Personal tools

Coexpression cluster:C797: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C797_mesenchymal_skeletal_Endothelial_Pericytes_Skeletal_Astrocyte_left |id=C797 }}")
 
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C797_mesenchymal_skeletal_Endothelial_Pericytes_Skeletal_Astrocyte_left
|full_id=C797_mesenchymal_skeletal_Endothelial_Pericytes_Skeletal_Astrocyte_left
|gostat_on_coexpression_clusters=GO:0048625!myoblast cell fate commitment!0.00777087685934379!4654$GO:0007518!myoblast cell fate determination!0.00777087685934379!4654$GO:0045445!myoblast differentiation!0.026461784800824!4654$GO:0003705!RNA polymerase II transcription factor activity, enhancer binding!0.026461784800824!4654$GO:0001709!cell fate determination!0.026461784800824!4654$GO:0048731!system development!0.026461784800824!10763;4654$GO:0048741!skeletal muscle fiber development!0.026461784800824!4654$GO:0048747!muscle fiber development!0.026461784800824!4654$GO:0042692!muscle cell differentiation!0.026461784800824!4654$GO:0048856!anatomical structure development!0.0306211131946604!10763;4654$GO:0007519!skeletal muscle development!0.0306211131946604!4654$GO:0045165!cell fate commitment!0.0306211131946604!4654$GO:0007275!multicellular organismal development!0.0309883796995485!10763;4654$GO:0014706!striated muscle development!0.032522933917594!4654
|id=C797
|id=C797
}}
}}

Revision as of 17:41, 18 May 2012


Full id: C797_mesenchymal_skeletal_Endothelial_Pericytes_Skeletal_Astrocyte_left



Phase1 CAGE Peaks

Hg19::chr11:17741206..17741215,+p6@MYOD1
Hg19::chr11:17741228..17741243,+p4@MYOD1
Hg19::chr1:156641398..156641410,-p@chr1:156641398..156641410
-
Hg19::chr1:156641522..156641541,-p@chr1:156641522..156641541
-
Hg19::chr1:156641620..156641633,-p@chr1:156641620..156641633
-
Hg19::chr1:156641913..156641932,-p3@NES
Hg19::chr1:156642431..156642448,-p5@NES
Hg19::chr1:156642464..156642497,-p4@NES
Hg19::chr1:156642538..156642550,-p10@NES
Hg19::chr1:203139551..203139560,-p@chr1:203139551..203139560
-


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:0048625myoblast cell fate commitment0.00777087685934379
GO:0007518myoblast cell fate determination0.00777087685934379
GO:0045445myoblast differentiation0.026461784800824
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.026461784800824
GO:0001709cell fate determination0.026461784800824
GO:0048731system development0.026461784800824
GO:0048741skeletal muscle fiber development0.026461784800824
GO:0048747muscle fiber development0.026461784800824
GO:0042692muscle cell differentiation0.026461784800824
GO:0048856anatomical structure development0.0306211131946604
GO:0007519skeletal muscle development0.0306211131946604
GO:0045165cell fate commitment0.0306211131946604
GO:0007275multicellular organismal development0.0309883796995485
GO:0014706striated muscle development0.032522933917594



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

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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.