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Coexpression cluster:C4266: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326494309506867!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323329997503036!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187034094662395!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00721613305953624!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295331843485478!PRDM1#639;3:131.830955777461:4.35536935195671e-07:2.08369408955111e-05!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00615768566099476!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330280281138543!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140584842343134
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326494309506867!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323329997503036!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187034094662395!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00721613305953624!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295331843485478!PRDM1#639;3:131.830955777461:4.35536935195671e-07:2.08369408955111e-05!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00615768566099476!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330280281138543!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140584842343134
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}}
}}

Revision as of 16:38, 26 November 2012


Full id: C4266_immature_thyroid_Small_smallcell_Renal_chorionic_pancreas



Phase1 CAGE Peaks

Hg19::chr3:111805212..111805258,+p1@C3orf52
Hg19::chr3:111805262..111805289,+p2@C3orf52
Hg19::chr3:111805316..111805323,+p4@C3orf52


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 cell3.13e-22253
endo-epithelial cell1.95e-1242
endodermal cell3.33e-0858
epithelial cell of alimentary canal3.67e-0720
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.06e-11160
endoderm1.06e-11160
presumptive endoderm1.06e-11160
digestive system1.23e-09145
digestive tract1.23e-09145
primitive gut1.23e-09145
reproductive structure3.08e-0959
reproductive system3.08e-0959
anatomical space4.22e-0995
subdivision of digestive tract9.04e-09118
female organism2.19e-0841
epithelial bud1.13e-0737
organism subdivision1.42e-07264
reproductive organ1.93e-0748
organ3.06e-07503
endo-epithelium3.07e-0782
female reproductive organ4.09e-0737
female reproductive system4.09e-0737
respiratory tract5.51e-0754
respiratory system5.78e-0774
body cavity7.91e-0746
trunk8.79e-07199
Disease
Ontology termp-valuen
carcinoma5.66e-19106
cell type cancer1.90e-13143
reproductive organ cancer3.38e-0929
disease of cellular proliferation3.80e-09239
squamous cell carcinoma8.01e-0914
female reproductive organ cancer8.40e-0927
cancer3.89e-08235


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#186934.907389214879320.008460985347239390.0326494309506867
E2F6#187635.017155731697390.00791769806886330.0323329997503036
MAX#414936.452555509007120.003721913834265510.0187034094662395
MXI1#460139.96157162875930.001011470541259020.00721613305953624
MYC#460935.22228187160940.007020843755740150.0295331843485478
PRDM1#6393131.8309557774614.35536935195671e-072.08369408955111e-05
TCF7L2#6934310.77017656313730.0008003181298398380.00615768566099476
YY1#752834.911170749853860.008441455341808260.0330280281138543
ZBTB7A#5134137.35190930787590.002516255860282270.0140584842343134



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.