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Coexpression cluster:C2510

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Full id: C2510_Preadipocyte_Chondrocyte_Osteoblast_Wilms_rhabdomyosarcoma_adrenal_Lens



Phase1 CAGE Peaks

Hg19::chr1:103574001..103574014,-p3@COL11A1
Hg19::chr1:103574024..103574063,-p1@COL11A1
Hg19::chr1:103574068..103574099,-p2@COL11A1
Hg19::chr1:103574154..103574165,-p4@COL11A1


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
non-terminally differentiated cell1.92e-14106
fibroblast8.64e-0876
neurectodermal cell3.40e-0759
columnar/cuboidal epithelial cell5.69e-0727
Uber Anatomy
Ontology termp-valuen
central nervous system1.19e-2081
nervous system4.95e-1989
ectoderm-derived structure3.93e-17171
ectoderm3.93e-17171
presumptive ectoderm3.93e-17171
brain7.75e-1668
future brain7.75e-1668
neural plate3.62e-1582
presumptive neural plate3.62e-1582
pre-chordal neural plate3.40e-1461
neurectoderm3.74e-1486
neural tube6.23e-1456
neural rod6.23e-1456
future spinal cord6.23e-1456
neural keel6.23e-1456
structure with developmental contribution from neural crest4.07e-13132
regional part of nervous system7.66e-1353
regional part of brain7.66e-1353
ecto-epithelium1.94e-12104
regional part of forebrain1.57e-1041
forebrain1.57e-1041
anterior neural tube1.57e-1041
future forebrain1.57e-1041
multi-tissue structure4.54e-10342
brain grey matter6.52e-1034
gray matter6.52e-1034
telencephalon9.98e-1034
cerebral hemisphere2.34e-0932
regional part of telencephalon2.52e-0932
organ system subdivision1.41e-08223
pigment epithelium of eye1.45e-0811
cerebral cortex7.18e-0825
pallium7.18e-0825
vasculature of organ7.82e-0711


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
EGR1#195844.988179094810140.001615011500076050.0101455751011394
TAF1#687243.343046285745290.008005664898701650.0322309716801782



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.