Coexpression cluster:C3670

Full id: C3670_CD14_Mesenchymal_Eosinophils_CD14CD16_Monocytederived_Neutrophils_Macrophage

Phase1 CAGE Peaks

Hg19::chr17:6915808..6915823,+	p5@RNASEK p8@C17orf49
Hg19::chr8:146078860..146078917,-	p3@COMMD5
Hg19::chr8:146078927..146078951,-	p4@COMMD5

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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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>

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Cell Type

Ontology term	p-value	n
myeloid leukocyte	3.61e-37	72
macrophage dendritic cell progenitor	3.85e-33	61
monopoietic cell	5.05e-32	59
monocyte	5.05e-32	59
monoblast	5.05e-32	59
promonocyte	5.05e-32	59
granulocyte monocyte progenitor cell	7.37e-32	67
defensive cell	9.87e-31	48
phagocyte	9.87e-31	48
myeloid lineage restricted progenitor cell	7.97e-30	66
classical monocyte	2.52e-27	42
CD14-positive, CD16-negative classical monocyte	2.52e-27	42
stuff accumulating cell	2.41e-22	87
myeloid cell	1.14e-21	108
common myeloid progenitor	1.14e-21	108
multi fate stem cell	4.84e-11	427
leukocyte	1.56e-10	136
somatic stem cell	2.53e-10	433
stem cell	2.74e-09	441
endothelial cell	3.07e-09	36
connective tissue cell	4.94e-09	361
mesenchymal cell	5.85e-09	354
hematopoietic lineage restricted progenitor cell	2.68e-07	120
lining cell	3.19e-07	58
barrier cell	3.19e-07	58
nongranular leukocyte	5.73e-07	115

Uber Anatomy

Ontology term	p-value	n
lateral plate mesoderm	4.45e-31	203
hemolymphoid system	3.71e-29	108
bone marrow	9.06e-29	76
mesoderm	1.14e-28	315
mesoderm-derived structure	1.14e-28	315
presumptive mesoderm	1.14e-28	315
immune system	4.29e-28	93
hematopoietic system	1.39e-26	98
blood island	1.39e-26	98
bone element	1.53e-24	82
skeletal element	2.23e-23	90
skeletal system	2.01e-21	100
musculoskeletal system	1.13e-20	167
embryonic structure	1.66e-08	564
connective tissue	1.81e-08	371
germ layer	3.39e-08	560
germ layer / neural crest	3.39e-08	560
embryonic tissue	3.39e-08	560
presumptive structure	3.39e-08	560
germ layer / neural crest derived structure	3.39e-08	560
epiblast (generic)	3.39e-08	560
circulatory system	4.84e-08	112
cardiovascular system	4.90e-08	109
vessel	5.56e-07	68

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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321794944395849
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0461773430412823
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0294217920313677
SMARCB1#6598	2	12.1684771874383	0.00867500222192174	0.0329841472642815
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190104655259953
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00421321342244233
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328998452977241
ZBTB33#10009	2	21.1098166866541	0.00292859706060324	0.0156346035072505

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.