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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1475_Sebocyte_Prostate_Tracheal_Bronchial_Preadipocyte_Urothelial_Small
|full_id=C1475_Sebocyte_Prostate_Tracheal_Bronchial_Preadipocyte_Urothelial_Small
|id=C1475
|id=C1475

Revision as of 14:02, 12 September 2012


Full id: C1475_Sebocyte_Prostate_Tracheal_Bronchial_Preadipocyte_Urothelial_Small



Phase1 CAGE Peaks

Hg19::chr1:31898174..31898188,+p@chr1:31898174..31898188
+
Hg19::chr1:31898628..31898663,+p@chr1:31898628..31898663
+
Hg19::chr1:31899496..31899521,+p@chr1:31899496..31899521
+
Hg19::chr1:31899590..31899619,+p@chr1:31899590..31899619
+
Hg19::chr1:31901841..31901876,+p3@SERINC2
Hg19::chr1:31902298..31902318,+p5@SERINC2


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
epithelial cell4.39e-20254
embryonic cell8.22e-16248
endo-epithelial cell9.96e-1243
endodermal cell1.30e-1159
animal cell1.86e-11679
eukaryotic cell1.86e-11679
ecto-epithelial cell2.97e-0933
general ecto-epithelial cell7.91e-0913
somatic cell8.82e-09591
respiratory epithelial cell4.71e-0813
non-terminally differentiated cell6.30e-08180
fibroblast9.54e-0775
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.92e-21169
endoderm3.92e-21169
presumptive endoderm3.92e-21169
surface structure1.79e-1795
trunk2.78e-17216
mesenchyme9.13e-17238
entire embryonic mesenchyme9.13e-17238
digestive system1.41e-16155
digestive tract1.41e-16155
primitive gut1.41e-16155
trunk mesenchyme7.28e-14143
multi-cellular organism2.58e-13659
anatomical system9.29e-13625
anatomical group1.74e-12626
organism subdivision1.90e-12365
multi-tissue structure2.76e-11347
respiratory system4.20e-1172
subdivision of digestive tract6.57e-11129
endodermal part of digestive tract6.57e-11129
orifice7.73e-1135
subdivision of head3.03e-1048
mouth3.71e-1028
stomodeum3.71e-1028
mixed endoderm/mesoderm-derived structure5.26e-10130
embryo6.04e-10612
subdivision of trunk1.01e-09113
germ layer1.27e-09604
embryonic tissue1.27e-09604
presumptive structure1.27e-09604
epiblast (generic)1.27e-09604
embryonic structure1.55e-09605
developing anatomical structure1.55e-09605
urinary system structure2.37e-0944
immaterial anatomical entity2.73e-09126
renal system2.96e-0945
anatomical space8.24e-09104
mesoderm1.29e-08448
mesoderm-derived structure1.29e-08448
presumptive mesoderm1.29e-08448
somite3.51e-0883
paraxial mesoderm3.51e-0883
presomitic mesoderm3.51e-0883
presumptive segmental plate3.51e-0883
trunk paraxial mesoderm3.51e-0883
presumptive paraxial mesoderm3.51e-0883
organ5.58e-08511
oral opening9.05e-0821
multilaminar epithelium1.60e-0782


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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