C4323
|id=C4323
|ontology_enrichment_celltype=CL:0000055!7.76e-21!180;CL:0000057!2.74e-16!75;CL:0002620!1.83e-12!23;CL:0002334!7.58e-08!12;CL:0002570!7.04e-07!8
|ontology_enrichment_celltype=CL:0002620!9.19e-32!23;CL:0000057!1.40e-23!76;CL:0002580!2.74e-14!3;CL:0002579!3.40e-14!3;CL:0002334!5.20e-13!12;CL:0000136!1.63e-09!15;CL:0002617!1.89e-09!2;CL:0000048!6.00e-09!427;CL:0000723!1.07e-08!433;CL:0000134!1.43e-08!354;CL:0000034!2.26e-08!441;CL:0002320!3.03e-08!361;CL:0000219!4.23e-07!386;CL:0000667!5.07e-07!6;CL:0000058!5.07e-07!6;CL:0000138!5.07e-07!6
|ontology_enrichment_disease=DOID:17!2.33e-08!5;DOID:450!2.33e-08!5;DOID:66!2.33e-08!5;DOID:423!2.33e-08!5;DOID:0080000!2.33e-08!5;DOID:11722!2.33e-08!5
|ontology_enrichment_disease=DOID:17!5.33e-20!5;DOID:450!5.33e-20!5;DOID:66!5.33e-20!5;DOID:423!5.33e-20!5;DOID:0080000!5.33e-20!5;DOID:11722!5.33e-20!5
|ontology_enrichment_uberon=UBERON:0003688!1.79e-10!6;UBERON:0002358!1.79e-10!6;UBERON:0003684!1.79e-10!6;UBERON:0001178!1.79e-10!6
|ontology_enrichment_uberon=UBERON:0002097!5.55e-19!41;UBERON:0003688!2.52e-18!6;UBERON:0002358!2.52e-18!6;UBERON:0003684!2.52e-18!6;UBERON:0001178!2.52e-18!6;UBERON:0002199!1.52e-16!46;UBERON:0002416!1.52e-16!46;UBERON:0000310!7.71e-11!10;UBERON:0001443!8.02e-10!11;UBERON:0002384!2.53e-09!371;UBERON:0004457!5.38e-09!12;UBERON:0000042!5.38e-09!12
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}}
}}

Revision as of 15:51, 19 October 2012


Full id: C4323_Preadipocyte_Ewing_Adipocyte_rectum_Fibroblast_basal_osteoclastoma



Phase1 CAGE Peaks

Hg19::chr3:29739726..29739732,+p14@RBMS3
Hg19::chr5:111312488..111312498,-p35@C5orf13
Hg19::chr5:111312622..111312634,-p17@C5orf13


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:0017015regulation of transforming growth factor beta receptor signaling pathway0.021247165877831
GO:0007179transforming growth factor beta receptor signaling pathway0.027944037936819
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0283057811010493



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>

Cell Type
Ontology termp-valuen
skin fibroblast9.19e-3223
fibroblast1.40e-2376
preadipocyte of the breast2.74e-143
omentum preadipocyte3.40e-143
preadipocyte5.20e-1312
fat cell1.63e-0915
adipocyte of breast1.89e-092
multi fate stem cell6.00e-09427
somatic stem cell1.07e-08433
mesenchymal cell1.43e-08354
stem cell2.26e-08441
connective tissue cell3.03e-08361
motile cell4.23e-07386
collagen secreting cell5.07e-076
chondroblast5.07e-076
chondrocyte5.07e-076
Uber Anatomy
Ontology termp-valuen
skin of body5.55e-1941
omentum2.52e-186
peritoneum2.52e-186
abdominal cavity2.52e-186
visceral peritoneum2.52e-186
integument1.52e-1646
integumental system1.52e-1646
breast7.71e-1110
chest8.02e-1011
connective tissue2.53e-09371
cavity lining5.38e-0912
serous membrane5.38e-0912
Disease
Ontology termp-valuen
musculoskeletal system disease5.33e-205
myotonic disease5.33e-205
muscle tissue disease5.33e-205
myopathy5.33e-205
muscular disease5.33e-205
myotonic dystrophy5.33e-205


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.

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