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Coexpression cluster:C617: Difference between revisions

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|tf_chipseq_enrich=NR3C1#2908;4:4.27800666604944:0.0115683845516382:0.0422873023061334
|tf_chipseq_enrich=NR3C1#2908;4:4.27800666604944:0.0115683845516382:0.0422873023061334
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}}
}}

Revision as of 14:21, 26 November 2012


Full id: C617_mucinous_gall_signet_bile_maxillary_keratoacanthoma_Alveolar



Phase1 CAGE Peaks

Hg19::chr10:88106150..88106156,+p@chr10:88106150..88106156
+
Hg19::chr11:70781237..70781270,-p@chr11:70781237..70781270
-
Hg19::chr13:99644885..99644901,+p@chr13:99644885..99644901
+
Hg19::chr14:102196739..102196744,+p1@LINC00239
Hg19::chr16:16011740..16011741,-p@chr16:16011740..16011741
-
Hg19::chr16:52028463..52028468,-p@chr16:52028463..52028468
-
Hg19::chr16:52028472..52028487,-p@chr16:52028472..52028487
-
Hg19::chr16:52028503..52028515,-p@chr16:52028503..52028515
-
Hg19::chr1:240996509..240996525,-p@chr1:240996509..240996525
-
Hg19::chr20:62321640..62321645,+p1@BC131817
Hg19::chr5:172722414..172722417,-p@chr5:172722414..172722417
-
Hg19::chr6:31080343..31080359,-p1@C6orf15
Hg19::chr7:55757275..55757282,-p1@FKBP9L
Hg19::chr7:73118172..73118185,-p3@STX1A


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:0050796regulation of insulin secretion0.0214651323421493
GO:0030073insulin secretion0.0214651323421493
GO:0046883regulation of hormone secretion0.0214651323421493
GO:0030072peptide hormone secretion0.0214651323421493
GO:0002790peptide secretion0.0214651323421493
GO:0005484SNAP receptor activity0.0274245201189629
GO:0046879hormone secretion0.0274245201189629
GO:0015833peptide transport0.0275212931074951
GO:0051046regulation of secretion0.0369868979872323
GO:0003001generation of a signal involved in cell-cell signaling0.0394816897354447
GO:0006836neurotransmitter transport0.0399850147348268



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
bile duct9.07e-186
digestive system duct9.07e-186
biliary system2.45e-129
biliary tree2.45e-129
biliary bud2.45e-129
female gonad5.28e-0913
Disease
Ontology termp-valuen
cystadenocarcinoma9.37e-991
mucinous cystadenocarcinoma9.37e-991


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
NR3C1#290844.278006666049440.01156838455163820.0422873023061334



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.