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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3648_acute_malignant_embryonic_small_transitionalcell_lens_Renal
|full_id=C3648_acute_malignant_embryonic_small_transitionalcell_lens_Renal
|id=C3648
|id=C3648

Revision as of 16:36, 12 September 2012


Full id: C3648_acute_malignant_embryonic_small_transitionalcell_lens_Renal



Phase1 CAGE Peaks

Hg19::chr17:46724016..46724042,-p3@ENST00000433510
Hg19::chr17:46724108..46724134,-p6@ENST00000433510
Hg19::chr17:46724136..46724151,-p5@ENST00000433510


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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell3.15e-13254
epithelial cell of nephron1.17e-1216
kidney cell2.64e-1218
kidney epithelial cell2.64e-1218
kidney tubule cell4.70e-1112
nephron tubule epithelial cell4.70e-1112
kidney cortical cell1.27e-0913
renal cortical epithelial cell1.27e-0913
Uber Anatomy
Ontology termp-valuen
urinary system structure8.44e-1744
renal system3.48e-1645
cavitated compound organ3.77e-1532
kidney1.41e-1427
kidney mesenchyme1.41e-1427
kidney rudiment1.41e-1427
kidney field1.41e-1427
mesonephros2.68e-1418
pronephros2.68e-1418
nephrogenic cord2.68e-1418
pronephric mesoderm2.68e-1418
rostral part of nephrogenic cord2.68e-1418
presumptive pronephric mesoderm2.68e-1418
intraembryonic coelom3.76e-1421
duct5.49e-1426
excretory tube2.25e-1317
mesonephric epithelium2.25e-1317
mesonephric tubule2.25e-1317
nephric duct2.25e-1317
kidney epithelium2.25e-1317
renal duct2.25e-1317
mesonephric duct2.25e-1317
pronephric duct2.25e-1317
abdominal segment of trunk8.54e-1361
abdomen8.54e-1361
nephron epithelium1.17e-1216
nephron1.17e-1216
uriniferous tubule1.17e-1216
metanephric mesenchyme1.17e-1216
nephrogenic mesenchyme1.17e-1216
body cavity precursor1.42e-1263
urogenital ridge2.66e-1220
intermediate mesoderm1.85e-1137
renal tubule4.70e-1112
nephron tubule4.70e-1112
nephron tubule epithelium4.70e-1112
anatomical cavity3.28e-1070
cortex3.89e-1016
larynx9.21e-109
cortex of kidney1.27e-0913
renal parenchyma1.27e-0913
subdivision of trunk3.37e-09113
abdomen element3.80e-0955
abdominal segment element3.80e-0955
anatomical space4.11e-09104
subdivision of digestive tract5.27e-08129
endodermal part of digestive tract5.27e-08129
trunk region element6.03e-08107
endoderm-derived structure8.33e-08169
endoderm8.33e-08169
presumptive endoderm8.33e-08169
parenchyma1.08e-0717
immaterial anatomical entity2.04e-07126
transitional epithelium2.25e-076
gastrointestinal system2.73e-0735
digestive system3.47e-07155
digestive tract3.47e-07155
primitive gut3.47e-07155
upper respiratory tract7.51e-0719
omentum8.45e-076
peritoneum8.45e-076
abdominal cavity8.45e-076
visceral peritoneum8.45e-076
Disease
Ontology termp-valuen
carcinoma1.03e-22106
cell type cancer4.95e-22143
cancer4.96e-17235
disease of cellular proliferation1.43e-16239
squamous cell carcinoma3.90e-0714


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
E2F1#186934.907389214879320.008460985347239390.0324921624018361
EGR1#195834.988179094810140.008056488137383440.0320244943510767
ELF1#199734.258097958807540.01295179875054610.0461710383216126
GABPB1#255337.067683836182170.002832212825417420.0153954861434326
ZBTB7A#5134137.35190930787590.002516255860282270.0140008122425157
ZZZ3#260092159.6088082901555.21262599582697e-050.00088650292522093



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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