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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4828_large_medial_gastric_papillary_embryonic_hippocampus_endometrioid
|full_id=C4828_large_medial_gastric_papillary_embryonic_hippocampus_endometrioid
|id=C4828
|id=C4828

Revision as of 17:58, 12 September 2012


Full id: C4828_large_medial_gastric_papillary_embryonic_hippocampus_endometrioid



Phase1 CAGE Peaks

Hg19::chr9:74838100..74838111,+p@chr9:74838100..74838111
+
Hg19::chr9:74864446..74864464,+p9@GDA
Hg19::chr9:74865515..74865533,+p7@GDA


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 uterus8.83e-086
stromal cell of endometrium8.83e-086
Uber Anatomy
Ontology termp-valuen
regional part of cerebral cortex2.04e-3022
telencephalon1.86e-2834
cerebral hemisphere2.05e-2832
regional part of telencephalon3.50e-2733
neocortex6.24e-2720
cerebral cortex4.11e-2625
pallium4.11e-2625
regional part of forebrain3.87e-2441
forebrain3.87e-2441
future forebrain3.87e-2441
gray matter3.95e-2434
brain grey matter3.95e-2434
anterior neural tube2.24e-2342
larynx1.11e-169
neural tube2.19e-1657
neural rod2.19e-1657
future spinal cord2.19e-1657
neural keel2.19e-1657
regional part of brain1.47e-1559
pre-chordal neural plate6.87e-1561
brain3.10e-1469
future brain3.10e-1469
adult organism5.28e-14115
central nervous system8.82e-1282
neurectoderm1.03e-1190
temporal lobe2.03e-117
gyrus4.64e-116
regional part of nervous system1.38e-1094
nervous system1.38e-1094
limbic system4.25e-105
neural plate4.67e-1086
presumptive neural plate4.67e-1086
small intestine6.79e-1014
upper respiratory tract1.19e-0919
subdivision of digestive tract2.21e-09129
endodermal part of digestive tract2.21e-09129
digestive system2.45e-09155
digestive tract2.45e-09155
primitive gut2.45e-09155
organ4.32e-09511
organ part5.23e-09219
endoderm-derived structure8.43e-09169
endoderm8.43e-09169
presumptive endoderm8.43e-09169
intestine8.90e-0927
multi-tissue structure1.08e-08347
occipital lobe2.71e-085
viscus1.14e-0718
duodenum1.26e-0712
gastrointestinal system2.82e-0735
middle temporal gyrus8.83e-073
Disease
Ontology termp-valuen
carcinoma6.43e-21106
cell type cancer4.11e-16143
adenocarcinoma1.87e-1425
disease of cellular proliferation3.95e-08239
female reproductive endometrioid cancer8.83e-086
cancer1.23e-07235


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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