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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4200_Mast_immature_CD4_Natural_CD8_Basophils_hairy
|full_id=C4200_Mast_immature_CD4_Natural_CD8_Basophils_hairy
|id=C4200
|id=C4200

Revision as of 17:15, 12 September 2012


Full id: C4200_Mast_immature_CD4_Natural_CD8_Basophils_hairy



Phase1 CAGE Peaks

Hg19::chr2:235403097..235403137,+p@chr2:235403097..235403137
+
Hg19::chr6:159071015..159071096,+p1@SYTL3
Hg19::chr6:159071097..159071104,+p9@SYTL3


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
leukocyte9.48e-41140
hematopoietic cell3.91e-36182
hematopoietic stem cell6.31e-36172
angioblastic mesenchymal cell6.31e-36172
hematopoietic oligopotent progenitor cell9.59e-34165
hematopoietic multipotent progenitor cell9.59e-34165
hematopoietic lineage restricted progenitor cell2.96e-32124
nongranular leukocyte9.05e-30119
myeloid leukocyte1.18e-2376
myeloid cell7.45e-21112
common myeloid progenitor7.45e-21112
granulocyte monocyte progenitor cell2.43e-2071
CD14-positive, CD16-negative classical monocyte4.66e-1942
myeloid lineage restricted progenitor cell2.85e-1870
macrophage dendritic cell progenitor2.95e-1765
monopoietic cell3.49e-1663
monocyte3.49e-1663
monoblast3.49e-1663
promonocyte3.49e-1663
classical monocyte5.65e-1645
mesenchymal cell7.39e-14358
connective tissue cell1.20e-12365
lymphoid lineage restricted progenitor cell1.38e-1252
mature alpha-beta T cell1.43e-1218
alpha-beta T cell1.43e-1218
immature T cell1.43e-1218
mature T cell1.43e-1218
immature alpha-beta T cell1.43e-1218
lymphocyte6.95e-1253
common lymphoid progenitor6.95e-1253
T cell1.60e-1125
pro-T cell1.60e-1125
multi fate stem cell2.06e-10430
somatic stem cell4.01e-09436
motile cell4.82e-09390
stem cell1.17e-08444
CD8-positive, alpha-beta T cell3.19e-0811
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.41e-29102
blood island2.41e-29102
hemolymphoid system6.41e-27112
bone marrow6.53e-1980
bone element3.37e-1786
adult organism1.85e-14115
lateral plate mesoderm1.57e-13216
skeletal element5.84e-13101
skeletal system5.84e-13101
immune system1.94e-12115
connective tissue4.03e-12375
blood3.52e-0915
haemolymphatic fluid3.52e-0915
organism substance3.52e-0915
musculoskeletal system8.65e-08167


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
BCL11A#53335218.91297006907140.003639406248379680.0183914428400119
BCL3#602223.03140186915890.002464674760842910.0138577748235624
MEF2A#4205212.4954872730960.008235029478029740.0324930387871075
MEF2C#4208227.54090299508270.001729119938369690.010649735050032



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.