Coexpression cluster:C412

Full id: C412_serous_breast_papillotubular_ductus_seminal_kidney_clear

Phase1 CAGE Peaks

Hg19::chr11:13974012..13974015,-	p@chr11:13974012..13974015 -
Hg19::chr11:61897513..61897534,+	p4@INCENP
Hg19::chr11:61897578..61897585,+	p10@INCENP
Hg19::chr16:34981388..34981402,+	p1@ENST00000516373
Hg19::chr17:37809300..37809309,+	p13@STARD3
Hg19::chr17:37856184..37856193,+	p6@ERBB2
Hg19::chr17:37856299..37856329,+	p1@ERBB2
Hg19::chr19:23732661..23732689,+	p@chr19:23732661..23732689 +
Hg19::chr1:159836049..159836056,+	p@chr1:159836049..159836056 +
Hg19::chr1:180240503..180240504,-	p@chr1:180240503..180240504 -
Hg19::chr20:30943898..30943899,-	p@chr20:30943898..30943899 -
Hg19::chr20:39536980..39536981,+	p@chr20:39536980..39536981 +
Hg19::chr2:22353663..22353666,+	p@chr2:22353663..22353666 +
Hg19::chr2:235157093..235157098,+	p@chr2:235157093..235157098 +
Hg19::chr3:168726935..168726936,-	p@chr3:168726935..168726936 -
Hg19::chr5:173377093..173377094,-	p@chr5:173377093..173377094 -
Hg19::chr6:11768690..11768702,-	p@chr6:11768690..11768702 -
Hg19::chr6:11768713..11768725,-	p@chr6:11768713..11768725 -
Hg19::chr6:42724431..42724435,+	p@chr6:42724431..42724435 +
Hg19::chr7:119683648..119683658,+	p@chr7:119683648..119683658 +
Hg19::chr7:150006580..150006590,+	p6@LRRC61
Hg19::chr7:150037547..150037552,-	p10@RARRES2
Hg19::chr7:154497207..154497243,-	p@chr7:154497207..154497243 -
Hg19::chr8:101588316..101588317,-	p1@AK127517
Hg19::chr9:88496176..88496181,+	p@chr9:88496176..88496181 +

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:0033087	negative regulation of immature T cell proliferation	0.00747674555516307
GO:0033080	immature T cell proliferation in the thymus	0.00747674555516307
GO:0033079	immature T cell proliferation	0.00747674555516307
GO:0033083	regulation of immature T cell proliferation	0.00747674555516307
GO:0033088	negative regulation of immature T cell proliferation in the thymus	0.00747674555516307
GO:0033084	regulation of immature T cell proliferation in the thymus	0.00747674555516307
GO:0005006	epidermal growth factor receptor activity	0.0168202015612282
GO:0005721	centric heterochromatin	0.0168202015612282
GO:0043125	ErbB-3 class receptor binding	0.0199335866525098
GO:0008045	motor axon guidance	0.0224236346827391
GO:0033077	T cell differentiation in the thymus	0.0313723029195121
GO:0007528	neuromuscular junction development	0.0313723029195121
GO:0016101	diterpenoid metabolic process	0.0313723029195121
GO:0017127	cholesterol transporter activity	0.0313723029195121
GO:0001523	retinoid metabolic process	0.0313723029195121
GO:0006700	C21-steroid hormone biosynthetic process	0.0313723029195121
GO:0004716	receptor signaling protein tyrosine kinase activity	0.0313723029195121
GO:0015248	sterol transporter activity	0.0313723029195121
GO:0030879	mammary gland development	0.0313723029195121
GO:0006721	terpenoid metabolic process	0.0313723029195121
GO:0008207	C21-steroid hormone metabolic process	0.0346241181710792
GO:0015485	cholesterol binding	0.0346241181710792
GO:0050679	positive regulation of epithelial cell proliferation	0.035064301385311
GO:0000792	heterochromatin	0.0373314928407595
GO:0008289	lipid binding	0.0413396373469942
GO:0007422	peripheral nervous system development	0.0413396373469942
GO:0042552	myelination	0.0417436404705552
GO:0032934	sterol binding	0.0417436404705552
GO:0031902	late endosome membrane	0.0417436404705552
GO:0050678	regulation of epithelial cell proliferation	0.0417436404705552
GO:0007272	ensheathment of neurons	0.0417436404705552
GO:0008366	axon ensheathment	0.0417436404705552
GO:0050673	epithelial cell proliferation	0.0417436404705552
GO:0042129	regulation of T cell proliferation	0.0417436404705552
GO:0000910	cytokinesis	0.0417436404705552
GO:0045765	regulation of angiogenesis	0.0417436404705552
GO:0042098	T cell proliferation	0.0417436404705552
GO:0050808	synapse organization and biogenesis	0.0417436404705552
GO:0001508	regulation of action potential	0.0417436404705552
GO:0044255	cellular lipid metabolic process	0.0417436404705552
GO:0030217	T cell differentiation	0.0417436404705552
GO:0048741	skeletal muscle fiber development	0.0417436404705552
GO:0050670	regulation of lymphocyte proliferation	0.0417436404705552
GO:0032944	regulation of mononuclear cell proliferation	0.0417436404705552
GO:0048747	muscle fiber development	0.0417436404705552
GO:0042446	hormone biosynthetic process	0.0418053836348106
GO:0006720	isoprenoid metabolic process	0.0428126721177308
GO:0048732	gland development	0.0428491605705884
GO:0006839	mitochondrial transport	0.043793229394858
GO:0005770	late endosome	0.0446891448334533
GO:0032943	mononuclear cell proliferation	0.0446891448334533
GO:0019748	secondary metabolic process	0.0446891448334533
GO:0046651	lymphocyte proliferation	0.0446891448334533
GO:0007411	axon guidance	0.0463340700446233
GO:0007059	chromosome segregation	0.0470624258525105
GO:0050863	regulation of T cell activation	0.0470624258525105
GO:0006629	lipid metabolic process	0.0480588986131011
GO:0030098	lymphocyte differentiation	0.0492722668622572
GO:0043406	positive regulation of MAP kinase activity	0.0497624591336918
GO:0007519	skeletal muscle development	0.0497624591336918
GO:0016324	apical plasma membrane	0.0497624591336918

