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Coexpression cluster:C2275: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2275_MCF7_breast_Hepatocyte_pancreatic_liver_parietal_temporal
|full_id=C2275_MCF7_breast_Hepatocyte_pancreatic_liver_parietal_temporal
|id=C2275
|id=C2275

Revision as of 14:58, 12 September 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
organism subdivision4.45e-19365
neural tube6.15e-1957
neural rod6.15e-1957
future spinal cord6.15e-1957
neural keel6.15e-1957
central nervous system3.45e-1782
regional part of nervous system4.00e-1794
nervous system4.00e-1794
neural plate1.69e-1686
presumptive neural plate1.69e-1686
neurectoderm9.60e-1690
regional part of brain1.04e-1559
anterior neural tube1.29e-1542
brain1.39e-1569
future brain1.39e-1569
tube1.44e-15194
regional part of forebrain4.07e-1541
forebrain4.07e-1541
future forebrain4.07e-1541
anatomical conduit1.32e-14241
pre-chordal neural plate4.81e-1461
ectoderm-derived structure1.10e-13169
head1.93e-13123
telencephalon2.31e-1334
ectoderm2.34e-13173
presumptive ectoderm2.34e-13173
anterior region of body2.39e-13129
craniocervical region2.39e-13129
anatomical cluster2.73e-13286
cerebral hemisphere6.75e-1332
cell layer6.86e-13312
regional part of telencephalon7.06e-1333
gray matter8.26e-1334
brain grey matter8.26e-1334
epithelium1.15e-12309
adult organism3.02e-11115
cerebral cortex7.77e-1125
pallium7.77e-1125
neocortex1.13e-1020
regional part of cerebral cortex1.29e-1022
multi-tissue structure8.03e-10347
organ part4.41e-07219


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.