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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3106_immature_Eosinophils_CD133_Neutrophils_Basophils_CD34_Natural
|full_id=C3106_immature_Eosinophils_CD133_Neutrophils_Basophils_CD34_Natural
|id=C3106
|id=C3106

Revision as of 15:58, 12 September 2012


Full id: C3106_immature_Eosinophils_CD133_Neutrophils_Basophils_CD34_Natural



Phase1 CAGE Peaks

Hg19::chr11:12257748..12257755,-p@chr11:12257748..12257755
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Hg19::chr15:74683456..74683465,-p@chr15:74683456..74683465
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Hg19::chr1:176176907..176176911,+p3@ENST00000456125


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
leukocyte5.03e-49140
hematopoietic stem cell1.31e-41172
angioblastic mesenchymal cell1.31e-41172
hematopoietic cell6.96e-38182
hematopoietic oligopotent progenitor cell7.27e-36165
hematopoietic multipotent progenitor cell7.27e-36165
nongranular leukocyte7.99e-32119
hematopoietic lineage restricted progenitor cell8.78e-32124
myeloid leukocyte7.38e-2176
myeloid cell1.58e-18112
common myeloid progenitor1.58e-18112
lymphocyte8.76e-1753
common lymphoid progenitor8.76e-1753
lymphoid lineage restricted progenitor cell4.82e-1652
granulocyte monocyte progenitor cell5.33e-1671
CD14-positive, CD16-negative classical monocyte5.41e-1642
macrophage dendritic cell progenitor1.92e-1465
classical monocyte2.09e-1445
myeloid lineage restricted progenitor cell9.38e-1470
dendritic cell7.50e-1310
monopoietic cell1.43e-1263
monocyte1.43e-1263
monoblast1.43e-1263
promonocyte1.43e-1263
mesenchymal cell2.42e-12358
connective tissue cell3.70e-12365
granulocyte2.08e-108
conventional dendritic cell4.77e-108
mature alpha-beta T cell1.43e-0918
alpha-beta T cell1.43e-0918
immature T cell1.43e-0918
mature T cell1.43e-0918
immature alpha-beta T cell1.43e-0918
motile cell3.18e-09390
stem cell8.34e-09444
Langerhans cell3.40e-085
multi fate stem cell5.15e-08430
somatic stem cell1.37e-07436
lymphocyte of B lineage2.75e-0724
pro-B cell2.75e-0724
blood cell4.05e-0711
T cell4.71e-0725
pro-T cell4.71e-0725
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.67e-22102
blood island1.67e-22102
hemolymphoid system3.90e-19112
bone marrow3.69e-1580
bone element3.51e-1486
connective tissue1.13e-11375
immune system2.22e-11115
skeletal element2.95e-11101
skeletal system2.95e-11101
lateral plate mesoderm5.14e-07216


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
ZEB1#6935211.25895467836260.01010222676646330.0377943280291825



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.