Personal tools

Coexpression cluster:C3635

From FANTOM5_SSTAR

Revision as of 03:39, 5 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3635_testicular_hepatoblastoma_hepatocellular_lung_gastric_prostate_Trabecular



Phase1 CAGE Peaks

  Short description
Hg19::chr17:41623667..41623682,- p8@ETV4
Hg19::chr17:41623692..41623715,- p1@ETV4
Hg19::chr17:41623716..41623727,- p12@ETV4


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data
disease_data


Cell Type
Ontology termp-valuen
epithelial cell8.14e-37254
embryonic cell6.62e-26248
animal cell6.48e-12679
eukaryotic cell6.48e-12679
endodermal cell1.00e-0959
squamous epithelial cell9.22e-0962
ectodermal cell3.57e-0871
endo-epithelial cell3.99e-0843
non-terminally differentiated cell5.26e-08180
mesodermal cell1.65e-07119
Uber Anatomy
Ontology termp-valuen
cell layer1.79e-13312
epithelium1.42e-12309
mesenchyme1.51e-11238
entire embryonic mesenchyme1.51e-11238
epithelial tube2.06e-11118
multi-tissue structure3.02e-11347
endoderm-derived structure5.77e-10169
endoderm5.77e-10169
presumptive endoderm5.77e-10169
unilaminar epithelium2.61e-09138
trunk6.22e-09216
primordium7.90e-09168
trunk mesenchyme1.30e-08143
digestive system2.08e-08155
digestive tract2.08e-08155
primitive gut2.08e-08155
organism subdivision3.87e-08365
immaterial anatomical entity5.07e-08126
anatomical cluster7.54e-08286
trunk region element1.45e-07107
mixed endoderm/mesoderm-derived structure1.95e-07130
simple squamous epithelium2.06e-0722
anatomical conduit2.28e-07241
vasculature2.81e-0779
vascular system2.81e-0779
endo-epithelium8.14e-0782
Disease
Ontology termp-valuen
cancer5.21e-15235
disease of cellular proliferation4.28e-14239
carcinoma4.35e-13106
cell type cancer2.90e-12143


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CCNT2#90536.336201576962630.003930750035764890.0189837504270635
EGR1#195834.988179094810140.008056488137383440.0320232755311204
ETS1#211339.728760922202340.001085840092584840.00761458762032282
FOXA1#3169311.08141974938550.000734755275698670.0058081370147361
IRF1#365937.63716375356390.002244692747297240.0127930949978159
NFYA#4800318.42558069983050.0001598135507814160.00199387975511413
NFYB#4801316.75979325353650.0002123649923296180.00245562305512766
SIN3A#2594235.408884726815140.006318961977991520.0276336182069951
TCF7L2#6934310.77017656313730.0008003181298398380.00612968797025102



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.