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Coexpression cluster:C2268: Difference between revisions

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|full_id=C2268_cholangiocellular_testis_bronchioalveolar_gall_squamous_chronic_gastric
|full_id=C2268_cholangiocellular_testis_bronchioalveolar_gall_squamous_chronic_gastric
|id=C2268
|id=C2268
|ontology_enrichment_celltype=CL:0000054!2.39e-08!2;CL:0000137!2.39e-08!2;CL:0000092!2.39e-08!2
|ontology_enrichment_celltype=CL:1000415!5.49e-09!2;CL:0000054!6.42e-09!2;CL:0000137!6.42e-09!2;CL:0000092!6.42e-09!2
|ontology_enrichment_disease=DOID:1036!3.91e-11!8;DOID:200!2.39e-08!2;DOID:4305!2.39e-08!2
|ontology_enrichment_disease=DOID:1036!1.69e-30!8;DOID:3910!4.02e-09!2;DOID:200!6.42e-09!2;DOID:4305!6.42e-09!2;DOID:8692!4.03e-08!31;DOID:2531!1.91e-07!51;DOID:0060083!1.91e-07!51
|ontology_enrichment_uberon=UBERON:0003135!3.91e-08!11;UBERON:0000473!1.40e-07!8
|ontology_enrichment_uberon=UBERON:0000473!7.02e-18!8;UBERON:0001282!4.72e-17!1;UBERON:0009842!4.72e-17!1;UBERON:0003704!4.72e-17!1;UBERON:0001171!4.72e-17!1;UBERON:0001172!4.72e-17!1;UBERON:0003135!3.48e-13!11;UBERON:0004903!4.02e-09!2;UBERON:0002173!4.02e-09!2;UBERON:0002186!4.02e-09!2;UBERON:0002294!7.77e-08!9;UBERON:0001173!7.77e-08!9;UBERON:0004912!7.77e-08!9;UBERON:0000991!3.57e-07!21;UBERON:0009196!3.57e-07!21;UBERON:0009117!3.57e-07!21;UBERON:0005564!3.57e-07!21;UBERON:0004176!7.18e-07!22;UBERON:0003101!7.18e-07!22;UBERON:0000079!7.18e-07!22
|tf_chipseq_enrich=CHD2#1106;3:7.75801712558764:0.00335152246453634:0.0172922465504254!GABPB1#2553;3:5.30076287713663:0.0101267882423427:0.0378469005991065!ZBTB33#10009;3:23.7485437724859:0.000122945190881838:0.00165467432867375
|tf_chipseq_enrich=CHD2#1106;3:7.75801712558764:0.00335152246453634:0.0172922465504254!GABPB1#2553;3:5.30076287713663:0.0101267882423427:0.0378469005991065!ZBTB33#10009;3:23.7485437724859:0.000122945190881838:0.00165467432867375
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}}
}}

Revision as of 13:48, 19 October 2012


Full id: C2268_cholangiocellular_testis_bronchioalveolar_gall_squamous_chronic_gastric



Phase1 CAGE Peaks

Hg19::chr13:64385967..64385986,-p1@PPP1R2P10
Hg19::chrX:147062844..147062871,+p1@FMR1NB
Hg19::chrX:147062877..147062885,+p2@FMR1NB
Hg19::chrX:147062891..147062896,+p3@FMR1NB


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

Cell Type
Ontology termp-valuen
epithelial cell of gall bladder5.49e-092
bone matrix secreting cell6.42e-092
osteocyte6.42e-092
osteoclast6.42e-092
Uber Anatomy
Ontology termp-valuen
testis7.02e-188
intralobular bile duct4.72e-171
acinus4.72e-171
intrahepatic bile duct4.72e-171
portal lobule4.72e-171
hepatic acinus4.72e-171
male reproductive organ3.48e-1311
bronchoalveolar duct junction4.02e-092
alveolar duct4.02e-092
bronchiole4.02e-092
biliary system7.77e-089
biliary tree7.77e-089
biliary bud7.77e-089
gonad3.57e-0721
indifferent external genitalia3.57e-0721
indifferent gonad3.57e-0721
gonad primordium3.57e-0721
external genitalia7.18e-0722
male organism7.18e-0722
male reproductive system7.18e-0722
Disease
Ontology termp-valuen
chronic leukemia1.69e-308
lung adenocarcinoma4.02e-092
giant cell tumor6.42e-092
bone giant cell tumor6.42e-092
myeloid leukemia4.03e-0831
hematologic cancer1.91e-0751
immune system cancer1.91e-0751


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

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

TF#promotersEnrichmentp-valueq-value
CHD2#110637.758017125587640.003351522464536340.0172922465504254
GABPB1#255335.300762877136630.01012678824234270.0378469005991065
ZBTB33#10009323.74854377248590.0001229451908818380.00165467432867375



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:C2268&oldid=2248366"