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Coexpression cluster:C3950

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Full id: C3950_Hepatic_Hair_Ewing_Preadipocyte_Adipocyte_corpus_neurofibroma



Phase1 CAGE Peaks

Hg19::chr1:231004162..231004173,-p4@C1orf198
Hg19::chr1:231004220..231004294,-p1@C1orf198
Hg19::chr1:231004738..231004754,-p11@C1orf198


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
fibroblast7.54e-1676
fat cell3.34e-0915
skin fibroblast1.28e-0723
non-terminally differentiated cell2.78e-07106
Uber Anatomy
Ontology termp-valuen
structure with developmental contribution from neural crest1.69e-08132
dense mesenchyme tissue4.68e-0873
paraxial mesoderm1.29e-0772
presumptive paraxial mesoderm1.29e-0772
neural tube1.89e-0756
neural rod1.89e-0756
future spinal cord1.89e-0756
neural keel1.89e-0756
somite2.18e-0771
presomitic mesoderm2.18e-0771
presumptive segmental plate2.18e-0771
dermomyotome2.18e-0771
trunk paraxial mesoderm2.18e-0771
central nervous system2.70e-0781
skin of body3.00e-0741
neural plate3.16e-0782
presumptive neural plate3.16e-0782
brain3.85e-0768
future brain3.85e-0768
omentum7.38e-076
peritoneum7.38e-076
abdominal cavity7.38e-076
visceral peritoneum7.38e-076
skeletal muscle tissue8.10e-0762
striated muscle tissue8.10e-0762
myotome8.10e-0762
nervous system8.12e-0789
integument9.35e-0746
integumental system9.35e-0746
epithelial vesicle9.57e-0778


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#186934.907389214879320.008460985347239390.0325604056406034
E2F6#187635.017155731697390.00791769806886330.0322485168323069
SIN3A#2594235.408884726815140.006318961977991520.027700892797996
SMARCB1#6598212.16847718743830.008675002221921740.0329925551529546
THAP1#55145220.91276306856750.002983447413736940.0158698311318769
YY1#752834.911170749853860.008441455341808260.0329662773227803



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.