Coexpression cluster:C974

Full id: C974_Dendritic_CD8_CD4_Natural_NK_B_Basophils

Phase1 CAGE Peaks

Hg19::chr10:129979299..129979317,+	p1@uc001lkg.1
Hg19::chr10:129979342..129979357,+	p2@uc001lkg.1
Hg19::chr10:129979383..129979404,+	p3@uc001lkg.1
Hg19::chr20:62367972..62367984,+	p3@LIME1
Hg19::chr20:62368028..62368039,+	p4@LIME1
Hg19::chr2:102972753..102972800,+	p4@IL18R1
Hg19::chrX:70838306..70838369,-	p1@CXCR3
Hg19::chrX:70838380..70838395,-	p2@CXCR3

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:0019955	cytokine binding	0.00183758911621637
GO:0004908	interleukin-1 receptor activity	0.0154665555303623
GO:0019966	interleukin-1 binding	0.0154665555303623
GO:0016494	C-X-C chemokine receptor activity	0.0154665555303623
GO:0019958	C-X-C chemokine binding	0.0154665555303623
GO:0005886	plasma membrane	0.01723178285095
GO:0016493	C-C chemokine receptor activity	0.0187002886462243
GO:0019957	C-C chemokine binding	0.0187002886462243
GO:0004907	interleukin receptor activity	0.0187002886462243
GO:0001637	G-protein chemoattractant receptor activity	0.0187002886462243
GO:0004950	chemokine receptor activity	0.0187002886462243
GO:0019956	chemokine binding	0.0187002886462243
GO:0019965	interleukin binding	0.0187002886462243
GO:0006955	immune response	0.0187002886462243
GO:0002376	immune system process	0.0236252975438142
GO:0004896	hematopoietin/interferon-class (D200-domain) cytokine receptor activity	0.0250187790858287
GO:0051480	cytosolic calcium ion homeostasis	0.0250187790858287
GO:0007204	elevation of cytosolic calcium ion concentration	0.0250187790858287
GO:0016021	integral to membrane	0.0272501061713494
GO:0031224	intrinsic to membrane	0.0272501061713494
GO:0019838	growth factor binding	0.0272501061713494
GO:0045087	innate immune response	0.0292619805128171
GO:0055074	calcium ion homeostasis	0.0292619805128171
GO:0006874	cellular calcium ion homeostasis	0.0292619805128171
GO:0004888	transmembrane receptor activity	0.0292619805128171
GO:0006875	cellular metal ion homeostasis	0.0292619805128171
GO:0055065	metal ion homeostasis	0.0292619805128171
GO:0044425	membrane part	0.029686163485034
GO:0042330	taxis	0.029686163485034
GO:0006935	chemotaxis	0.029686163485034
GO:0001653	peptide receptor activity	0.029686163485034
GO:0008528	peptide receptor activity, G-protein coupled	0.029686163485034
GO:0030005	cellular di-, tri-valent inorganic cation homeostasis	0.0335256500190761
GO:0007626	locomotory behavior	0.0335256500190761
GO:0055066	di-, tri-valent inorganic cation homeostasis	0.0335256500190761
GO:0030003	cellular cation homeostasis	0.0350714466327775
GO:0055080	cation homeostasis	0.0350714466327775
GO:0042277	peptide binding	0.0350714466327775
GO:0055082	cellular chemical homeostasis	0.0379306900088159
GO:0006873	cellular ion homeostasis	0.0379306900088159
GO:0004872	receptor activity	0.0400874681138121
GO:0050801	ion homeostasis	0.0400874681138121
GO:0016020	membrane	0.0400874681138121
GO:0007610	behavior	0.0427037919488679
GO:0048878	chemical homeostasis	0.0428808753857429
GO:0019725	cellular homeostasis	0.048826880339797
GO:0060089	molecular transducer activity	0.048826880339797
GO:0004871	signal transducer activity	0.048826880339797
GO:0051674	localization of cell	0.048826880339797
GO:0006928	cell motility	0.048826880339797

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
lymphoid lineage restricted progenitor cell	4.21e-39	52
lymphocyte	4.30e-38	53
common lymphoid progenitor	4.30e-38	53
nucleate cell	3.45e-36	55
leukocyte	3.28e-28	136
T cell	1.26e-27	25
pro-T cell	1.26e-27	25
mature alpha-beta T cell	2.62e-27	18
alpha-beta T cell	2.62e-27	18
immature T cell	2.62e-27	18
mature T cell	2.62e-27	18
immature alpha-beta T cell	2.62e-27	18
nongranular leukocyte	9.74e-25	115
hematopoietic stem cell	1.06e-21	168
angioblastic mesenchymal cell	1.06e-21	168
hematopoietic cell	1.35e-19	177
hematopoietic lineage restricted progenitor cell	1.44e-19	120
CD8-positive, alpha-beta T cell	1.35e-17	11
hematopoietic oligopotent progenitor cell	1.42e-16	161
hematopoietic multipotent progenitor cell	1.42e-16	161
lymphocyte of B lineage	1.51e-10	24
pro-B cell	1.51e-10	24
CD4-positive, alpha-beta T cell	4.86e-10	6

Uber Anatomy

Ontology term	p-value	n
blood	4.30e-13	15
haemolymphatic fluid	4.30e-13	15
organism substance	4.30e-13	15
adult organism	8.11e-11	114
hemopoietic organ	7.18e-08	7
immune organ	7.18e-08	7
thymus	3.00e-07	4
hemolymphoid system gland	3.00e-07	4
thymic region	3.00e-07	4
pharyngeal gland	3.00e-07	4
thymus primordium	3.00e-07	4

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)
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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
EBF1#1879	5	5.56654177910563	0.000744581328255861	0.0058636200679923

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.