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{{Coexpression_clusters
 
{{Coexpression_clusters
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|full_id=C3971_Mast_breast_lung_Wilms_salivary_mesothelioma_oral
 
|full_id=C3971_Mast_breast_lung_Wilms_salivary_mesothelioma_oral
 
|id=C3971
 
|id=C3971

Revision as of 07:58, 12 September 2012


Full id: C3971_Mast_breast_lung_Wilms_salivary_mesothelioma_oral



Phase1 CAGE Peaks

Hg19::chr1:33219558..33219569,+p5@KIAA1522
Hg19::chr1:33219575..33219586,+p4@KIAA1522
Hg19::chr1:33219592..33219626,+p1@KIAA1522


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 cell9.93e-20254
endo-epithelial cell2.67e-1043
respiratory epithelial cell5.14e-0713
squamous epithelial cell7.81e-0762
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure1.82e-18169
ectoderm2.69e-18173
presumptive ectoderm2.69e-18173
anterior region of body2.45e-15129
craniocervical region2.45e-15129
head3.23e-15123
neural plate1.36e-1386
presumptive neural plate1.36e-1386
central nervous system1.48e-1382
anatomical space2.16e-13104
pre-chordal neural plate2.87e-1361
neurectoderm2.94e-1390
regional part of nervous system1.53e-1294
nervous system1.53e-1294
organism subdivision5.42e-12365
neural tube5.95e-1257
neural rod5.95e-1257
future spinal cord5.95e-1257
neural keel5.95e-1257
brain7.33e-1269
future brain7.33e-1269
regional part of brain2.11e-1159
cerebral hemisphere3.45e-1132
anterior neural tube5.61e-1142
regional part of forebrain8.82e-1141
forebrain8.82e-1141
future forebrain8.82e-1141
telencephalon1.32e-1034
organ part1.49e-10219
gray matter2.09e-1034
brain grey matter2.09e-1034
regional part of telencephalon3.42e-1033
regional part of cerebral cortex5.59e-1022
immaterial anatomical entity9.55e-10126
multi-tissue structure1.04e-09347
cerebral cortex1.34e-0925
pallium1.34e-0925
adult organism1.53e-09115
organ1.88e-09511
neocortex1.94e-0920
anatomical cavity2.60e-0870
endoderm-derived structure7.65e-08169
endoderm7.65e-08169
presumptive endoderm7.65e-08169
reproductive structure1.12e-0759
reproductive system1.12e-0759
cell layer1.91e-07312
epithelium2.15e-07309
embryo2.64e-07612
reproductive organ2.98e-0748
trunk region element9.18e-07107
Disease
Ontology termp-valuen
cell type cancer2.36e-10143
carcinoma1.13e-09106
adenocarcinoma6.31e-0825
squamous cell carcinoma9.15e-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
CCNT2#90536.336201576962630.003930750035764890.0190224550755409
E2F1#186934.907389214879320.008460985347239390.0325664055679345
EGR1#195834.988179094810140.008056488137383440.0320941207834683
HMGN3#932438.178547723350590.001827766942164210.0108812718276628
IRF1#365937.63716375356390.002244692747297240.0128203798444152
MYC#460935.22228187160940.007020843755740150.0294809384450686
NFYB#4801316.75979325353650.0002123649923296180.00246079967091013
SP1#666735.69838137814090.005403962701712170.0246790179108888
TAF7#6879311.43306940492390.0006690181981945830.00543663177725211
USF1#739136.361499277207960.00388404057290560.0190470635955152
USF2#7392312.99219738506960.0004558979393427810.00421956087265338
ZBTB7A#5134137.35190930787590.002516255860282270.0140352085981638



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.