Personal tools

Coexpression cluster:C1157

From FANTOM5_SSTAR

Revision as of 16:57, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1157_Hepatic_neuroectodermal_liver_Hepatocyte_Adipocyte_spleen_kidney



Phase1 CAGE Peaks

Hg19::chr11:940729..940745,+p5@AP2A2
Hg19::chr19:7861495..7861500,+p@chr19:7861495..7861500
+
Hg19::chr3:58196639..58196653,-p2@DNASE1L3
Hg19::chr3:58196655..58196668,-p3@DNASE1L3
Hg19::chr3:58196822..58196832,-p9@DNASE1L3
Hg19::chr3:58196939..58196956,-p7@DNASE1L3
Hg19::chr7:158330204..158330217,+p2@ENST00000448698


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:0030128clathrin coat of endocytic vesicle0.00906548923612662
GO:0030669clathrin-coated endocytic vesicle membrane0.00906548923612662
GO:0030122AP-2 adaptor complex0.00906548923612662
GO:0030666endocytic vesicle membrane0.00906548923612662
GO:0045334clathrin-coated endocytic vesicle0.00906548923612662
GO:0030132clathrin coat of coated pit0.0124081634475196
GO:0006309DNA fragmentation during apoptosis0.0124081634475196
GO:0006921cell structure disassembly during apoptosis0.0124081634475196
GO:0030139endocytic vesicle0.0124081634475196
GO:0030125clathrin vesicle coat0.0124081634475196
GO:0030262apoptotic nuclear changes0.0124081634475196
GO:0030665clathrin coated vesicle membrane0.0124081634475196
GO:0006308DNA catabolic process0.0166393790457123
GO:0006997nuclear organization and biogenesis0.0166393790457123
GO:0005905coated pit0.0166393790457123
GO:0022411cellular component disassembly0.0166393790457123
GO:0030120vesicle coat0.0166393790457123
GO:0004536deoxyribonuclease activity0.0166393790457123
GO:0030662coated vesicle membrane0.0166393790457123
GO:0030131clathrin adaptor complex0.0166393790457123
GO:0030119AP-type membrane coat adaptor complex0.0166393790457123
GO:0030118clathrin coat0.0194091775309714
GO:0008632apoptotic program0.0250265430168767
GO:0030659cytoplasmic vesicle membrane0.0258598402874453
GO:0044433cytoplasmic vesicle part0.0258598402874453
GO:0012506vesicle membrane0.0258598402874453
GO:0030136clathrin-coated vesicle0.0258598402874453
GO:0030117membrane coat0.0258598402874453
GO:0048475coated membrane0.0258598402874453
GO:0030135coated vesicle0.0310077056707032
GO:0004519endonuclease activity0.0310077056707032
GO:0008565protein transporter activity0.0310077056707032
GO:0016043cellular component organization and biogenesis0.0310077056707032
GO:0010324membrane invagination0.0363450338784508
GO:0006897endocytosis0.0363450338784508
GO:0004518nuclease activity0.0440925552788139
GO:0016044membrane organization and biogenesis0.0495000262251407



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>


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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1157&oldid=1987605"