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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1571_renal_parietal_insula_occipital_temporal_duodenum_mesothelioma
|full_id=C1571_renal_parietal_insula_occipital_temporal_duodenum_mesothelioma
|id=C1571
|id=C1571

Revision as of 14:09, 12 September 2012


Full id: C1571_renal_parietal_insula_occipital_temporal_duodenum_mesothelioma



Phase1 CAGE Peaks

Hg19::chr10:14278992..14278993,-p@chr10:14278992..14278993
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Hg19::chr10:14283679..14283683,-p@chr10:14283679..14283683
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Hg19::chr10:14302020..14302023,-p@chr10:14302020..14302023
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Hg19::chr10:14372855..14372869,-p10@FRMD4A
Hg19::chr10:14372870..14372944,-p2@FRMD4A


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
mesothelial cell1.14e-1019
Uber Anatomy
Ontology termp-valuen
neural tube7.24e-4457
neural rod7.24e-4457
future spinal cord7.24e-4457
neural keel7.24e-4457
central nervous system6.03e-4382
regional part of brain1.79e-3759
regional part of nervous system1.01e-3694
nervous system1.01e-3694
neural plate8.48e-3686
presumptive neural plate8.48e-3686
regional part of forebrain2.37e-3541
forebrain2.37e-3541
future forebrain2.37e-3541
neurectoderm2.61e-3490
anterior neural tube3.66e-3442
brain9.10e-3469
future brain9.10e-3469
gray matter9.91e-3434
brain grey matter9.91e-3434
telencephalon1.12e-3334
regional part of telencephalon1.68e-3233
cerebral hemisphere3.08e-3232
regional part of cerebral cortex1.25e-2722
adult organism1.33e-27115
pre-chordal neural plate4.19e-2661
neocortex2.39e-2520
cerebral cortex5.52e-2525
pallium5.52e-2525
anterior region of body2.23e-20129
craniocervical region2.23e-20129
head7.32e-20123
ectoderm-derived structure1.08e-19169
ectoderm2.71e-19173
presumptive ectoderm2.71e-19173
tube1.27e-12194
posterior neural tube1.21e-1015
chordal neural plate1.21e-1015
basal ganglion1.79e-109
nuclear complex of neuraxis1.79e-109
aggregate regional part of brain1.79e-109
collection of basal ganglia1.79e-109
cerebral subcortex1.79e-109
temporal lobe1.98e-107
nucleus of brain4.10e-109
neural nucleus4.10e-109
segmental subdivision of nervous system9.78e-0913
gyrus1.84e-086
organ part2.16e-08219
anatomical conduit3.42e-08241
telencephalic nucleus3.64e-087
segmental subdivision of hindbrain5.56e-0812
hindbrain5.56e-0812
presumptive hindbrain5.56e-0812
anatomical cluster1.41e-07286
epithelium1.79e-07309
occipital lobe2.18e-075
limbic system2.50e-075
parietal lobe2.90e-075
cell layer3.44e-07312
organ7.76e-07511
Disease
Ontology termp-valuen
ovarian cancer6.17e-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

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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