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Coexpression cluster:C4873: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002390!9.80e-14!98;UBERON:0003061!9.80e-14!98;UBERON:0002193!1.46e-12!108;UBERON:0000178!2.05e-08!15;UBERON:0000179!2.05e-08!15;UBERON:0000463!2.05e-08!15;UBERON:0002405!1.31e-07!93
|ontology_enrichment_uberon=UBERON:0002390!9.80e-14!98;UBERON:0003061!9.80e-14!98;UBERON:0002193!1.46e-12!108;UBERON:0000178!2.05e-08!15;UBERON:0000179!2.05e-08!15;UBERON:0000463!2.05e-08!15;UBERON:0002405!1.31e-07!93
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}}
}}

Revision as of 17:01, 26 November 2012


Full id: C4873_lymphangiectasia_Eosinophils_Mast_Neutrophils_CD4_b_H9



Phase1 CAGE Peaks

Hg19::chrX:48770828..48770832,-p@chrX:48770828..48770832
-
Hg19::chrX:48771830..48771849,-p2@PIM2
Hg19::chrX:48776292..48776309,-p1@PIM2


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>


Cell Type
Ontology termp-valuen
hematopoietic stem cell3.56e-46168
angioblastic mesenchymal cell3.56e-46168
hematopoietic cell4.10e-45177
hematopoietic oligopotent progenitor cell2.95e-43161
hematopoietic multipotent progenitor cell2.95e-43161
leukocyte1.17e-36136
hematopoietic lineage restricted progenitor cell4.97e-29120
nongranular leukocyte4.57e-28115
nucleate cell4.89e-2655
lymphocyte4.06e-2553
common lymphoid progenitor4.06e-2553
lymphoid lineage restricted progenitor cell1.65e-2452
myeloid cell1.12e-18108
common myeloid progenitor1.12e-18108
lymphocyte of B lineage1.58e-1224
pro-B cell1.58e-1224
T cell1.04e-1125
pro-T cell1.04e-1125
mature alpha-beta T cell5.91e-1118
alpha-beta T cell5.91e-1118
immature T cell5.91e-1118
mature T cell5.91e-1118
immature alpha-beta T cell5.91e-1118
myeloid leukocyte9.86e-1072
B cell2.18e-0814
myeloid lineage restricted progenitor cell2.33e-0766
granulocyte monocyte progenitor cell2.57e-0767
CD8-positive, alpha-beta T cell2.75e-0711
classical monocyte3.94e-0742
CD14-positive, CD16-negative classical monocyte3.94e-0742
macrophage dendritic cell progenitor9.33e-0761
Uber Anatomy
Ontology termp-valuen
hematopoietic system9.80e-1498
blood island9.80e-1498
hemolymphoid system1.46e-12108
blood2.05e-0815
haemolymphatic fluid2.05e-0815
organism substance2.05e-0815
immune system1.31e-0793
Disease
Ontology termp-valuen
hematologic cancer4.23e-1251
immune system cancer4.23e-1251
leukemia1.94e-0939
myeloid leukemia4.63e-0831


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.