Coexpression cluster:C2743

Full id: C2743_immature_migratory_cord_CD19_CD14_Dendritic_Natural

Phase1 CAGE Peaks

Hg19::chr3:5229456..5229471,+	p7@EDEM1
Hg19::chr3:5229484..5229499,+	p4@EDEM1
Hg19::chr3:71114592..71114612,-	p@chr3:71114592..71114612 -
Hg19::chr9:5438330..5438382,-	p3@C9orf46

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

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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

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GO ID	GO name	FDR corrected p-value
GO:0030433	ER-associated protein catabolic process	0.018538133087335
GO:0006515	misfolded or incompletely synthesized protein catabolic process	0.018538133087335
GO:0004571	mannosyl-oligosaccharide 1,2-alpha-mannosidase activity	0.018538133087335
GO:0043161	proteasomal ubiquitin-dependent protein catabolic process	0.018538133087335
GO:0015924	mannosyl-oligosaccharide mannosidase activity	0.018538133087335
GO:0015923	mannosidase activity	0.0216246375331606
GO:0030176	integral to endoplasmic reticulum membrane	0.0226045344575232
GO:0051789	response to protein stimulus	0.0226045344575232
GO:0006986	response to unfolded protein	0.0226045344575232
GO:0031227	intrinsic to endoplasmic reticulum membrane	0.0226045344575232
GO:0031301	integral to organelle membrane	0.0467722791504351
GO:0031300	intrinsic to organelle membrane	0.0468754537772942

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>

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Cell Type

Ontology term	p-value	n
leukocyte	5.69e-46	140
hematopoietic stem cell	2.02e-37	172
angioblastic mesenchymal cell	2.02e-37	172
hematopoietic cell	9.65e-37	182
hematopoietic lineage restricted progenitor cell	5.86e-34	124
nongranular leukocyte	6.79e-34	119
hematopoietic oligopotent progenitor cell	9.09e-34	165
hematopoietic multipotent progenitor cell	9.09e-34	165
myeloid leukocyte	2.89e-25	76
granulocyte monocyte progenitor cell	4.74e-23	71
CD14-positive, CD16-negative classical monocyte	4.99e-22	42
mesenchymal cell	1.40e-20	358
macrophage dendritic cell progenitor	2.35e-20	65
myeloid cell	9.19e-20	112
common myeloid progenitor	9.19e-20	112
myeloid lineage restricted progenitor cell	1.05e-19	70
classical monocyte	3.50e-19	45
monopoietic cell	4.20e-19	63
monocyte	4.20e-19	63
monoblast	4.20e-19	63
promonocyte	4.20e-19	63
connective tissue cell	4.68e-19	365
motile cell	3.75e-16	390
multi fate stem cell	1.05e-15	430
somatic stem cell	2.00e-15	436
stem cell	6.36e-15	444
somatic cell	8.68e-15	591
lymphocyte	4.41e-13	53
common lymphoid progenitor	4.41e-13	53
lymphoid lineage restricted progenitor cell	1.17e-12	52
lymphocyte of B lineage	1.94e-09	24
pro-B cell	1.94e-09	24
animal cell	2.96e-09	679
eukaryotic cell	2.96e-09	679
native cell	6.28e-09	722
dendritic cell	2.03e-08	10
conventional dendritic cell	3.19e-07	8

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	6.03e-21	102
blood island	6.03e-21	102
hemolymphoid system	5.65e-20	112
bone marrow	1.43e-19	80
bone element	3.76e-18	86
connective tissue	4.00e-18	375
immune system	1.63e-17	115
skeletal element	3.02e-15	101
skeletal system	3.02e-15	101
lateral plate mesoderm	5.06e-09	216
musculoskeletal system	6.52e-07	167

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

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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

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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

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This analysis result is provided for C0 - C305 clusters.