Personal tools

Coexpression cluster:C4058

From FANTOM5_SSTAR

Revision as of 19:41, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C4058_Smooth_gastric_giant_embryonic_squamous_mucinous_papillotubular



Phase1 CAGE Peaks

Hg19::chr20:61340152..61340173,+p2@NTSR1
Hg19::chr20:61340179..61340195,+p1@NTSR1
Hg19::chr20:61340492..61340503,+p6@NTSR1


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
CD14-positive, CD16-negative classical monocyte2.30e-0842
classical monocyte3.54e-0745
Uber Anatomy
Ontology termp-valuen
regional part of cerebral cortex5.71e-0922
embryo1.44e-08612
gray matter2.16e-0834
brain grey matter2.16e-0834
germ layer2.54e-08604
embryonic tissue2.54e-08604
presumptive structure2.54e-08604
epiblast (generic)2.54e-08604
embryonic structure3.30e-08605
developing anatomical structure3.30e-08605
neocortex3.95e-0820
cerebral hemisphere7.40e-0832
telencephalon1.08e-0734
anatomical system1.14e-07625
anatomical group1.47e-07626
regional part of telencephalon2.23e-0733
dermis2.52e-079
dermatome2.52e-079
future dermis2.52e-079
cerebral cortex3.75e-0725
pallium3.75e-0725
artery7.44e-0742
arterial blood vessel7.44e-0742
arterial system7.44e-0742


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


No analysis results for this cluster

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.