Coexpression cluster:C1754

Full id: C1754_immature_CD14_Dendritic_CD34_Basophils_Mast_migratory

Phase1 CAGE Peaks

Hg19::chr15:86123791..86123808,+	p22@AKAP13
Hg19::chr15:86124854..86124875,+	p30@AKAP13
Hg19::chr19:3136115..3136165,+	p2@GNA15
Hg19::chr3:119013434..119013460,+	p3@ARHGAP31
Hg19::chr3:119013476..119013540,+	p2@ARHGAP31

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
3.28059829023111e-05	0.0133922329919482	2	95	G Protein Signaling Pathways (Wikipathways):WP35
5.33094045966131e-05	0.0133922329919482	2	121	Signaling by Rho GTPases (Reactome):REACT_11044
6.34702985400389e-05	0.0133922329919482	2	132	{RAC1,133} (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:0007207	muscarinic acetylcholine receptor, phospholipase C activating pathway	0.0192505813106471
GO:0004691	cAMP-dependent protein kinase activity	0.0256625304030679
GO:0004690	cyclic nucleotide-dependent protein kinase activity	0.0256625304030679
GO:0007202	phospholipase C activation	0.0256625304030679
GO:0006471	protein amino acid ADP-ribosylation	0.0333563781795267
GO:0005834	heterotrimeric G-protein complex	0.0395508365680418
GO:0019897	extrinsic to plasma membrane	0.0405964492107154
GO:0007242	intracellular signaling cascade	0.0405964492107154
GO:0019992	diacylglycerol binding	0.0405964492107154
GO:0051480	cytosolic calcium ion homeostasis	0.0405964492107154
GO:0007204	elevation of cytosolic calcium ion concentration	0.0405964492107154
GO:0051345	positive regulation of hydrolase activity	0.0405964492107154
GO:0007200	G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)	0.0433828646488185
GO:0019898	extrinsic to membrane	0.043486306495677
GO:0055074	calcium ion homeostasis	0.043486306495677
GO:0006874	cellular calcium ion homeostasis	0.043486306495677
GO:0006875	cellular metal ion homeostasis	0.043486306495677
GO:0055065	metal ion homeostasis	0.043486306495677
GO:0048015	phosphoinositide-mediated signaling	0.043486306495677
GO:0005089	Rho guanyl-nucleotide exchange factor activity	0.0448398258562391
GO:0035023	regulation of Rho protein signal transduction	0.0448398258562391
GO:0005088	Ras guanyl-nucleotide exchange factor activity	0.0448398258562391
GO:0030005	cellular di-, tri-valent inorganic cation homeostasis	0.0448398258562391
GO:0055066	di-, tri-valent inorganic cation homeostasis	0.0448398258562391
GO:0007266	Rho protein signal transduction	0.0448398258562391
GO:0030003	cellular cation homeostasis	0.0448398258562391
GO:0055080	cation homeostasis	0.0448398258562391
GO:0060089	molecular transducer activity	0.0448398258562391
GO:0004871	signal transducer activity	0.0448398258562391
GO:0055082	cellular chemical homeostasis	0.0488889669249315
GO:0006873	cellular ion homeostasis	0.0488889669249315

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
granulocyte monocyte progenitor cell	1.20e-55	67
leukocyte	2.11e-53	136
myeloid leukocyte	1.06e-51	72
macrophage dendritic cell progenitor	6.22e-50	61
myeloid lineage restricted progenitor cell	6.57e-50	66
defensive cell	7.29e-49	48
phagocyte	7.29e-49	48
monopoietic cell	1.43e-47	59
monocyte	1.43e-47	59
monoblast	1.43e-47	59
promonocyte	1.43e-47	59
hematopoietic lineage restricted progenitor cell	6.13e-44	120
classical monocyte	9.43e-44	42
CD14-positive, CD16-negative classical monocyte	9.43e-44	42
nongranular leukocyte	5.82e-42	115
hematopoietic stem cell	2.05e-40	168
angioblastic mesenchymal cell	2.05e-40	168
myeloid cell	2.41e-37	108
common myeloid progenitor	2.41e-37	108
hematopoietic oligopotent progenitor cell	2.76e-37	161
hematopoietic multipotent progenitor cell	2.76e-37	161
hematopoietic cell	1.80e-36	177
stuff accumulating cell	5.02e-23	87
dendritic cell	3.27e-12	10
conventional dendritic cell	2.86e-10	8
intermediate monocyte	3.46e-09	9
CD14-positive, CD16-positive monocyte	3.46e-09	9
mesenchymal cell	9.33e-08	354
immature conventional dendritic cell	1.13e-07	5
common dendritic progenitor	1.13e-07	5
connective tissue cell	4.41e-07	361

Uber Anatomy

Ontology term	p-value	n
bone marrow	8.27e-48	76
hematopoietic system	1.84e-45	98
blood island	1.84e-45	98
immune system	4.20e-43	93
bone element	2.21e-42	82
hemolymphoid system	4.15e-41	108
skeletal element	1.38e-37	90
skeletal system	2.42e-32	100
lateral plate mesoderm	1.01e-19	203
adult organism	1.97e-18	114
musculoskeletal system	4.05e-13	167
mesoderm	4.94e-08	315
mesoderm-derived structure	4.94e-08	315
presumptive mesoderm	4.94e-08	315

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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No analysis results for this cluster

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.