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Coexpression cluster:C4118

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Full id: C4118_thyroid_clear_kidney_anaplastic_Renal_serous_endometrioid



Phase1 CAGE Peaks

Hg19::chr2:113984760..113984792,+p@chr2:113984760..113984792
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Hg19::chr2:113999199..113999214,+p@chr2:113999199..113999214
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Hg19::chr2:114036488..114036504,-p1@PAX8


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
cavitated compound organ2.87e-2132
kidney3.42e-1827
kidney mesenchyme3.42e-1827
kidney rudiment3.42e-1827
kidney field3.42e-1827
mesonephros4.03e-1818
pronephros4.03e-1818
nephrogenic cord4.03e-1818
pronephric mesoderm4.03e-1818
rostral part of nephrogenic cord4.03e-1818
presumptive pronephric mesoderm4.03e-1818
urogenital ridge6.40e-1820
reproductive organ2.25e-1748
excretory tube8.60e-1717
mesonephric epithelium8.60e-1717
mesonephric tubule8.60e-1717
nephric duct8.60e-1717
kidney epithelium8.60e-1717
renal duct8.60e-1717
mesonephric duct8.60e-1717
pronephric duct8.60e-1717
reproductive structure6.59e-1659
reproductive system6.59e-1659
renal system9.46e-1645
renal tubule1.22e-1512
nephron tubule1.22e-1512
nephron tubule epithelium1.22e-1512
nephron epithelium1.89e-1516
nephron1.89e-1516
uriniferous tubule1.89e-1516
metanephric mesenchyme1.89e-1516
nephrogenic mesenchyme1.89e-1516
intraembryonic coelom7.94e-1521
urinary system structure8.46e-1544
body cavity precursor1.17e-1363
intermediate mesoderm1.79e-1337
female reproductive organ4.72e-1337
female reproductive system4.72e-1337
duct8.56e-1326
anatomical cavity2.29e-1270
cortex of kidney2.48e-1113
renal parenchyma2.48e-1113
female organism3.68e-1141
compound organ6.54e-1169
internal genitalia1.78e-0925
gonad3.47e-0921
indifferent external genitalia3.47e-0921
indifferent gonad3.47e-0921
gonad primordium3.47e-0921
posterior neural tube4.34e-0915
chordal neural plate4.34e-0915
cortex1.08e-0816
external genitalia1.30e-0822
female gonad4.10e-0813
parenchyma5.04e-0817
abdomen element2.20e-0755
abdominal segment element2.20e-0755
anatomical space2.27e-07104


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.