Personal tools

Coexpression cluster:C2121: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C2121_spinal_epididymis_glioma_thalamus_locus_pineal_medulla |id=C2121 }}")
 
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C2121_spinal_epididymis_glioma_thalamus_locus_pineal_medulla
|full_id=C2121_spinal_epididymis_glioma_thalamus_locus_pineal_medulla
|gostat_on_coexpression_clusters=GO:0008294!calcium- and calmodulin-responsive adenylate cyclase activity!0.00397386082656305!114$GO:0004016!adenylate cyclase activity!0.00647592134699164!114$GO:0006171!cAMP biosynthetic process!0.00647592134699164!114$GO:0046058!cAMP metabolic process!0.00647592134699164!114$GO:0016849!phosphorus-oxygen lyase activity!0.00647592134699164!114$GO:0009975!cyclase activity!0.00647592134699164!114$GO:0004289!subtilase activity!0.00647592134699164!114$GO:0009190!cyclic nucleotide biosynthetic process!0.00647592134699164!114$GO:0007611!learning and/or memory!0.00647592134699164!114$GO:0009187!cyclic nucleotide metabolic process!0.00662310137760509!114$GO:0009165!nucleotide biosynthetic process!0.0277434357706346!114$GO:0016829!lyase activity!0.0277434357706346!114$GO:0007610!behavior!0.0277434357706346!114$GO:0004252!serine-type endopeptidase activity!0.0277434357706346!114$GO:0009117!nucleotide metabolic process!0.0277434357706346!114$GO:0055086!nucleobase, nucleoside and nucleotide metabolic process!0.0277434357706346!114$GO:0008236!serine-type peptidase activity!0.0277434357706346!114$GO:0017171!serine hydrolase activity!0.0277434357706346!114$GO:0000287!magnesium ion binding!0.0311634349030471!114$GO:0005624!membrane fraction!0.0452357824090427!114
|id=C2121
|id=C2121
}}
}}

Revision as of 17:36, 18 May 2012


Full id: C2121_spinal_epididymis_glioma_thalamus_locus_pineal_medulla



Phase1 CAGE Peaks

Hg19::chr11:24518492..24518510,+p5@LUZP2
Hg19::chr8:132053091..132053127,-p1@ADCY8
Hg19::chr8:132053777..132053790,-p@chr8:132053777..132053790
-
Hg19::chr8:132053800..132053811,-p@chr8:132053800..132053811
-


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:0008294calcium- and calmodulin-responsive adenylate cyclase activity0.00397386082656305
GO:0004016adenylate cyclase activity0.00647592134699164
GO:0006171cAMP biosynthetic process0.00647592134699164
GO:0046058cAMP metabolic process0.00647592134699164
GO:0016849phosphorus-oxygen lyase activity0.00647592134699164
GO:0009975cyclase activity0.00647592134699164
GO:0004289subtilase activity0.00647592134699164
GO:0009190cyclic nucleotide biosynthetic process0.00647592134699164
GO:0007611learning and/or memory0.00647592134699164
GO:0009187cyclic nucleotide metabolic process0.00662310137760509
GO:0009165nucleotide biosynthetic process0.0277434357706346
GO:0016829lyase activity0.0277434357706346
GO:0007610behavior0.0277434357706346
GO:0004252serine-type endopeptidase activity0.0277434357706346
GO:0009117nucleotide metabolic process0.0277434357706346
GO:0055086nucleobase, nucleoside and nucleotide metabolic process0.0277434357706346
GO:0008236serine-type peptidase activity0.0277434357706346
GO:0017171serine hydrolase activity0.0277434357706346
GO:0000287magnesium ion binding0.0311634349030471
GO:0005624membrane fraction0.0452357824090427



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.