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Coexpression cluster:C2630: Difference between revisions

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|tf_chipseq_enrich=E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00997681656524783!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101516813756511!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.00142531332413321!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00888428329639242!SUZ12#23512;4:50.1157809110629:1.5827390373096e-07:8.82539681353859e-06!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322620634494329!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00508413432353775!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249235469315124
|tf_chipseq_enrich=E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00997681656524783!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101516813756511!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.00142531332413321!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00888428329639242!SUZ12#23512;4:50.1157809110629:1.5827390373096e-07:8.82539681353859e-06!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322620634494329!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00508413432353775!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249235469315124
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}}
}}

Revision as of 15:37, 26 November 2012


Full id: C2630_extraskeletal_Fibroblast_Smooth_Aortic_mesothelioma_prostate_small



Phase1 CAGE Peaks

Hg19::chr21:38071403..38071428,+p2@SIM2
Hg19::chr21:38071430..38071456,+p1@SIM2
Hg19::chr21:38071462..38071474,+p3@SIM2
Hg19::chr21:38071488..38071502,+p4@SIM2


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 cell4.31e-18253
kidney tubule cell5.69e-0710
nephron tubule epithelial cell5.69e-0710
Uber Anatomy
Ontology termp-valuen
multi-tissue structure1.41e-11342
trunk5.60e-11199
trunk region element1.40e-09101
mesenchyme2.91e-09160
entire embryonic mesenchyme2.91e-09160
organism subdivision3.32e-09264
segment of respiratory tract1.50e-0747
larynx1.53e-079
kidney2.58e-0726
kidney mesenchyme2.58e-0726
upper urinary tract2.58e-0726
kidney rudiment2.58e-0726
kidney field2.58e-0726
nephron tubule epithelium5.69e-0710
digestive system9.08e-07145
digestive tract9.08e-07145
primitive gut9.08e-07145
Disease
Ontology termp-valuen
cell type cancer7.98e-37143
carcinoma2.20e-34106
cancer3.07e-28235
disease of cellular proliferation1.18e-26239
adenocarcinoma1.68e-1325
squamous cell carcinoma7.52e-0814
gastrointestinal system cancer6.44e-0714


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
E2F6#187645.017155731697390.00157802193473060.00997681656524783
EGR1#195844.988179094810140.001615011500076050.0101516813756511
MXI1#460149.96157162875930.0001015224754950450.00142531332413321
MYC#460945.22228187160940.001344309395272740.00888428329639242
SUZ12#23512450.11578091106291.5827390373096e-078.82539681353859e-06
TAF1#687243.343046285745290.008005664898701650.0322620634494329
USF1#739146.361499277207960.0006105011399140830.00508413432353775
ZNF263#1012748.221841637010680.0002187871180958320.00249235469315124



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.

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