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Coexpression cluster:C4093: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4093_pancreas_breast_MCF7_salivary_Mast_parotid_submaxillary
|full_id=C4093_pancreas_breast_MCF7_salivary_Mast_parotid_submaxillary
|id=C4093
|id=C4093

Revision as of 17:08, 12 September 2012


Full id: C4093_pancreas_breast_MCF7_salivary_Mast_parotid_submaxillary



Phase1 CAGE Peaks

Hg19::chr22:29196433..29196445,-p4@XBP1
Hg19::chr22:29196492..29196503,-p3@XBP1
Hg19::chr22:29196547..29196563,-p2@XBP1


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><br>

Cell Type
Ontology termp-valuen
mesenchymal cell1.54e-07358
CD14-positive, CD16-negative classical monocyte8.36e-0742
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.35e-07169
endoderm3.35e-07169
presumptive endoderm3.35e-07169
subdivision of digestive tract5.16e-07129
endodermal part of digestive tract5.16e-07129
mesoderm9.04e-07448
mesoderm-derived structure9.04e-07448
presumptive mesoderm9.04e-07448


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
CCNT2#90536.336201576962630.003930750035764890.0190374514461718
CHD2#1106310.34402283411690.0009033701102746880.00661295794119143
E2F1#186934.907389214879320.008460985347239390.0326000460665659
FOS#235338.99795530889440.001372499272417130.00898811459192203
GATA1#2623313.56030814380040.0004009615963782630.00388352296801905
GTF2B#2959331.94382993432423.06634405746243e-050.000628549375892677
GTF2F1#2962312.73966087675770.0004835525047438590.00434722734294085
HNF4A#3172323.13229036295378.07584663437677e-050.00122967392717258
MYC#460935.22228187160940.007020843755740150.0295046636490321
NFKB1#479035.488063424193840.006049381815655430.0270019398002068
NFYA#4800318.42558069983050.0001598135507814160.00199937319478442
NFYB#4801316.75979325353650.0002123649923296180.00246243892904552
PAX5#507936.669565531177830.003370290999677260.0173189245087234
REST#597839.650028716128020.001112636247114590.0076899356106413
RFX5#5993312.04791082719510.0005717246050312580.00485410503413215
SP1#666735.69838137814090.005403962701712170.0246995387572918
SP2#6668326.15353049384465.58768218891694e-050.000941245064723058
TAF7#6879311.43306940492390.0006690181981945830.00544044161031255
USF1#739136.361499277207960.00388404057290560.0190676559835333
YY1#752834.911170749853860.008441455341808260.0329995940426379



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:C4093&oldid=2138955"