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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3824_small_colon_heart_skeletal_pancreas_left_salivary
|full_id=C3824_small_colon_heart_skeletal_pancreas_left_salivary
|id=C3824
|id=C3824

Revision as of 16:48, 12 September 2012


Full id: C3824_small_colon_heart_skeletal_pancreas_left_salivary



Phase1 CAGE Peaks

Hg19::chr19:56187987..56188005,+p7@EPN1
Hg19::chr1:16062747..16062758,+p2@SLC25A34
Hg19::chr1:16062768..16062798,+p1@SLC25A34


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><br>

Uber Anatomy
Ontology termp-valuen
adult organism5.42e-51115
neural tube3.59e-2157
neural rod3.59e-2157
future spinal cord3.59e-2157
neural keel3.59e-2157
regional part of forebrain7.61e-2041
forebrain7.61e-2041
future forebrain7.61e-2041
anterior neural tube3.42e-1942
telencephalon1.40e-1734
regional part of brain2.93e-1759
regional part of telencephalon1.00e-1633
gray matter5.47e-1634
brain grey matter5.47e-1634
cerebral hemisphere8.46e-1632
neural plate4.97e-1586
presumptive neural plate4.97e-1586
regional part of cerebral cortex8.42e-1522
neocortex1.88e-1420
brain2.70e-1469
future brain2.70e-1469
neurectoderm6.69e-1490
central nervous system1.39e-1282
cerebral cortex1.48e-1225
pallium1.48e-1225
pre-chordal neural plate4.02e-1261
anterior region of body6.56e-11129
craniocervical region6.56e-11129
regional part of nervous system1.46e-1094
nervous system1.46e-1094
head2.45e-10123
multi-tissue structure3.11e-10347
gyrus1.41e-086
anatomical conduit3.08e-08241
tube4.45e-08194
ectoderm-derived structure7.04e-08169
organism subdivision1.09e-07365
ectoderm1.91e-07173
presumptive ectoderm1.91e-07173
epithelium9.06e-07309


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
RXRA#6256213.38307809275550.007196434429465730.0298296719867825



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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