Coexpression cluster:C979

Full id: C979_Mast_CD14_Eosinophils_immature_Neutrophils_CD4_Basophils

Phase1 CAGE Peaks

Hg19::chr10:35484090..35484104,+	p6@CREM
Hg19::chr14:91976671..91976682,-	p6@SMEK1
Hg19::chr15:52313600..52313611,+	p12@MAPK6
Hg19::chr16:80404220..80404224,+	p@chr16:80404220..80404224 +
Hg19::chr1:178569076..178569079,+	p@chr1:178569076..178569079 +
Hg19::chr21:36260463..36260480,-	p9@RUNX1
Hg19::chr3:182971089..182971100,+	p12@B3GNT5
Hg19::chr3:182971130..182971148,+	p3@B3GNT5

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:0008457	beta-galactosyl-N-acetylglucosaminylgalactosylglucosyl-ceramide beta-1,3-acetylglucosaminyltransferase activity	0.0057400211939244
GO:0030854	positive regulation of granulocyte differentiation	0.0057400211939244
GO:0008917	lipopolysaccharide N-acetylglucosaminyltransferase activity	0.0057400211939244
GO:0030852	regulation of granulocyte differentiation	0.0057400211939244
GO:0008140	cAMP response element binding protein binding	0.0137744288177509
GO:0030851	granulocyte differentiation	0.0153040198506013
GO:0002763	positive regulation of myeloid leukocyte differentiation	0.0157923462251457
GO:0016563	transcription activator activity	0.0157923462251457
GO:0045766	positive regulation of angiogenesis	0.0286764594625967
GO:0045639	positive regulation of myeloid cell differentiation	0.0286764594625967
GO:0009247	glycolipid biosynthetic process	0.0286764594625967
GO:0002761	regulation of myeloid leukocyte differentiation	0.0286764594625967
GO:0007275	multicellular organismal development	0.0334812275315464
GO:0006664	glycolipid metabolic process	0.0458310383064836
GO:0002573	myeloid leukocyte differentiation	0.0458310383064836
GO:0045637	regulation of myeloid cell differentiation	0.0458310383064836
GO:0004707	MAP kinase activity	0.0458310383064836
GO:0045765	regulation of angiogenesis	0.0482261591889499
GO:0008378	galactosyltransferase activity	0.0482261591889499

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
classical monocyte	8.57e-37	42
CD14-positive, CD16-negative classical monocyte	8.57e-37	42
myeloid leukocyte	8.43e-34	72
defensive cell	1.48e-33	48
phagocyte	1.48e-33	48
granulocyte monocyte progenitor cell	5.58e-33	67
myeloid lineage restricted progenitor cell	2.22e-30	66
macrophage dendritic cell progenitor	1.08e-29	61
monopoietic cell	6.92e-28	59
monocyte	6.92e-28	59
monoblast	6.92e-28	59
promonocyte	6.92e-28	59
myeloid cell	1.80e-19	108
common myeloid progenitor	1.80e-19	108
stuff accumulating cell	7.48e-19	87
leukocyte	2.03e-16	136
hematopoietic lineage restricted progenitor cell	6.76e-13	120
nongranular leukocyte	3.54e-11	115
hematopoietic stem cell	1.44e-10	168
angioblastic mesenchymal cell	1.44e-10	168
hematopoietic cell	1.71e-09	177
hematopoietic oligopotent progenitor cell	5.86e-09	161
hematopoietic multipotent progenitor cell	5.86e-09	161

Uber Anatomy

Ontology term	p-value	n
immune system	1.18e-29	93
bone marrow	2.36e-29	76
bone element	5.84e-27	82
skeletal element	7.57e-26	90
hemolymphoid system	7.81e-26	108
hematopoietic system	2.39e-24	98
blood island	2.39e-24	98
skeletal system	3.65e-21	100
musculoskeletal system	8.19e-13	167
lateral plate mesoderm	3.30e-10	203
mesoderm	5.05e-07	315
mesoderm-derived structure	5.05e-07	315
presumptive mesoderm	5.05e-07	315

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
EGR1#1958	5	3.11761193425634	0.0105139099038836	0.038925954002329
FOSL2#2355	3	6.34882522671063	0.00921194665864107	0.0348279212670799
STAT1#6772	3	7.7649703114497	0.00524867388918618	0.024314315915401

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.