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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C1354_CD4_CD19_CD8_cord_Natural_Mast_thymus
|full_id=C1354_CD4_CD19_CD8_cord_Natural_Mast_thymus
|gostat_on_coexpression_clusters=GO:0006355!regulation of transcription, DNA-dependent!0.0283845759598042!170959;9988;80264$GO:0006351!transcription, DNA-dependent!0.0283845759598042!170959;9988;80264$GO:0032774!RNA biosynthetic process!0.0283845759598042!170959;9988;80264$GO:0003677!DNA binding!0.0283845759598042!170959;9988;80264$GO:0045449!regulation of transcription!0.0283845759598042!170959;9988;80264$GO:0019219!regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0283845759598042!170959;9988;80264$GO:0006350!transcription!0.0283845759598042!170959;9988;80264$GO:0010468!regulation of gene expression!0.0283845759598042!170959;9988;80264$GO:0031323!regulation of cellular metabolic process!0.0283845759598042!170959;9988;80264$GO:0019222!regulation of metabolic process!0.0283845759598042!170959;9988;80264$GO:0016070!RNA metabolic process!0.0283845759598042!170959;9988;80264$GO:0043229!intracellular organelle!0.0364791675777369!9662;170959;9988;80264$GO:0043226!organelle!0.0364791675777369!9662;170959;9988;80264$GO:0010467!gene expression!0.0463822808005125!170959;9988;80264$GO:0005813!centrosome!0.0463822808005125!9662$GO:0050794!regulation of cellular process!0.0463822808005125!170959;9988;80264$GO:0005815!microtubule organizing center!0.0463822808005125!9662$GO:0006139!nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0463822808005125!170959;9988;80264$GO:0005634!nucleus!0.0473610801434053!170959;9988;80264$GO:0050789!regulation of biological process!0.0473610801434053!170959;9988;80264$GO:0044424!intracellular part!0.0473610801434053!9662;170959;9988;80264$GO:0003676!nucleic acid binding!0.0485494265355204!170959;9988;80264
|id=C1354
|id=C1354
}}
}}

Revision as of 17:34, 18 May 2012


Full id: C1354_CD4_CD19_CD8_cord_Natural_Mast_thymus



Phase1 CAGE Peaks

Hg19::chr11:94227129..94227182,+p1@ANKRD49
Hg19::chr19:21203451..21203475,+p1@ZNF430
Hg19::chr19:21324829..21324855,+p1@ZNF431
Hg19::chr4:56814968..56815018,+p1@CEP135
Hg19::chr4:84376953..84377040,-p1@HELQ
Hg19::chr7:86781734..86781777,+p1@DMTF1


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:0006355regulation of transcription, DNA-dependent0.0283845759598042
GO:0006351transcription, DNA-dependent0.0283845759598042
GO:0032774RNA biosynthetic process0.0283845759598042
GO:0003677DNA binding0.0283845759598042
GO:0045449regulation of transcription0.0283845759598042
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0283845759598042
GO:0006350transcription0.0283845759598042
GO:0010468regulation of gene expression0.0283845759598042
GO:0031323regulation of cellular metabolic process0.0283845759598042
GO:0019222regulation of metabolic process0.0283845759598042
GO:0016070RNA metabolic process0.0283845759598042
GO:0043229intracellular organelle0.0364791675777369
GO:0043226organelle0.0364791675777369
GO:0010467gene expression0.0463822808005125
GO:0005813centrosome0.0463822808005125
GO:0050794regulation of cellular process0.0463822808005125
GO:0005815microtubule organizing center0.0463822808005125
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0463822808005125
GO:0005634nucleus0.0473610801434053
GO:0050789regulation of biological process0.0473610801434053
GO:0044424intracellular part0.0473610801434053
GO:0003676nucleic acid binding0.0485494265355204



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.