Coexpression cluster:C691

Full id: C691_Monocytederived_CD14_Macrophage_CD19_Dendritic_immature_Whole

Phase1 CAGE Peaks

Hg19::chr11:67771024..67771043,-	p2@UNC93B1
Hg19::chr11:67771513..67771604,-	p1@UNC93B1
Hg19::chr14:21249200..21249248,+	p1@RNASE6
Hg19::chr14:21249254..21249267,+	p3@RNASE6
Hg19::chr14:21249300..21249314,+	p2@RNASE6
Hg19::chr14:21249998..21250018,+	p5@RNASE6
Hg19::chr5:66492562..66492635,-	p1@CD180
Hg19::chr6:32908739..32908746,-	p3@HLA-DMB
Hg19::chr6:32908765..32908786,-	p2@HLA-DMB
Hg19::chr6:32908792..32908830,-	p1@HLA-DMB
Hg19::chr6:6588941..6588960,+	p1@LY86
Hg19::chr6:6588974..6589011,+	p2@LY86

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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p.value	FDR	nGenes	nPathway	Name
5.55202746254732e-05	0.0175721669189623	3	511	Signaling in Immune system (Reactome):REACT_6900
3.63134547651233e-05	0.0175721669189623	2	55	{TRAF6,55} (Static Module):NA

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:0006952	defense response	0.00398983501859937
GO:0006955	immune response	0.0145573104414221
GO:0002376	immune system process	0.0145573104414221
GO:0006954	inflammatory response	0.0145573104414221
GO:0009611	response to wounding	0.0244421873004799
GO:0009605	response to external stimulus	0.0357037352160071
GO:0004522	pancreatic ribonuclease activity	0.0357037352160071
GO:0016892	endoribonuclease activity, producing 3'-phosphomonoesters	0.0357037352160071
GO:0031902	late endosome membrane	0.0357037352160071
GO:0016894	endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters	0.0357037352160071
GO:0006401	RNA catabolic process	0.0466318094114567
GO:0005765	lysosomal membrane	0.0466318094114567
GO:0005770	late endosome	0.0466318094114567
GO:0005774	vacuolar membrane	0.0485780051467031
GO:0044437	vacuolar part	0.0485780051467031
GO:0004521	endoribonuclease activity	0.0485780051467031
GO:0006959	humoral immune response	0.0485780051467031
GO:0005886	plasma membrane	0.0485780051467031
GO:0006950	response to stress	0.0485780051467031
GO:0010008	endosome membrane	0.0485780051467031
GO:0044440	endosomal part	0.0485780051467031

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
leukocyte	9.48e-49	140
nongranular leukocyte	6.82e-45	119
hematopoietic stem cell	4.10e-43	172
angioblastic mesenchymal cell	4.10e-43	172
hematopoietic cell	3.32e-41	182
hematopoietic oligopotent progenitor cell	1.77e-40	165
hematopoietic multipotent progenitor cell	1.77e-40	165
hematopoietic lineage restricted progenitor cell	1.12e-39	124
macrophage dendritic cell progenitor	1.33e-30	65
myeloid leukocyte	3.74e-30	76
monopoietic cell	1.52e-29	63
monocyte	1.52e-29	63
monoblast	1.52e-29	63
promonocyte	1.52e-29	63
granulocyte monocyte progenitor cell	2.04e-28	71
myeloid cell	3.83e-25	112
common myeloid progenitor	3.83e-25	112
myeloid lineage restricted progenitor cell	8.29e-25	70
CD14-positive, CD16-negative classical monocyte	2.56e-24	42
classical monocyte	3.00e-22	45
lymphocyte	9.33e-14	53
common lymphoid progenitor	9.33e-14	53
lymphoid lineage restricted progenitor cell	2.40e-13	52
lymphocyte of B lineage	3.15e-13	24
pro-B cell	3.15e-13	24
B cell	1.46e-09	14

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	3.07e-34	102
blood island	3.07e-34	102
hemolymphoid system	2.68e-30	112
adult organism	1.35e-28	115
bone marrow	1.35e-25	80
bone element	8.59e-22	86
immune system	1.20e-19	115
skeletal element	3.49e-15	101
skeletal system	3.49e-15	101
neural tube	2.33e-11	57
neural rod	2.33e-11	57
future spinal cord	2.33e-11	57
neural keel	2.33e-11	57
regional part of brain	7.05e-09	59
anterior neural tube	1.51e-08	42
regional part of forebrain	2.48e-08	41
forebrain	2.48e-08	41
future forebrain	2.48e-08	41
lateral plate mesoderm	6.52e-08	216
brain	1.88e-07	69
future brain	1.88e-07	69
blood	3.35e-07	15
haemolymphatic fluid	3.35e-07	15
organism substance	3.35e-07	15
telencephalon	4.83e-07	34
gray matter	5.27e-07	34
brain grey matter	5.27e-07	34
regional part of telencephalon	7.20e-07	33

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	3	6.08945044807591	0.0115136703549497	0.042112356174287
BCL11A#53335	5	11.8206062931696	3.49540037901642e-05	0.00068145626317733
IRF4#3662	5	9.13104695281005	0.000119452296579471	0.00162145547211637
MEF2C#4208	3	10.327838623156	0.00264680895377695	0.0146205151702285
NANOG#79923	3	7.31119462025316	0.00697119958520868	0.02948109465013
NFKB1#4790	7	3.20137033077974	0.00222865791151487	0.0128023103031022
PAX5#5079	6	3.33478276558891	0.00462982151105892	0.0218615575003835
POLR2A#5430	11	1.96849874517823	0.0015351588645567	0.0097601787700394
POU2F2#5452	5	3.79421835739272	0.00649961629267657	0.0278350525276109
SP1#6667	9	4.27378603360567	2.0740195727163e-05	0.000458333749798811
SPI1#6688	8	5.46954900568182	1.52450635998341e-05	0.000360466198166871
TBP#6908	8	2.47118045806426	0.00467271370660667	0.0220551157772989
USF2#7392	6	6.4960986925348	0.000127663267259117	0.00169782554046542

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.