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Coexpression cluster:C2275: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106340167127633!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00995692561873665!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101327758053853!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0185703515303345!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00886409046864634!NRF1#4899;4:12.2102794477109:4.49717228915276e-05:0.000792709158998861!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321578321675193!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0243731395725165!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00507280838185114!USF2#7392;4:12.9921973850696:3.50833029870167e-05:0.000680547006066314
|tf_chipseq_enrich=E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106340167127633!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00995692561873665!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101327758053853!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0185703515303345!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00886409046864634!NRF1#4899;4:12.2102794477109:4.49717228915276e-05:0.000792709158998861!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321578321675193!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0243731395725165!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00507280838185114!USF2#7392;4:12.9921973850696:3.50833029870167e-05:0.000680547006066314
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}}
}}

Revision as of 15:24, 26 November 2012


Full id: C2275_MCF7_breast_Hepatocyte_pancreatic_liver_parietal_temporal



Phase1 CAGE Peaks

Hg19::chr14:100437780..100437791,+p10@EVL
Hg19::chr14:100437793..100437811,+p8@EVL
Hg19::chr14:100437825..100437840,+p9@EVL
Hg19::chr14:100437931..100437940,+p17@EVL


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neural tube4.72e-1856
neural rod4.72e-1856
future spinal cord4.72e-1856
neural keel4.72e-1856
regional part of nervous system2.76e-1753
regional part of brain2.76e-1753
neural plate4.86e-1682
presumptive neural plate4.86e-1682
central nervous system5.19e-1681
nervous system9.62e-1689
neurectoderm1.86e-1586
brain7.81e-1568
future brain7.81e-1568
regional part of forebrain1.00e-1441
forebrain1.00e-1441
anterior neural tube1.00e-1441
future forebrain1.00e-1441
tube1.05e-14192
structure with developmental contribution from neural crest7.75e-14132
anatomical conduit1.65e-13240
pre-chordal neural plate5.27e-1361
telencephalon9.99e-1334
anatomical cluster2.08e-12373
cerebral hemisphere2.92e-1232
brain grey matter2.95e-1234
gray matter2.95e-1234
ectoderm-derived structure3.60e-12171
ectoderm3.60e-12171
presumptive ectoderm3.60e-12171
regional part of telencephalon4.69e-1232
ecto-epithelium7.94e-12104
cell layer8.27e-12309
epithelium1.71e-11306
regional part of cerebral cortex8.99e-1122
neocortex1.02e-1020
cerebral cortex1.44e-1025
pallium1.44e-1025
adult organism1.77e-10114
multi-tissue structure6.52e-10342
organ system subdivision1.51e-07223


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#186944.907389214879320.001724022357361790.0106340167127633
E2F6#187645.017155731697390.00157802193473060.00995692561873665
EGR1#195844.988179094810140.001615011500076050.0101327758053853
HEY1#2346244.040111043105710.00375304636917980.0185703515303345
MYC#460945.22228187160940.001344309395272740.00886409046864634
NRF1#4899412.21027944771094.49717228915276e-050.000792709158998861
TAF1#687243.343046285745290.008005664898701650.0321578321675193
TBP#690843.706770687096390.005296377814784350.0243731395725165
USF1#739146.361499277207960.0006105011399140830.00507280838185114
USF2#7392412.99219738506963.50833029870167e-050.000680547006066314



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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