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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1873_skeletal_MCF7_serous_left_brain_heart_tongue
|full_id=C1873_skeletal_MCF7_serous_left_brain_heart_tongue
|id=C1873
|id=C1873

Revision as of 14:30, 12 September 2012


Full id: C1873_skeletal_MCF7_serous_left_brain_heart_tongue



Phase1 CAGE Peaks

Hg19::chr20:62127314..62127345,-p6@EEF1A2
Hg19::chr20:62128967..62129009,+p@chr20:62128967..62129009
+
Hg19::chr20:62129099..62129111,-p10@EEF1A2
Hg19::chr20:62129135..62129160,-p7@EEF1A2
Hg19::chr20:62130428..62130472,-p1@EEF1A2


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
regional part of nervous system8.38e-2594
nervous system8.38e-2594
neural tube1.13e-2457
neural rod1.13e-2457
future spinal cord1.13e-2457
neural keel1.13e-2457
central nervous system1.25e-2482
neurectoderm1.11e-2290
adult organism3.15e-22115
neural plate6.80e-2286
presumptive neural plate6.80e-2286
regional part of forebrain1.15e-2041
forebrain1.15e-2041
future forebrain1.15e-2041
brain1.72e-2069
future brain1.72e-2069
anterior neural tube1.76e-1942
regional part of brain1.47e-1859
gray matter9.66e-1834
brain grey matter9.66e-1834
telencephalon1.45e-1734
cerebral hemisphere3.91e-1732
regional part of telencephalon5.33e-1733
tube1.36e-16194
pre-chordal neural plate4.41e-1561
anatomical conduit7.30e-15241
ectoderm5.78e-14173
presumptive ectoderm5.78e-14173
regional part of cerebral cortex7.50e-1422
cerebral cortex8.29e-1425
pallium8.29e-1425
ectoderm-derived structure3.04e-13169
neocortex5.79e-1320
epithelium9.43e-12309
cell layer2.22e-11312
head6.66e-11123
anatomical cluster8.76e-11286
anterior region of body9.73e-11129
craniocervical region9.73e-11129
multi-tissue structure2.15e-09347
organ part6.03e-09219
organism subdivision1.08e-08365
multi-cellular organism2.89e-08659
embryo4.77e-08612
organ1.21e-07511
anatomical system1.29e-07625
anatomical group2.03e-07626
Disease
Ontology termp-valuen
cell type cancer3.29e-15143
carcinoma5.17e-12106
cancer1.42e-08235
disease of cellular proliferation6.28e-08239


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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