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Coexpression cluster:C2762: Difference between revisions

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|tf_chipseq_enrich=POU2F2#5452;3:6.82959304330689:0.00486047377520374:0.0227715333127805
|tf_chipseq_enrich=POU2F2#5452;3:6.82959304330689:0.00486047377520374:0.0227715333127805
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}}
}}

Revision as of 15:42, 26 November 2012


Full id: C2762_splenic_CD4_b_plasma_xeroderma_NK_lymphoma



Phase1 CAGE Peaks

Hg19::chr3:98250809..98250829,+p1@GPR15
Hg19::chr3:98250848..98250859,+p3@GPR15
Hg19::chr3:98251121..98251133,+p4@GPR15
Hg19::chr3:98252740..98252746,+p@chr3:98252740..98252746
+


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
lymphoid lineage restricted progenitor cell2.79e-4152
lymphocyte2.49e-4053
common lymphoid progenitor2.49e-4053
nucleate cell1.55e-3855
mature alpha-beta T cell2.56e-3018
alpha-beta T cell2.56e-3018
immature T cell2.56e-3018
mature T cell2.56e-3018
immature alpha-beta T cell2.56e-3018
T cell4.65e-2725
pro-T cell4.65e-2725
nongranular leukocyte4.00e-21115
leukocyte1.26e-18136
CD8-positive, alpha-beta T cell2.79e-1811
hematopoietic lineage restricted progenitor cell3.51e-16120
lymphocyte of B lineage6.18e-1624
pro-B cell6.18e-1624
hematopoietic cell9.97e-14177
hematopoietic stem cell3.46e-13168
angioblastic mesenchymal cell3.46e-13168
hematopoietic oligopotent progenitor cell1.72e-11161
hematopoietic multipotent progenitor cell1.72e-11161
CD4-positive, alpha-beta T cell3.38e-116
circulating cell1.31e-096
B cell2.46e-0814
single nucleate cell9.97e-083
mononuclear cell9.97e-083
Uber Anatomy
Ontology termp-valuen
blood1.41e-1415
haemolymphatic fluid1.41e-1415
organism substance1.41e-1415
hemopoietic organ3.81e-137
immune organ3.81e-137
thymus1.18e-104
hemolymphoid system gland1.18e-104
thymic region1.18e-104
pharyngeal gland1.18e-104
thymus primordium1.18e-104
chordate pharynx8.52e-0910
pharyngeal region of foregut8.52e-0910
pharynx6.26e-0811
pharyngeal epithelium4.23e-076


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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
POU2F2#545236.829593043306890.004860473775203740.0227715333127805



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.

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