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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3830_CD4_Hep2_serous_testicular_meningioma_hairy_mesothelioma
|full_id=C3830_CD4_Hep2_serous_testicular_meningioma_hairy_mesothelioma
|id=C3830
|id=C3830

Revision as of 16:48, 12 September 2012


Full id: C3830_CD4_Hep2_serous_testicular_meningioma_hairy_mesothelioma



Phase1 CAGE Peaks

Hg19::chr19:6590873..6590879,-p8@CD70
Hg19::chr19:6590884..6590916,-p3@CD70
Hg19::chr19:6590918..6590923,-p9@CD70


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
lymphocyte1.26e-2353
common lymphoid progenitor1.26e-2353
lymphoid lineage restricted progenitor cell7.44e-2352
lymphocyte of B lineage2.99e-1624
pro-B cell2.99e-1624
B cell4.97e-0914
T cell6.41e-0825
pro-T cell6.41e-0825
mature alpha-beta T cell2.52e-0718
alpha-beta T cell2.52e-0718
immature T cell2.52e-0718
mature T cell2.52e-0718
immature alpha-beta T cell2.52e-0718
Uber Anatomy
Ontology termp-valuen
larynx1.40e-099
upper respiratory tract3.97e-0919
Disease
Ontology termp-valuen
disease of cellular proliferation9.01e-10239
cancer1.41e-09235


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
BCL3#602334.54710280373832.42397750207122e-050.00052708262822989
CTCF#1066435.360256373075030.0064925092527670.0279455643690131
EBF1#187938.9064668465690.00141523283560980.00915147681990294
EGR1#195834.988179094810140.008056488137383440.0320659895038182
ELF1#199734.258097958807540.01295179875054610.0462325828733435
MAX#414936.452555509007120.003721913834265510.0186522533079105
NFKB1#479035.488063424193840.006049381815655430.0269627597919613
PAX5#507936.669565531177830.003370290999677260.0172916988463005
PBX3#5090321.91451268674419.49854535978121e-050.0013664167752482
POU2F2#545239.106124057742520.001324165192682130.0088231777822208
SRF#6722313.79717826216780.0003806615025800190.00375126501867849
TCF12#6938310.63446490218640.0008313523990202070.00629353531467609
USF1#739136.361499277207960.00388404057290560.0190283006564259
ZEB1#6935316.88843201754390.0002075486917327580.00242788730016549



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.