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Coexpression cluster:C1865

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Full id: C1865_adult_CD4_CD8_cord_lymphangiectasia_B_xeroderma



Phase1 CAGE Peaks

Hg19::chr20:21538047..21538060,+p@chr20:21538047..21538060
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Hg19::chr20:21538062..21538073,+p@chr20:21538062..21538073
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Hg19::chr20:21538183..21538198,+p@chr20:21538183..21538198
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Hg19::chr20:21538200..21538210,+p@chr20:21538200..21538210
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Hg19::chr3:39371213..39371253,+p1@CCR8


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
mature alpha-beta T cell7.11e-4618
alpha-beta T cell7.11e-4618
immature T cell7.11e-4618
mature T cell7.11e-4618
immature alpha-beta T cell7.11e-4618
T cell1.64e-4125
pro-T cell1.64e-4125
lymphoid lineage restricted progenitor cell1.46e-2752
lymphocyte6.08e-2753
common lymphoid progenitor6.08e-2753
nucleate cell9.05e-2655
CD4-positive, alpha-beta T cell7.58e-246
circulating cell1.95e-226
CD8-positive, alpha-beta T cell1.61e-2111
nongranular leukocyte2.05e-14115
naive T cell4.38e-133
single nucleate cell1.59e-113
mononuclear cell1.59e-113
leukocyte2.69e-11136
hematopoietic cell4.25e-10177
hematopoietic lineage restricted progenitor cell5.17e-10120
regulatory T cell1.87e-092
CD4-positive, CD25-positive, alpha-beta regulatory T cell1.87e-092
naive regulatory T cell1.87e-092
thymocyte9.20e-092
double negative thymocyte9.20e-092
double-positive, alpha-beta thymocyte9.20e-092
DN4 thymocyte9.20e-092
DN1 thymic pro-T cell9.20e-092
DN2 thymocyte9.20e-092
DN3 thymocyte9.20e-092
immature single positive thymocyte9.20e-092
early T lineage precursor9.20e-092
hematopoietic stem cell4.44e-08168
angioblastic mesenchymal cell4.44e-08168
Uber Anatomy
Ontology termp-valuen
blood1.52e-2815
haemolymphatic fluid1.52e-2815
organism substance1.52e-2815
thymus5.29e-094
hemolymphoid system gland5.29e-094
thymic region5.29e-094
pharyngeal gland5.29e-094
thymus primordium5.29e-094


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.