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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2919_smallcell_Smooth_skeletal_small_Urothelial_pituitary_gastrointestinal
|full_id=C2919_smallcell_Smooth_skeletal_small_Urothelial_pituitary_gastrointestinal
|id=C2919
|id=C2919

Revision as of 15:43, 12 September 2012


Full id: C2919_smallcell_Smooth_skeletal_small_Urothelial_pituitary_gastrointestinal



Phase1 CAGE Peaks

Hg19::chr8:139926246..139926269,-p2@COL22A1
Hg19::chr8:139926277..139926290,-p1@COL22A1
Hg19::chr8:139926293..139926315,-p3@COL22A1
Hg19::chr8:139926319..139926328,-p4@COL22A1


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><br>

Cell Type
Ontology termp-valuen
ectodermal cell2.10e-0871
embryonic cell6.65e-08248
non-terminally differentiated cell7.12e-08180
Uber Anatomy
Ontology termp-valuen
epithelium1.85e-15309
cell layer7.61e-15312
anatomical conduit6.57e-14241
tube3.16e-13194
embryo3.89e-13612
organism subdivision1.31e-12365
multi-cellular organism1.72e-12659
multi-tissue structure2.60e-11347
embryonic structure7.26e-11605
developing anatomical structure7.26e-11605
anatomical group1.09e-10626
germ layer1.65e-10604
embryonic tissue1.65e-10604
presumptive structure1.65e-10604
epiblast (generic)1.65e-10604
anatomical cluster1.66e-10286
anatomical system2.17e-10625
regional part of nervous system2.38e-0894
nervous system2.38e-0894
ectoderm3.15e-08173
presumptive ectoderm3.15e-08173
compound organ3.19e-0869
ectoderm-derived structure4.70e-08169
posterior neural tube7.76e-0815
chordal neural plate7.76e-0815
neurectoderm8.90e-0890
systemic artery9.74e-0833
systemic arterial system9.74e-0833
neural plate1.19e-0786
presumptive neural plate1.19e-0786
central nervous system1.68e-0782
neural tube4.52e-0757
neural rod4.52e-0757
future spinal cord4.52e-0757
neural keel4.52e-0757
artery5.21e-0742
arterial blood vessel5.21e-0742
arterial system5.21e-0742
anterior region of body7.08e-07129
craniocervical region7.08e-07129
epithelial tube9.09e-07118


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
TAF1#687243.343046285745290.008005664898701650.0323431834882791



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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