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Coexpression cluster:C4801: Difference between revisions

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|tf_chipseq_enrich=CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00663201679649783!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0465315758413582!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157784164642296!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0296406298409631!SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000223831865251574!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00617908073943542
|tf_chipseq_enrich=CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00663201679649783!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0465315758413582!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157784164642296!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0296406298409631!SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000223831865251574!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00617908073943542
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}}
}}

Revision as of 16:58, 26 November 2012


Full id: C4801_Trabecular_Wilms_parotid_MCF7_salivary_breast_submaxillary



Phase1 CAGE Peaks

Hg19::chr9:129376073..129376080,-p2@ENST00000451449
Hg19::chr9:129376201..129376225,+p1@LMX1B
Hg19::chr9:129376233..129376251,+p2@LMX1B


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:0009953dorsal/ventral pattern formation0.0313199105145414
GO:0001701in utero embryonic development0.0313199105145414
GO:0003002regionalization0.0313199105145414
GO:0009792embryonic development ending in birth or egg hatching0.0313199105145414
GO:0043009chordate embryonic development0.0313199105145414
GO:0007389pattern specification process0.0340672710859924
GO:0030182neuron differentiation0.0431885081832097
GO:0009790embryonic development0.0431885081832097
GO:0048699generation of neurons0.0431885081832097
GO:0022008neurogenesis0.0431885081832097



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 cell4.43e-08253
embryonic stem cell2.62e-075
mammary gland epithelial cell2.78e-074
Uber Anatomy
Ontology termp-valuen
cavitated compound organ1.76e-0731
mammary gland2.78e-074
mammary bud2.78e-074
mammary ridge2.78e-074
mammary placode2.78e-074
stroma3.06e-074
Disease
Ontology termp-valuen
cell type cancer9.01e-13143
carcinoma2.41e-10106
cancer1.43e-08235
disease of cellular proliferation4.42e-08239
thoracic cancer9.29e-084
breast cancer9.29e-084
disease of anatomical entity9.87e-0839


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#1106310.34402283411690.0009033701102746880.00663201679649783
ELF1#199734.258097958807540.01295179875054610.0465315758413582
JUND#372736.994663941871030.002921845042734990.0157784164642296
MYC#460935.22228187160940.007020843755740150.0296406298409631
SUZ12#23512350.11578091106297.93834897779404e-060.000223831865251574
TCF7L2#6934310.77017656313730.0008003181298398380.00617908073943542



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.