Personal tools

Coexpression cluster:C3294

From FANTOM5_SSTAR

Revision as of 19:03, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3294_smallcell_hepatoblastoma_thyroid_hepatocellular_Melanocyte_liver_small



Phase1 CAGE Peaks

Hg19::chr12:53497240..53497249,+p3@SOAT2
Hg19::chr7:130600638..130600649,+p@chr7:130600638..130600649
+
Hg19::chr7:130600673..130600688,+p@chr7:130600673..130600688
+


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
melanocyte1.78e-1510
melanoblast1.78e-1510
pigment cell1.84e-1014
neurecto-epithelial cell3.61e-0820
light melanocyte1.86e-073
Uber Anatomy
Ontology termp-valuen
digestive system3.35e-13155
digestive tract3.35e-13155
primitive gut3.35e-13155
endoderm-derived structure1.41e-12169
endoderm1.41e-12169
presumptive endoderm1.41e-12169
prostate gland2.00e-1211
male accessory sex gland2.00e-1211
embryonic cloacal epithelium2.00e-1211
epithelium of hindgut2.00e-1211
urogenital sinus epithelium2.00e-1211
prostate bud2.00e-1211
prostate field2.00e-1211
sex gland3.12e-1112
male reproductive gland3.12e-1112
large intestine4.61e-1111
subdivision of digestive tract1.37e-10129
endodermal part of digestive tract1.37e-10129
colon1.56e-109
hindgut5.52e-1019
cloaca2.31e-0914
anal region2.31e-0914
embryonic cloaca2.31e-0914
terminal part of digestive tract2.31e-0914
primitive urogenital sinus2.31e-0914
proctodeum2.31e-0914
gut epithelium1.10e-0854
orifice1.21e-0835
genitourinary system1.29e-0815
endo-epithelium1.65e-0782
gland1.82e-0759


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.