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Coexpression cluster:C4325: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!9.68e-07!114
|ontology_enrichment_uberon=UBERON:0007023!9.68e-07!114
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}}
}}

Revision as of 16:40, 26 November 2012


Full id: C4325_Basophils_CD8_Mast_Natural_CD4_Peripheral_optic



Phase1 CAGE Peaks

Hg19::chr3:3151947..3151970,-p5@IL5RA
Hg19::chrX:3631503..3631514,-p7@PRKX
Hg19::chrX:3631533..3631552,-p2@PRKX


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


GO IDGO nameFDR corrected p-value
GO:0019980interleukin-5 binding0.00459188178052133
GO:0004914interleukin-5 receptor activity0.00459188178052133
GO:0004691cAMP-dependent protein kinase activity0.00816274461151255
GO:0004690cyclic nucleotide-dependent protein kinase activity0.00918254698947879
GO:0004907interleukin receptor activity0.0203972491114866
GO:0019965interleukin binding0.0203972491114866
GO:0004896hematopoietin/interferon-class (D200-domain) cytokine receptor activity0.0301459095476488
GO:0019838growth factor binding0.0336262182582139
GO:0019955cytokine binding0.0336262182582139



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
leukocyte6.09e-15136
hematopoietic stem cell2.06e-13168
angioblastic mesenchymal cell2.06e-13168
hematopoietic oligopotent progenitor cell8.96e-13161
hematopoietic multipotent progenitor cell8.96e-13161
hematopoietic cell3.91e-12177
hematopoietic lineage restricted progenitor cell8.25e-12120
nongranular leukocyte1.15e-11115
lymphocyte1.76e-1153
common lymphoid progenitor1.76e-1153
lymphoid lineage restricted progenitor cell5.05e-1152
nucleate cell1.05e-1055
mature alpha-beta T cell2.78e-0918
alpha-beta T cell2.78e-0918
immature T cell2.78e-0918
mature T cell2.78e-0918
immature alpha-beta T cell2.78e-0918
histamine secreting cell1.72e-075
biogenic amine secreting cell1.72e-075
granulocytopoietic cell1.72e-075
mast cell1.72e-075
mast cell progenitor1.72e-075
basophil mast progenitor cell1.72e-075
Uber Anatomy
Ontology termp-valuen
adult organism9.68e-07114


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)

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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.