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Coexpression cluster:C4054

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Full id: C4054_Osteoblast_Fibroblast_leiomyoblastoma_meningioma_Smooth_salivary_Chondrocyte



Phase1 CAGE Peaks

Hg19::chr20:57089878..57089902,-p4@APCDD1L
Hg19::chr20:57089913..57089929,-p5@APCDD1L
Hg19::chr20:57089934..57089974,-p2@APCDD1L


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>


Uber Anatomy
Ontology termp-valuen
somite6.62e-2883
paraxial mesoderm6.62e-2883
presomitic mesoderm6.62e-2883
presumptive segmental plate6.62e-2883
trunk paraxial mesoderm6.62e-2883
presumptive paraxial mesoderm6.62e-2883
dermomyotome7.93e-2770
multilaminar epithelium1.70e-2382
muscle tissue1.92e-2363
musculature1.92e-2363
musculature of body1.92e-2363
skeletal muscle tissue4.57e-2361
striated muscle tissue4.57e-2361
myotome4.57e-2361
trunk mesenchyme1.68e-21143
multi-tissue structure5.12e-12347
artery8.82e-1242
arterial blood vessel8.82e-1242
arterial system8.82e-1242
trunk3.08e-11216
systemic artery8.24e-1133
systemic arterial system8.24e-1133
organism subdivision9.08e-11365
mesenchyme1.35e-10238
entire embryonic mesenchyme1.35e-10238
splanchnic layer of lateral plate mesoderm7.20e-1084
epithelial tube1.15e-09118
blood vessel4.23e-0960
epithelial tube open at both ends4.23e-0960
blood vasculature4.23e-0960
vascular cord4.23e-0960
vasculature5.64e-0979
vascular system5.64e-0979
surface structure7.54e-0995
unilaminar epithelium7.83e-09138
cardiovascular system5.14e-08110
vessel1.64e-0769
circulatory system2.69e-07113
multi-cellular organism3.20e-07659
smooth muscle tissue6.09e-0715
Disease
Ontology termp-valuen
ovarian cancer4.32e-0714


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
SUZ12#23512350.11578091106297.93834897779404e-060.000222929074722192



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.