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Coexpression cluster:C3648

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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 cell1.52e-18253
kidney tubule cell4.13e-1510
nephron tubule epithelial cell4.13e-1510
epithelial cell of nephron1.04e-1315
kidney cell1.48e-1317
kidney epithelial cell1.48e-1317
kidney cortical cell8.55e-1012
renal cortical epithelial cell8.55e-1012
Uber Anatomy
Ontology termp-valuen
cavitated compound organ6.36e-1831
urinary system structure5.48e-1747
kidney1.15e-1626
kidney mesenchyme1.15e-1626
upper urinary tract1.15e-1626
kidney rudiment1.15e-1626
kidney field1.15e-1626
renal system1.89e-1648
nephron tubule epithelium4.13e-1510
excretory tube1.43e-1416
kidney epithelium1.43e-1416
abdominal segment of trunk1.54e-1460
abdomen1.54e-1460
nephron epithelium1.04e-1315
renal tubule1.04e-1315
nephron tubule1.04e-1315
nephron1.04e-1315
uriniferous tubule1.04e-1315
nephrogenic mesenchyme1.04e-1315
larynx3.07e-129
cortex1.08e-1015
abdomen element3.91e-1054
abdominal segment element3.91e-1054
subdivision of trunk5.79e-10112
cortex of kidney8.55e-1012
renal parenchyma8.55e-1012
endoderm-derived structure2.15e-09160
endoderm2.15e-09160
presumptive endoderm2.15e-09160
trunk region element2.51e-09101
subdivision of digestive tract2.74e-09118
gastrointestinal system3.19e-0925
transitional epithelium5.03e-096
digestive system2.09e-08145
digestive tract2.09e-08145
primitive gut2.09e-08145
omentum4.85e-086
peritoneum4.85e-086
abdominal cavity4.85e-086
visceral peritoneum4.85e-086
urothelium9.69e-085
parenchyma2.26e-0715
organ segment4.90e-0798
upper respiratory tract5.42e-0719
respiratory primordium5.60e-0738
endoderm of foregut5.60e-0738
Disease
Ontology termp-valuen
carcinoma2.65e-28106
cell type cancer1.24e-27143
cancer4.66e-20235
disease of cellular proliferation3.76e-19239
squamous cell carcinoma4.05e-0914
adenocarcinoma4.25e-0725


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.