Coexpression cluster:C909

Full id: C909_Whole_CD19_CD8_Neutrophils_Eosinophils_CD4_blood

Phase1 CAGE Peaks

Hg19::chr15:40600231..40600255,+	p@chr15:40600231..40600255 +
Hg19::chr17:29151686..29151766,-	p1@CRLF3
Hg19::chr19:18391246..18391315,+	p1@AB593186
Hg19::chr19:2290149..2290192,+	p2@uc002lvo.1
Hg19::chr21:44204140..44204160,+	p@chr21:44204140..44204160 +
Hg19::chr2:85822676..85822691,-	p@chr2:85822676..85822691 -
Hg19::chr5:162932571..162932661,+	p1@MAT2B
Hg19::chr5:176784837..176784936,+	p1@RGS14
Hg19::chr6:32812568..32812631,+	p2@PSMB9

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:0008831	dTDP-4-dehydrorhamnose reductase activity	0.00173083716001413
GO:0045226	extracellular polysaccharide biosynthetic process	0.00173083716001413
GO:0046379	extracellular polysaccharide metabolic process	0.00173083716001413
GO:0048269	methionine adenosyltransferase complex	0.00173083716001413
GO:0048270	methionine adenosyltransferase regulator activity	0.00173083716001413
GO:0006556	S-adenosylmethionine biosynthetic process	0.00288464368263519
GO:0046500	S-adenosylmethionine metabolic process	0.00370871841460287
GO:0000097	sulfur amino acid biosynthetic process	0.0216233659096436
GO:0000096	sulfur amino acid metabolic process	0.025928944303149
GO:0008277	regulation of G-protein coupled receptor protein signaling pathway	0.025928944303149
GO:0004298	threonine endopeptidase activity	0.025928944303149
GO:0033692	cellular polysaccharide biosynthetic process	0.025928944303149
GO:0000271	polysaccharide biosynthetic process	0.025928944303149
GO:0005839	proteasome core complex (sensu Eukaryota)	0.025928944303149
GO:0044272	sulfur compound biosynthetic process	0.025928944303149
GO:0000502	proteasome complex (sensu Eukaryota)	0.0369922818669568
GO:0044264	cellular polysaccharide metabolic process	0.0369922818669568
GO:0008652	amino acid biosynthetic process	0.0369922818669568
GO:0005976	polysaccharide metabolic process	0.0369922818669568
GO:0006790	sulfur metabolic process	0.0369922818669568
GO:0006575	amino acid derivative metabolic process	0.0369922818669568
GO:0043284	biopolymer biosynthetic process	0.0390134412752236
GO:0009968	negative regulation of signal transduction	0.0390134412752236
GO:0009309	amine biosynthetic process	0.0427614578009655
GO:0046483	heterocycle metabolic process	0.0448310930447899
GO:0016051	carbohydrate biosynthetic process	0.045748758593867
GO:0044271	nitrogen compound biosynthetic process	0.046045758423692
GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	0.046045758423692
GO:0006730	one-carbon compound metabolic process	0.046045758423692
GO:0016614	oxidoreductase activity, acting on CH-OH group of donors	0.0473686029795388
GO:0005057	receptor signaling protein activity	0.0491570475788475
GO:0006725	aromatic compound metabolic process	0.049226446731777

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
hematopoietic stem cell	5.39e-65	172
angioblastic mesenchymal cell	5.39e-65	172
hematopoietic oligopotent progenitor cell	3.00e-61	165
hematopoietic multipotent progenitor cell	3.00e-61	165
hematopoietic cell	1.27e-59	182
leukocyte	1.03e-57	140
hematopoietic lineage restricted progenitor cell	1.23e-49	124
nongranular leukocyte	5.34e-48	119
myeloid cell	3.09e-33	112
common myeloid progenitor	3.09e-33	112
myeloid leukocyte	1.06e-26	76
lymphocyte	3.91e-25	53
common lymphoid progenitor	3.91e-25	53
lymphoid lineage restricted progenitor cell	6.14e-25	52
granulocyte monocyte progenitor cell	3.69e-23	71
myeloid lineage restricted progenitor cell	5.06e-23	70
macrophage dendritic cell progenitor	5.34e-21	65
monopoietic cell	1.83e-20	63
monocyte	1.83e-20	63
monoblast	1.83e-20	63
promonocyte	1.83e-20	63
CD14-positive, CD16-negative classical monocyte	1.48e-17	42
classical monocyte	5.23e-17	45
T cell	2.57e-13	25
pro-T cell	2.57e-13	25
mature alpha-beta T cell	1.13e-11	18
alpha-beta T cell	1.13e-11	18
immature T cell	1.13e-11	18
mature T cell	1.13e-11	18
immature alpha-beta T cell	1.13e-11	18
lymphocyte of B lineage	3.04e-11	24
pro-B cell	3.04e-11	24
B cell	1.08e-08	14
CD8-positive, alpha-beta T cell	4.68e-08	11

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.62e-30	102
blood island	1.62e-30	102
hemolymphoid system	1.21e-29	112
bone marrow	1.61e-19	80
adult organism	1.16e-17	115
bone element	3.67e-17	86
immune system	5.70e-16	115
skeletal element	8.50e-12	101
skeletal system	8.50e-12	101
blood	2.60e-09	15
haemolymphatic fluid	2.60e-09	15
organism substance	2.60e-09	15

Disease

Ontology term	p-value	n
hematologic cancer	3.28e-10	51
immune system cancer	3.28e-10	51
leukemia	3.39e-08	39

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
CCNT2#905	5	3.52011198720146	0.00704556022641387	0.0293956241805065
EBF1#1879	4	3.95842970958622	0.01255739025408	0.0454161194288141
ELF1#1997	8	3.78497596338448	6.58614701323904e-05	0.00106726238621516
GABPB1#2553	6	4.71178922412145	0.000457630704900798	0.00421765735873054
MAX#4149	5	3.58475306055951	0.00650226248509667	0.0278429598885203
MYC#4609	7	4.06177478902954	0.000235555679657337	0.00256851113256762
NFKB1#4790	7	4.26849377437298	0.000169653664166286	0.00207306177978973
NFYA#4800	3	6.14186023327684	0.0104816316305809	0.0388188342505758
NFYB#4801	3	5.58659775117882	0.0135850027711194	0.0479520110995314
PAX5#5079	5	3.70531418398768	0.00561655707771942	0.0253934027982657
POLR2A#5430	8	1.90884726805162	0.011661228959883	0.0425849537166061
SMARCB1#6598	3	6.08423859371914	0.0107567140124601	0.0396982386214114
SP1#6667	5	3.1657674323005	0.0111972168609182	0.0411205081661604
SPI1#6688	5	4.55795750473485	0.00221269338710164	0.0127239007078245

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.