Coexpression cluster:C662

Full id: C662_Mast_CD8_Natural_Basophils_CD4_Peripheral_Dendritic

Phase1 CAGE Peaks

Hg19::chr12:9142131..9142229,+	p1@KLRG1
Hg19::chr12:9142239..9142262,+	p4@KLRG1
Hg19::chr12:9142310..9142328,+	p5@KLRG1
Hg19::chr12:9142330..9142341,+	p@chr12:9142330..9142341 +
Hg19::chr12:9144805..9144867,+	p3@KLRG1
Hg19::chr15:86126120..86126165,+	p3@AKAP13
Hg19::chr16:85588893..85588910,-	p@chr16:85588893..85588910 -
Hg19::chr1:23430065..23430077,+	p@chr1:23430065..23430077 +
Hg19::chr21:36421147..36421193,-	p10@RUNX1
Hg19::chr21:36421347..36421380,-	p8@RUNX1
Hg19::chr4:151749436..151749449,-	p@chr4:151749436..151749449 -
Hg19::chr4:151749450..151749479,-	p@chr4:151749450..151749479 -
Hg19::chr4:151749484..151749504,-	p@chr4:151749484..151749504 -

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:0030854	positive regulation of granulocyte differentiation	0.00596079123984457
GO:0030852	regulation of granulocyte differentiation	0.00596079123984457
GO:0030851	granulocyte differentiation	0.0149002234807402
GO:0002763	positive regulation of myeloid leukocyte differentiation	0.0149002234807402
GO:0004691	cAMP-dependent protein kinase activity	0.0190706017369349
GO:0045766	positive regulation of angiogenesis	0.0193657290530936
GO:0004690	cyclic nucleotide-dependent protein kinase activity	0.0193657290530936
GO:0045639	positive regulation of myeloid cell differentiation	0.0193657290530936
GO:0002761	regulation of myeloid leukocyte differentiation	0.0198611167149153
GO:0002573	myeloid leukocyte differentiation	0.0357342245604695
GO:0045637	regulation of myeloid cell differentiation	0.0368127436255965
GO:0045765	regulation of angiogenesis	0.0377105745980246
GO:0045597	positive regulation of cell differentiation	0.0430427686180983
GO:0019992	diacylglycerol binding	0.0446283343177092
GO:0031404	chloride ion binding	0.0446283343177092
GO:0043168	anion binding	0.0446283343177092
GO:0051094	positive regulation of developmental process	0.0475867330910966
GO:0006968	cellular defense response	0.0475867330910966
GO:0030099	myeloid cell differentiation	0.0482057734703268

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
hematopoietic stem cell	2.02e-30	168
angioblastic mesenchymal cell	2.02e-30	168
mature alpha-beta T cell	1.62e-28	18
alpha-beta T cell	1.62e-28	18
immature T cell	1.62e-28	18
mature T cell	1.62e-28	18
immature alpha-beta T cell	1.62e-28	18
hematopoietic cell	8.58e-28	177
leukocyte	8.89e-27	136
hematopoietic oligopotent progenitor cell	1.95e-26	161
hematopoietic multipotent progenitor cell	1.95e-26	161
hematopoietic lineage restricted progenitor cell	1.10e-20	120
CD8-positive, alpha-beta T cell	1.98e-19	11
T cell	7.73e-19	25
pro-T cell	7.73e-19	25
nongranular leukocyte	1.76e-18	115
lymphoid lineage restricted progenitor cell	3.30e-15	52
nucleate cell	3.85e-15	55
lymphocyte	9.08e-15	53
common lymphoid progenitor	9.08e-15	53
myeloid cell	2.36e-12	108
common myeloid progenitor	2.36e-12	108
myeloid leukocyte	3.40e-11	72
histamine secreting cell	3.56e-10	5
biogenic amine secreting cell	3.56e-10	5
granulocytopoietic cell	3.56e-10	5
mast cell	3.56e-10	5
mast cell progenitor	3.56e-10	5
basophil mast progenitor cell	3.56e-10	5
CD4-positive, alpha-beta T cell	6.96e-10	6
myeloid lineage restricted progenitor cell	1.01e-07	66
granulocyte	2.17e-07	8
granulocyte monocyte progenitor cell	8.56e-07	67

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	2.19e-18	98
blood island	2.19e-18	98
hemolymphoid system	1.37e-17	108
blood	2.17e-14	15
haemolymphatic fluid	2.17e-14	15
organism substance	2.17e-14	15
immune system	2.35e-09	93
adult organism	2.89e-07	114
hemopoietic organ	6.19e-07	7
immune organ	6.19e-07	7

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
BATF#10538	6	11.2420623656786	6.38699523402909e-06	0.000188326198545106
FOS#2353	5	3.46075204188246	0.0101121032593917	0.0378285676734585
GATA2#2624	7	6.86265554883676	2.05065762260648e-05	0.000454517469115871
IRF4#3662	4	6.74292698053666	0.00222199559447697	0.0127759853496796
JUN#3725	7	6.73767725741187	2.31332287642027e-05	0.000504913537911089
SPI1#6688	6	3.78661085008741	0.00261400033851087	0.0144530457596345

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.