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
epithelial cell	2.33e-19	254
embryonic cell	2.53e-13	248
endodermal cell	6.32e-09	59
endo-epithelial cell	1.79e-08	43

Uber Anatomy

Ontology term	p-value	n
multi-tissue structure	1.33e-17	347
multi-cellular organism	4.52e-17	659
organism subdivision	3.01e-15	365
mesenchyme	9.19e-14	238
entire embryonic mesenchyme	9.19e-14	238
endoderm-derived structure	2.34e-13	169
endoderm	2.34e-13	169
presumptive endoderm	2.34e-13	169
organ	3.77e-13	511
anatomical system	2.15e-12	625
anatomical group	4.24e-12	626
embryo	4.14e-11	612
trunk	8.05e-11	216
digestive system	1.12e-10	155
digestive tract	1.12e-10	155
primitive gut	1.12e-10	155
organ part	4.14e-10	219
primordium	6.35e-10	168
cell layer	7.77e-10	312
epithelium	1.20e-09	309
subdivision of digestive tract	2.29e-09	129
endodermal part of digestive tract	2.29e-09	129
mixed endoderm/mesoderm-derived structure	2.45e-09	130
subdivision of trunk	2.53e-09	113
embryonic structure	3.75e-09	605
developing anatomical structure	3.75e-09	605
anatomical cluster	4.62e-09	286
reproductive structure	5.87e-09	59
reproductive system	5.87e-09	59
germ layer	7.90e-09	604
embryonic tissue	7.90e-09	604
presumptive structure	7.90e-09	604
epiblast (generic)	7.90e-09	604
immaterial anatomical entity	2.41e-08	126
compound organ	4.17e-08	69
extraembryonic membrane	7.75e-08	14
membranous layer	7.75e-08	14
female organism	1.06e-07	41
female reproductive organ	1.95e-07	37
female reproductive system	1.95e-07	37
reproductive organ	1.98e-07	48
anatomical conduit	2.83e-07	241
trunk region element	3.11e-07	107
epithelial tube	3.33e-07	118
renal system	4.15e-07	45
anatomical space	4.82e-07	104
trunk mesenchyme	5.07e-07	143
urinary system structure	5.80e-07	44
organ component layer	9.46e-07	57

Disease

Ontology term	p-value	n
carcinoma	2.77e-08	106
adenocarcinoma	3.89e-08	25

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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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.