Personal tools

Coexpression cluster:C2772

From FANTOM5_SSTAR

Revision as of 14:18, 5 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2772_mesenchymal_Fibroblast_Cardiac_Smooth_Chondrocyte_Anulus_tenocyte



Phase1 CAGE Peaks

Hg19::chr4:114682288..114682309,-p5@CAMK2D
Hg19::chr4:114682310..114682325,-p6@CAMK2D
Hg19::chr4:114682326..114682356,-p2@CAMK2D
Hg19::chr4:114682364..114682379,-p3@CAMK2D


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 cell1.24e-16180
fibroblast1.76e-1275
multi fate stem cell7.64e-10430
skin fibroblast3.23e-0923
somatic stem cell1.34e-08436
muscle precursor cell1.74e-0757
myoblast1.74e-0757
multi-potent skeletal muscle stem cell1.74e-0757
stem cell3.69e-07444
Uber Anatomy
Ontology termp-valuen
somite1.40e-1283
paraxial mesoderm1.40e-1283
presomitic mesoderm1.40e-1283
presumptive segmental plate1.40e-1283
trunk paraxial mesoderm1.40e-1283
presumptive paraxial mesoderm1.40e-1283
dermomyotome4.16e-1070
muscle tissue2.83e-0963
musculature2.83e-0963
musculature of body2.83e-0963
skeletal muscle tissue1.03e-0861
striated muscle tissue1.03e-0861
myotome1.03e-0861
primary circulatory organ2.50e-0827
anatomical system5.12e-08625
anatomical group8.71e-08626
musculoskeletal system1.20e-07167
multilaminar epithelium2.92e-0782
multi-cellular organism2.94e-07659
heart3.06e-0724
primitive heart tube3.06e-0724
primary heart field3.06e-0724
anterior lateral plate mesoderm3.06e-0724
heart tube3.06e-0724
heart primordium3.06e-0724
cardiac mesoderm3.06e-0724
cardiogenic plate3.06e-0724
heart rudiment3.06e-0724
tissue4.41e-07787


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
CEBPB#105147.971147625824820.0002476385788090830.00268456773222356
CTBP2#1488462.71700033932816.45042639894877e-083.96513291747976e-06
NFKB1#479045.488063424193840.001102199566301980.00768955380795005
TAF1#687243.343046285745290.008005664898701650.0322994528453798



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.