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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4688_tubular_placenta_chorionic_liver_Multipotent_lung_mesenchymal
|full_id=C4688_tubular_placenta_chorionic_liver_Multipotent_lung_mesenchymal
|id=C4688
|id=C4688

Revision as of 17:48, 12 September 2012


Full id: C4688_tubular_placenta_chorionic_liver_Multipotent_lung_mesenchymal



Phase1 CAGE Peaks

Hg19::chr7:45927978..45927999,+p2@IGFBP1
Hg19::chr7:45928011..45928026,+p4@IGFBP1
Hg19::chr7:45928140..45928150,+p3@IGFBP1


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 cell of nephron1.71e-0716
stromal cell3.27e-0727
kidney tubule cell5.92e-0712
nephron tubule epithelial cell5.92e-0712
Uber Anatomy
Ontology termp-valuen
multi-tissue structure1.64e-08347
foregut4.62e-0898
anatomical cluster4.68e-08286
larynx1.20e-079
endocrine system1.26e-0745
nephron epithelium1.71e-0716
nephron1.71e-0716
uriniferous tubule1.71e-0716
metanephric mesenchyme1.71e-0716
nephrogenic mesenchyme1.71e-0716
mesenchyme1.79e-07238
entire embryonic mesenchyme1.79e-07238
brain vasculature4.10e-075
abdomen element5.45e-0755
abdominal segment element5.45e-0755
body cavity precursor5.67e-0763
renal tubule5.92e-0712
nephron tubule5.92e-0712
nephron tubule epithelium5.92e-0712
excretory tube6.88e-0717
mesonephric epithelium6.88e-0717
mesonephric tubule6.88e-0717
nephric duct6.88e-0717
kidney epithelium6.88e-0717
renal duct6.88e-0717
mesonephric duct6.88e-0717
pronephric duct6.88e-0717


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
EP300#203336.77394172622320.003216880500103790.0168480909959551
FOXA1#3169311.08141974938550.000734755275698670.00584218547687045
FOXA2#3170324.63046375266526.68983856509345e-050.00107704647741606
HNF4A#3172323.13229036295378.07584663437677e-050.00123417229535803
MAFF#23764356.31535648994525.59409009993116e-060.000169345268390351
NR3C1#2908314.9730233311730.0002978331194675480.00310247288690119
SIN3A#2594235.408884726815140.006318961977991520.0278258662570922
SP1#666735.69838137814090.005403962701712170.0247874065880854
TCF7L2#6934310.77017656313730.0008003181298398380.00617451615293956



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.