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Coexpression cluster:C2311: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106359011743463!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248287599987076
|tf_chipseq_enrich=E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106359011743463!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248287599987076
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}}
}}

Revision as of 15:25, 26 November 2012


Full id: C2311_neuroectodermal_eye_retina_neuroepithelioma_merkel_carcinoid_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr14:76842457..76842494,+p1@ESRRB
Hg19::chr14:76842508..76842518,+p4@ESRRB
Hg19::chr14:76842616..76842623,+p8@ESRRB
Hg19::chr14:76842634..76842646,+p5@ESRRB


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


No GOStat results

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><br>uberon_data<br>disease_data<br>


Uber Anatomy
Ontology termp-valuen
spleen3.69e-213
gastrointestinal system mesentery3.69e-213
stomach region3.69e-213
mesentery3.69e-213
gastrointestinal system serosa3.69e-213
mesentery of stomach3.69e-213
gut mesentery3.69e-213
dorsal mesentery3.69e-213
dorsal mesogastrium3.69e-213
peritoneal cavity3.69e-213
spleen primordium3.69e-213
hemopoietic organ2.14e-097
immune organ2.14e-097
stomach2.77e-088
food storage organ2.77e-088
corpus callosum3.53e-081
central nervous system cell part cluster3.53e-081
axon tract3.53e-081
intercerebral commissure3.53e-081
dorsal telencephalic commissure3.53e-081
brain white matter3.53e-081
brain commissure3.53e-081
white matter3.53e-081
nervous system commissure3.53e-081
cerebral hemisphere white matter3.53e-081
sympathetic nervous system7.71e-075
autonomic nervous system7.71e-075
Disease
Ontology termp-valuen
neuroectodermal tumor1.77e-1810
syndrome2.64e-081
germ cell and embryonal cancer2.76e-0822
germ cell cancer2.76e-0822


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)

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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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
E2F1#186944.907389214879320.001724022357361790.0106359011743463
ZNF263#1012748.221841637010680.0002187871180958320.00248287599987076



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.