Personal tools

Coexpression cluster:C3586: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C3586_serous_breast_choriocarcinoma_pancreatic_malignant_Prostate_maxillary |id=C3586 }}")
 
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C3586_serous_breast_choriocarcinoma_pancreatic_malignant_Prostate_maxillary
|full_id=C3586_serous_breast_choriocarcinoma_pancreatic_malignant_Prostate_maxillary
|gostat_on_coexpression_clusters=GO:0030054!cell junction!0.00429571419202788!153562;999$GO:0044459!plasma membrane part!0.0299164706866183!153562;999$GO:0005923!tight junction!0.0299164706866183!153562$GO:0043296!apical junction complex!0.0299164706866183!153562$GO:0016327!apicolateral plasma membrane!0.0299164706866183!153562$GO:0050954!sensory perception of mechanical stimulus!0.0299164706866183!153562$GO:0007605!sensory perception of sound!0.0299164706866183!153562$GO:0005911!intercellular junction!0.0340594182494116!153562$GO:0007156!homophilic cell adhesion!0.0340594182494116!999$GO:0005886!plasma membrane!0.0340594182494116!153562;999$GO:0016337!cell-cell adhesion!0.0498875417599653!999
|id=C3586
|id=C3586
}}
}}

Revision as of 17:39, 18 May 2012


Full id: C3586_serous_breast_choriocarcinoma_pancreatic_malignant_Prostate_maxillary



Phase1 CAGE Peaks

Hg19::chr16:68771187..68771201,+p1@CDH1
Hg19::chr5:68711023..68711075,+p2@MARVELD2
Hg19::chr5:68711076..68711103,+p3@MARVELD2


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:0030054cell junction0.00429571419202788
GO:0044459plasma membrane part0.0299164706866183
GO:0005923tight junction0.0299164706866183
GO:0043296apical junction complex0.0299164706866183
GO:0016327apicolateral plasma membrane0.0299164706866183
GO:0050954sensory perception of mechanical stimulus0.0299164706866183
GO:0007605sensory perception of sound0.0299164706866183
GO:0005911intercellular junction0.0340594182494116
GO:0007156homophilic cell adhesion0.0340594182494116
GO:0005886plasma membrane0.0340594182494116
GO:0016337cell-cell adhesion0.0498875417599653



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.