Coexpression cluster:C3462

Full id: C3462_Monocytederived_CD14_Macrophage_extraskeletal_schwannoma_Dendritic_Osteoblast

Phase1 CAGE Peaks

Hg19::chr14:93651576..93651587,+	p5@C14orf109
Hg19::chr15:65281775..65281821,-	p3@SPG21
Hg19::chr3:196065341..196065356,-	p4@TM4SF19

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:0042609	CD4 receptor binding	0.00971359607417973
GO:0050851	antigen receptor-mediated signaling pathway	0.0228754456591497
GO:0030140	trans-Golgi network transport vesicle	0.0228754456591497
GO:0002429	immune response-activating cell surface receptor signaling pathway	0.0228754456591497
GO:0002768	immune response-regulating cell surface receptor signaling pathway	0.0228754456591497
GO:0002757	immune response-activating signal transduction	0.0228754456591497
GO:0002764	immune response-regulating signal transduction	0.0228754456591497
GO:0030133	transport vesicle	0.0297609038989029
GO:0005798	Golgi-associated vesicle	0.0297609038989029
GO:0002253	activation of immune response	0.0297609038989029
GO:0050778	positive regulation of immune response	0.0297609038989029
GO:0010008	endosome membrane	0.0297609038989029
GO:0002684	positive regulation of immune system process	0.0297609038989029
GO:0044440	endosomal part	0.0297609038989029
GO:0050776	regulation of immune response	0.029907006894176
GO:0002682	regulation of immune system process	0.029907006894176
GO:0051240	positive regulation of multicellular organismal process	0.029907006894176
GO:0030136	clathrin-coated vesicle	0.0309264398045245
GO:0030135	coated vesicle	0.0374161160315025
GO:0005768	endosome	0.0466050765668934

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
monopoietic cell	1.20e-42	59
monocyte	1.20e-42	59
monoblast	1.20e-42	59
promonocyte	1.20e-42	59
defensive cell	6.39e-41	48
phagocyte	6.39e-41	48
macrophage dendritic cell progenitor	1.28e-40	61
myeloid leukocyte	4.84e-40	72
myeloid lineage restricted progenitor cell	4.20e-36	66
granulocyte monocyte progenitor cell	2.78e-35	67
classical monocyte	1.55e-33	42
CD14-positive, CD16-negative classical monocyte	1.55e-33	42
myeloid cell	1.23e-26	108
common myeloid progenitor	1.23e-26	108
stuff accumulating cell	2.78e-24	87
nongranular leukocyte	3.60e-16	115
leukocyte	1.86e-15	136
hematopoietic lineage restricted progenitor cell	4.30e-14	120
hematopoietic oligopotent progenitor cell	4.25e-13	161
hematopoietic multipotent progenitor cell	4.25e-13	161
hematopoietic stem cell	5.89e-13	168
angioblastic mesenchymal cell	5.89e-13	168
hematopoietic cell	2.49e-11	177
macrophage	5.66e-09	6

Uber Anatomy

Ontology term	p-value	n
immune system	2.29e-30	93
bone marrow	2.57e-30	76
bone element	9.85e-27	82
hemolymphoid system	3.19e-24	108
hematopoietic system	4.11e-23	98
blood island	4.11e-23	98
skeletal element	9.80e-23	90
skeletal system	1.27e-19	100
musculoskeletal system	1.29e-09	167
mesoderm	3.29e-09	315
mesoderm-derived structure	3.29e-09	315
presumptive mesoderm	3.29e-09	315
lateral plate mesoderm	1.55e-07	203

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
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324432517781083
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321319785744711
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319806752025918
ELK4#2005	2	10.823787772312	0.0109128471951648	0.0401878296267918
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293887735874046
SMARCB1#6598	2	12.1684771874383	0.00867500222192174	0.0329769439126187
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189917745865297

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.