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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C484_squamous_pharyngeal_bile_transitionalcell_Prostate_signet_trachea
|full_id=C484_squamous_pharyngeal_bile_transitionalcell_Prostate_signet_trachea
|id=C484
|id=C484

Revision as of 18:00, 12 September 2012


Full id: C484_squamous_pharyngeal_bile_transitionalcell_Prostate_signet_trachea



Phase1 CAGE Peaks

Hg19::chr9:130911723..130911741,+p1@LCN2
Hg19::chr9:130911770..130911779,+p2@LCN2
Hg19::chr9:130911904..130911915,-p@chr9:130911904..130911915
-
Hg19::chr9:130912519..130912545,+p@chr9:130912519..130912545
+
Hg19::chr9:130912567..130912578,-p@chr9:130912567..130912578
-
Hg19::chr9:130912602..130912627,+p@chr9:130912602..130912627
+
Hg19::chr9:130912603..130912639,-p@chr9:130912603..130912639
-
Hg19::chr9:130912628..130912633,+p@chr9:130912628..130912633
+
Hg19::chr9:130913926..130913932,+p4@LCN2
Hg19::chr9:130913939..130913973,+p3@LCN2
Hg19::chr9:130913945..130913957,-p@chr9:130913945..130913957
-
Hg19::chr9:130914190..130914206,+p@chr9:130914190..130914206
+
Hg19::chr9:130914212..130914239,+p@chr9:130914212..130914239
+
Hg19::chr9:130914227..130914253,-p@chr9:130914227..130914253
-
Hg19::chr9:130914276..130914284,+p@chr9:130914276..130914284
+
Hg19::chr9:130914283..130914293,-p@chr9:130914283..130914293
-
Hg19::chr9:130914494..130914509,+p@chr9:130914494..130914509
+
Hg19::chr9:130914521..130914530,+p@chr9:130914521..130914530
+
Hg19::chr9:130915632..130915647,+p@chr9:130915632..130915647
+
Hg19::chr9:130915665..130915685,-p@chr9:130915665..130915685
-


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 cell4.83e-18254
endodermal cell2.06e-1659
endo-epithelial cell3.65e-1643
respiratory epithelial cell4.97e-0813
epithelial cell of alimentary canal2.80e-0721
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure6.03e-23169
endoderm6.03e-23169
presumptive endoderm6.03e-23169
adult organism6.03e-21115
digestive system3.82e-19155
digestive tract3.82e-19155
primitive gut3.82e-19155
subdivision of digestive tract3.45e-17129
endodermal part of digestive tract3.45e-17129
mixed endoderm/mesoderm-derived structure3.42e-16130
foregut5.49e-1498
immaterial anatomical entity7.91e-12126
respiratory system9.95e-1272
organ1.79e-11511
trunk region element2.27e-10107
anatomical space2.54e-10104
endo-epithelium1.20e-0982
anatomical system5.40e-09625
multi-tissue structure5.91e-09347
anatomical group7.74e-09626
embryo1.27e-08612
embryonic structure1.55e-08605
developing anatomical structure1.55e-08605
germ layer2.80e-08604
embryonic tissue2.80e-08604
presumptive structure2.80e-08604
epiblast (generic)2.80e-08604
respiratory tract3.07e-0853
multi-cellular organism5.61e-08659
orifice5.73e-0835
primordium6.14e-07168
mesenchyme7.45e-07238
entire embryonic mesenchyme7.45e-07238
organ part7.68e-07219
anatomical cavity8.04e-0770
gland9.80e-0759
Disease
Ontology termp-valuen
carcinoma7.27e-13106
adenocarcinoma1.10e-0825
squamous cell carcinoma1.29e-0814


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
GATA1#262353.390077035950110.01323321252295330.0468178686546316
TAL1#688657.467154169360050.000427161752698430.00399072781913153



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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