Coexpression cluster:C2349

Full id: C2349_Mast_CD14_Smooth_Mesenchymal_Hair_mesothelioma_papillotubular

Phase1 CAGE Peaks

Hg19::chr15:75913265..75913337,-	p4@SNUPN
Hg19::chr16:27258633..27258637,+	p@chr16:27258633..27258637 +
Hg19::chr19:35646092..35646138,+	p2@FXYD5
Hg19::chr19:35646149..35646177,+	p5@FXYD5

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:0046588	negative regulation of calcium-dependent cell-cell adhesion	0.00259036853879666
GO:0046586	regulation of calcium-dependent cell-cell adhesion	0.00259036853879666
GO:0030033	microvillus biogenesis	0.006475540085248
GO:0032528	microvillus organization and biogenesis	0.006475540085248
GO:0000339	RNA cap binding	0.0072523913889013
GO:0022408	negative regulation of cell-cell adhesion	0.00805738235098189
GO:0045296	cadherin binding	0.00805738235098189
GO:0022407	regulation of cell-cell adhesion	0.00805738235098189
GO:0050839	cell adhesion molecule binding	0.00805738235098189
GO:0016339	calcium-dependent cell-cell adhesion	0.0122408727264318
GO:0007162	negative regulation of cell adhesion	0.0122408727264318
GO:0022892	substrate-specific transporter activity	0.0198064840396804
GO:0030155	regulation of cell adhesion	0.0262770403496228
GO:0005643	nuclear pore	0.0298227869868878
GO:0006606	protein import into nucleus	0.0298227869868878
GO:0046930	pore complex	0.0298227869868878
GO:0051170	nuclear import	0.0298227869868878
GO:0044453	nuclear membrane part	0.0318961541352686
GO:0017038	protein import	0.0332065413839154
GO:0031965	nuclear membrane	0.0341084762377736
GO:0006913	nucleocytoplasmic transport	0.0341084762377736
GO:0008565	protein transporter activity	0.0341084762377736
GO:0051169	nuclear transport	0.0341084762377736
GO:0016043	cellular component organization and biogenesis	0.0341084762377736
GO:0005635	nuclear envelope	0.0376325929129757
GO:0032990	cell part morphogenesis	0.0376325929129757
GO:0048858	cell projection morphogenesis	0.0376325929129757
GO:0030030	cell projection organization and biogenesis	0.0376325929129757
GO:0006605	protein targeting	0.0388204651484896
GO:0006810	transport	0.0413724656089171
GO:0051234	establishment of localization	0.0420472423208777
GO:0051179	localization	0.047836148453937

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
defensive cell	2.17e-23	48
phagocyte	2.17e-23	48
classical monocyte	3.99e-21	42
CD14-positive, CD16-negative classical monocyte	3.99e-21	42
somatic cell	1.85e-20	588
native cell	2.07e-20	722
myeloid lineage restricted progenitor cell	3.07e-20	66
granulocyte monocyte progenitor cell	4.06e-20	67
animal cell	9.63e-20	679
eukaryotic cell	9.63e-20	679
monopoietic cell	1.40e-19	59
monocyte	1.40e-19	59
monoblast	1.40e-19	59
promonocyte	1.40e-19	59
stem cell	2.78e-19	441
multi fate stem cell	3.18e-19	427
myeloid leukocyte	5.90e-19	72
somatic stem cell	7.86e-19	433
macrophage dendritic cell progenitor	1.22e-18	61
myeloid cell	1.27e-15	108
common myeloid progenitor	1.27e-15	108
mesenchymal cell	1.14e-13	354
connective tissue cell	2.18e-13	361
stuff accumulating cell	4.92e-13	87
vascular associated smooth muscle cell	9.28e-11	32
motile cell	1.11e-09	386
smooth muscle cell	3.94e-09	43
smooth muscle myoblast	3.94e-09	43
muscle cell	1.60e-08	55
muscle precursor cell	8.45e-08	58
myoblast	8.45e-08	58
multi-potent skeletal muscle stem cell	8.45e-08	58
contractile cell	2.19e-07	59
mesodermal cell	7.12e-07	121
fibroblast	9.67e-07	76

Uber Anatomy

Ontology term	p-value	n
lateral plate mesoderm	2.27e-28	203
mesoderm	1.74e-26	315
mesoderm-derived structure	1.74e-26	315
presumptive mesoderm	1.74e-26	315
musculoskeletal system	3.99e-19	167
bone marrow	9.66e-18	76
hematopoietic system	1.70e-17	98
blood island	1.70e-17	98
skeletal element	5.90e-16	90
bone element	6.12e-16	82
hemolymphoid system	1.09e-14	108
skeletal system	9.71e-14	100
connective tissue	5.14e-13	371
immune system	2.54e-12	93
artery	3.23e-12	42
arterial blood vessel	3.23e-12	42
arterial system	3.23e-12	42
splanchnic layer of lateral plate mesoderm	1.92e-10	83
systemic artery	2.04e-10	33
systemic arterial system	2.04e-10	33
cardiovascular system	1.47e-08	109
epithelial tube open at both ends	5.03e-08	59
blood vessel	5.03e-08	59
blood vasculature	5.03e-08	59
vascular cord	5.03e-08	59
circulatory system	6.56e-08	112

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
FOS#2353	3	6.7484664816708	0.00503245277631794	0.0234614916304736
THAP1#55145	2	15.6845723014257	0.00584046967835792	0.0262444201332942

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.