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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3934_glassy_epidermoid_oral_ductal_malignant_squamous_acantholytic
|full_id=C3934_glassy_epidermoid_oral_ductal_malignant_squamous_acantholytic
|id=C3934
|id=C3934

Revision as of 16:56, 12 September 2012


Full id: C3934_glassy_epidermoid_oral_ductal_malignant_squamous_acantholytic



Phase1 CAGE Peaks

Hg19::chr1:209944599..209944616,-p@chr1:209944599..209944616
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Hg19::chr1:209945462..209945477,-p@chr1:209945462..209945477
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Hg19::chr1:209945709..209945715,-p@chr1:209945709..209945715
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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 cell of alimentary canal7.37e-0921
endo-epithelial cell1.02e-0843
endodermal cell1.20e-0759
Uber Anatomy
Ontology termp-valuen
neural tube3.83e-2157
neural rod3.83e-2157
future spinal cord3.83e-2157
neural keel3.83e-2157
regional part of forebrain2.05e-1841
forebrain2.05e-1841
future forebrain2.05e-1841
anterior neural tube1.06e-1742
regional part of brain1.57e-1759
telencephalon2.36e-1634
central nervous system2.72e-1682
gray matter2.80e-1634
brain grey matter2.80e-1634
brain6.86e-1669
future brain6.86e-1669
neurectoderm7.34e-1690
ectoderm7.87e-16173
presumptive ectoderm7.87e-16173
regional part of telencephalon1.40e-1533
cerebral hemisphere1.01e-1432
regional part of nervous system2.40e-1494
nervous system2.40e-1494
ectoderm-derived structure3.34e-14169
neural plate6.13e-1486
presumptive neural plate6.13e-1486
anterior region of body6.14e-14129
craniocervical region6.14e-14129
head8.34e-14123
adult organism6.54e-13115
pre-chordal neural plate1.11e-1161
regional part of cerebral cortex2.08e-1022
cerebral cortex1.23e-0925
pallium1.23e-0925
basal ganglion3.72e-099
nuclear complex of neuraxis3.72e-099
aggregate regional part of brain3.72e-099
collection of basal ganglia3.72e-099
cerebral subcortex3.72e-099
nucleus of brain6.29e-099
neural nucleus6.29e-099
neocortex7.81e-0920
telencephalic nucleus2.58e-077
mucosa2.82e-0712
Disease
Ontology termp-valuen
squamous cell carcinoma1.91e-1414
carcinoma6.72e-10106
cell type cancer4.68e-09143
cancer8.70e-08235
disease of cellular proliferation3.40e-07239


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

No analysis results for this cluster

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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