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Coexpression cluster:C2433: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!6.95e-65!102;UBERON:0003061!6.95e-65!102;UBERON:0002193!7.17e-61!112;UBERON:0002371!6.31e-48!80;UBERON:0002405!1.35e-43!115;UBERON:0001474!2.21e-43!86;UBERON:0004765!7.35e-36!101;UBERON:0001434!7.35e-36!101;UBERON:0003081!6.38e-22!216;UBERON:0002204!1.11e-16!167;UBERON:0000178!2.29e-15!15;UBERON:0000179!2.29e-15!15;UBERON:0000463!2.29e-15!15;UBERON:0000926!1.17e-08!448;UBERON:0004120!1.17e-08!448;UBERON:0006603!1.17e-08!448;UBERON:0002384!3.43e-07!375
|ontology_enrichment_uberon=UBERON:0002390!6.95e-65!102;UBERON:0003061!6.95e-65!102;UBERON:0002193!7.17e-61!112;UBERON:0002371!6.31e-48!80;UBERON:0002405!1.35e-43!115;UBERON:0001474!2.21e-43!86;UBERON:0004765!7.35e-36!101;UBERON:0001434!7.35e-36!101;UBERON:0003081!6.38e-22!216;UBERON:0002204!1.11e-16!167;UBERON:0000178!2.29e-15!15;UBERON:0000179!2.29e-15!15;UBERON:0000463!2.29e-15!15;UBERON:0000926!1.17e-08!448;UBERON:0004120!1.17e-08!448;UBERON:0006603!1.17e-08!448;UBERON:0002384!3.43e-07!375
|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00817124111844175
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}}
}}

Revision as of 11:37, 5 September 2012


Full id: C2433_CD14_neuroectodermal_Whole_Macrophage_Peripheral_blood_Monocytederived



Phase1 CAGE Peaks

Hg19::chr17:7040609..7040638,+p@chr17:7040609..7040638
+
Hg19::chr17:7040645..7040665,+p@chr17:7040645..7040665
+
Hg19::chr17:7040766..7040776,+p@chr17:7040766..7040776
+
Hg19::chr17:7040783..7040800,+p@chr17:7040783..7040800
+


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
monopoietic cell1.66e-6563
monocyte1.66e-6563
monoblast1.66e-6563
promonocyte1.66e-6563
macrophage dendritic cell progenitor5.81e-6365
CD14-positive, CD16-negative classical monocyte1.25e-6242
myeloid leukocyte2.39e-5876
classical monocyte1.80e-5745
myeloid lineage restricted progenitor cell3.10e-5770
granulocyte monocyte progenitor cell3.47e-5671
nongranular leukocyte3.98e-49119
leukocyte3.20e-43140
hematopoietic lineage restricted progenitor cell4.56e-41124
myeloid cell3.57e-35112
common myeloid progenitor3.57e-35112
hematopoietic stem cell2.90e-32172
angioblastic mesenchymal cell2.90e-32172
hematopoietic oligopotent progenitor cell1.48e-30165
hematopoietic multipotent progenitor cell1.48e-30165
hematopoietic cell2.60e-29182
intermediate monocyte7.79e-129
CD14-positive, CD16-positive monocyte7.79e-129
mesenchymal cell5.75e-08358
connective tissue cell1.81e-07365
adult endothelial progenitor cell9.95e-073
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.95e-65102
blood island6.95e-65102
hemolymphoid system7.17e-61112
bone marrow6.31e-4880
immune system1.35e-43115
bone element2.21e-4386
skeletal element7.35e-36101
skeletal system7.35e-36101
lateral plate mesoderm6.38e-22216
musculoskeletal system1.11e-16167
blood2.29e-1515
haemolymphatic fluid2.29e-1515
organism substance2.29e-1515
mesoderm1.17e-08448
mesoderm-derived structure1.17e-08448
presumptive mesoderm1.17e-08448
connective tissue3.43e-07375


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
CTCF#1066445.360256373075030.001211145381643620.00817124111844175



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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