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Coexpression cluster:C3426: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278835090817392!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.0017142942337264!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293805305527806!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00483758778456287!SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000221795941383583
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278835090817392!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.0017142942337264!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293805305527806!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00483758778456287!SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000221795941383583
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}}
}}

Revision as of 16:07, 26 November 2012


Full id: C3426_bronchioalveolar_anaplastic_astrocytoma_small_somatostatinoma_large_prostate



Phase1 CAGE Peaks

Hg19::chr14:36989892..36989908,-p9@NKX2-1
Hg19::chr14:36989913..36989931,-p6@NKX2-1
Hg19::chr14:36989940..36989957,-p2@NKX2-1


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
respiratory tract3.02e-1954
respiratory primordium2.86e-1838
endoderm of foregut2.86e-1838
respiratory system1.96e-1674
telencephalic nucleus6.34e-127
larynx2.54e-119
segment of respiratory tract2.88e-1047
endoderm-derived structure4.98e-10160
endoderm4.98e-10160
presumptive endoderm4.98e-10160
lung5.70e-1022
respiratory tube5.70e-1022
respiration organ5.70e-1022
pair of lungs5.70e-1022
lung primordium5.70e-1022
lung bud5.70e-1022
corpus striatum6.76e-104
striatum6.76e-104
ventral part of telencephalon6.76e-104
future corpus striatum6.76e-104
basal ganglion4.16e-099
neural nucleus4.16e-099
nuclear complex of neuraxis4.16e-099
nucleus of brain4.16e-099
aggregate regional part of brain4.16e-099
collection of basal ganglia4.16e-099
cerebral subcortex4.16e-099
thyroid gland6.89e-095
pharyngeal pouch6.89e-095
thyroid diverticulum6.89e-095
pharyngeal pouch 26.89e-095
thyroid primordium6.89e-095
digestive system1.15e-08145
digestive tract1.15e-08145
primitive gut1.15e-08145
thoracic cavity element3.38e-0834
thoracic cavity3.38e-0834
caudate-putamen3.93e-083
dorsal striatum3.93e-083
thoracic segment organ6.93e-0835
foregut8.47e-0887
Disease
Ontology termp-valuen
squamous cell carcinoma5.43e-1514
carcinoma2.13e-13106
cell type cancer2.24e-10143
cancer5.04e-10235
disease of cellular proliferation1.38e-09239
respiratory system cancer5.63e-0716
lung carcinoma6.92e-079


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
CTCF#1066435.360256373075030.0064925092527670.0278835090817392
CTCFL#140690319.74647435897440.0001298372005551160.0017142942337264
MYC#460935.22228187160940.007020843755740150.0293805305527806
RFX5#5993312.04791082719510.0005717246050312580.00483758778456287
SUZ12#23512350.11578091106297.93834897779404e-060.000221795941383583



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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