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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3594_gall_Melanocyte_normal_smooth_Fibroblast_bladder_umbilical
|full_id=C3594_gall_Melanocyte_normal_smooth_Fibroblast_bladder_umbilical
|id=C3594
|id=C3594

Revision as of 16:32, 12 September 2012


Full id: C3594_gall_Melanocyte_normal_smooth_Fibroblast_bladder_umbilical



Phase1 CAGE Peaks

Hg19::chr16:84328580..84328591,+p9@WFDC1
Hg19::chr16:84328606..84328621,+p7@WFDC1
Hg19::chr16:84328632..84328654,+p6@WFDC1


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 organism7.12e-41115
neural tube3.29e-1757
neural rod3.29e-1757
future spinal cord3.29e-1757
neural keel3.29e-1757
neural plate2.75e-1686
presumptive neural plate2.75e-1686
regional part of brain3.19e-1659
neurectoderm2.32e-1590
brain4.09e-1469
future brain4.09e-1469
head4.80e-14123
anterior region of body2.15e-13129
craniocervical region2.15e-13129
central nervous system1.48e-1282
organ part3.73e-12219
regional part of forebrain5.28e-1241
forebrain5.28e-1241
future forebrain5.28e-1241
telencephalon8.06e-1234
gray matter1.71e-1134
brain grey matter1.71e-1134
anterior neural tube1.74e-1142
regional part of telencephalon3.18e-1133
ectoderm-derived structure7.07e-11169
cerebral hemisphere8.03e-1132
pre-chordal neural plate8.07e-1161
ectoderm1.69e-10173
presumptive ectoderm1.69e-10173
multi-tissue structure3.14e-10347
organ3.23e-10511
regional part of nervous system3.59e-1094
nervous system3.59e-1094
neocortex3.99e-0920
regional part of cerebral cortex5.84e-0922
organism subdivision1.50e-08365
larynx3.28e-089
anatomical cluster2.11e-07286
cerebral cortex2.89e-0725
pallium2.89e-0725
posterior neural tube3.13e-0715
chordal neural plate3.13e-0715
segmental subdivision of hindbrain4.01e-0712
hindbrain4.01e-0712
presumptive hindbrain4.01e-0712


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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