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Coexpression cluster:C1477: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;6:4.90738921487932:7.15746523583771e-05:0.00112747890160732!E2F6#1876;6:5.01715573169739:6.26776799983417e-05:0.00102489341182821!EGR1#1958;6:4.98817909481014:6.48943962979974e-05:0.00105535749843764!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380472869247424!ZBTB7A#51341;6:7.3519093078759:6.32958528301959e-06:0.000186791624010535
|tf_chipseq_enrich=E2F1#1869;6:4.90738921487932:7.15746523583771e-05:0.00112747890160732!E2F6#1876;6:5.01715573169739:6.26776799983417e-05:0.00102489341182821!EGR1#1958;6:4.98817909481014:6.48943962979974e-05:0.00105535749843764!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380472869247424!ZBTB7A#51341;6:7.3519093078759:6.32958528301959e-06:0.000186791624010535
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}}
}}

Revision as of 14:55, 26 November 2012


Full id: C1477_hairy_acute_B_carcinosarcoma_merkel_peripheral_b



Phase1 CAGE Peaks

Hg19::chr1:3568870..3568881,+p5@TP73
Hg19::chr1:3568911..3568925,+p9@TP73
Hg19::chr1:3568928..3568946,+p4@TP73
Hg19::chr1:3568961..3568973,+p6@TP73
Hg19::chr1:3569101..3569115,+p2@TP73
Hg19::chr1:3569135..3569150,+p3@TP73


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
lymphocyte of B lineage6.88e-0724
pro-B cell6.88e-0724
Uber Anatomy
Ontology termp-valuen
foregut1.07e-0887
subdivision of digestive tract2.11e-08118
digestive system7.47e-07145
digestive tract7.47e-07145
primitive gut7.47e-07145
Disease
Ontology termp-valuen
disease of cellular proliferation9.27e-41239
cancer2.64e-40235
cell type cancer1.85e-25143
carcinoma1.80e-23106
organ system cancer3.42e-21137
disease of anatomical entity9.28e-1139
hematologic cancer5.53e-1051
immune system cancer5.53e-1051
lymphoma6.66e-1010


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
E2F1#186964.907389214879327.15746523583771e-050.00112747890160732
E2F6#187665.017155731697396.26776799983417e-050.00102489341182821
EGR1#195864.988179094810146.48943962979974e-050.00105535749843764
POLR2A#543062.147453176558070.01019570676818780.0380472869247424
ZBTB7A#5134167.35190930787596.32958528301959e-060.000186791624010535



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.