Coexpression cluster:C525

Full id: C525_tubular_vagina_cervix_rectum_Placental_colon_Hair

Phase1 CAGE Peaks

Hg19::chr10:4007246..4007251,+	p@chr10:4007246..4007251 +
Hg19::chr11:65144695..65144697,-	p@chr11:65144695..65144697 -
Hg19::chr14:102027518..102027524,-	p@chr14:102027518..102027524 -
Hg19::chr14:102027537..102027598,-	p@chr14:102027537..102027598 -
Hg19::chr14:102027607..102027620,-	p@chr14:102027607..102027620 -
Hg19::chr14:102027691..102027715,-	p@chr14:102027691..102027715 -
Hg19::chr16:1128952..1128957,+	p4@SSTR5
Hg19::chr16:1129001..1129004,+	p6@SSTR5
Hg19::chr20:42980646..42980651,+	p@chr20:42980646..42980651 +
Hg19::chr21:36208874..36208890,+	p@chr21:36208874..36208890 +
Hg19::chr21:36208893..36208906,+	p@chr21:36208893..36208906 +
Hg19::chr2:109605543..109605554,-	p4@EDAR
Hg19::chr2:109605568..109605573,-	p6@EDAR
Hg19::chr2:109605588..109605606,-	p2@EDAR
Hg19::chr4:93623257..93623261,+	p@chr4:93623257..93623261 +
Hg19::chr6:137365402..137365416,-	p8@IL20RA
Hg19::chr7:45928212..45928215,+	p14@IGFBP1

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:0065008	regulation of biological quality	0.0119799206895422
GO:0007431	salivary gland development	0.0124043961038235
GO:0004994	somatostatin receptor activity	0.0124043961038235
GO:0042346	positive regulation of NF-kappaB import into nucleus	0.0124043961038235
GO:0035272	exocrine system development	0.0124043961038235
GO:0042993	positive regulation of transcription factor import into nucleus	0.0124043961038235
GO:0050796	regulation of insulin secretion	0.0124043961038235
GO:0042307	positive regulation of protein import into nucleus	0.0124043961038235
GO:0046824	positive regulation of nucleocytoplasmic transport	0.0124043961038235
GO:0051222	positive regulation of protein transport	0.0124043961038235
GO:0042345	regulation of NF-kappaB import into nucleus	0.0124043961038235
GO:0042348	NF-kappaB import into nucleus	0.0124043961038235
GO:0065007	biological regulation	0.0124043961038235
GO:0030073	insulin secretion	0.0124043961038235
GO:0042593	glucose homeostasis	0.0124043961038235
GO:0033500	carbohydrate homeostasis	0.0124043961038235
GO:0022404	molting cycle process	0.0124043961038235
GO:0001942	hair follicle development	0.0124043961038235
GO:0022405	hair cycle process	0.0124043961038235
GO:0042633	hair cycle	0.0124043961038235
GO:0042303	molting cycle	0.0124043961038235
GO:0046883	regulation of hormone secretion	0.0124043961038235
GO:0002790	peptide secretion	0.0124043961038235
GO:0042475	odontogenesis of dentine-containing teeth	0.0124043961038235
GO:0030072	peptide hormone secretion	0.0124043961038235
GO:0042990	regulation of transcription factor import into nucleus	0.0124043961038235
GO:0042991	transcription factor import into nucleus	0.0124043961038235
GO:0042306	regulation of protein import into nucleus	0.0124043961038235
GO:0033157	regulation of intracellular protein transport	0.0124043961038235
GO:0004872	receptor activity	0.0127727213189944
GO:0042476	odontogenesis	0.0127727213189944
GO:0032386	regulation of intracellular transport	0.0127727213189944
GO:0051223	regulation of protein transport	0.0138701117521645
GO:0046822	regulation of nucleocytoplasmic transport	0.0139423432406483
GO:0046879	hormone secretion	0.0158756554137676
GO:0051050	positive regulation of transport	0.0166232626728935
GO:0005520	insulin-like growth factor binding	0.0166232626728935
GO:0015833	peptide transport	0.0166232626728935
GO:0004871	signal transducer activity	0.0166232626728935
GO:0060089	molecular transducer activity	0.0166232626728935
GO:0048732	gland development	0.0180796828083034
GO:0009653	anatomical structure morphogenesis	0.0180796828083034
GO:0008188	neuropeptide receptor activity	0.0181876457184049
GO:0042923	neuropeptide binding	0.0181876457184049
GO:0051046	regulation of secretion	0.0214033011731342
GO:0003001	generation of a signal involved in cell-cell signaling	0.0248296422928927
GO:0045177	apical part of cell	0.0298348531050072
GO:0019838	growth factor binding	0.0302283557850762
GO:0006606	protein import into nucleus	0.0316777496862145
GO:0051170	nuclear import	0.0316777496862145
GO:0007596	blood coagulation	0.0316777496862145
GO:0050817	coagulation	0.0316777496862145
GO:0007165	signal transduction	0.0316777496862145
GO:0007599	hemostasis	0.0316777496862145
GO:0051049	regulation of transport	0.0325756316374623
GO:0007187	G-protein signaling, coupled to cyclic nucleotide second messenger	0.0340193783461287
GO:0019935	cyclic-nucleotide-mediated signaling	0.0342424189330173
GO:0017038	protein import	0.0342424189330173
GO:0050878	regulation of body fluid levels	0.0344852227673087
GO:0042060	wound healing	0.0350398057358722
GO:0007154	cell communication	0.0350398057358722
GO:0008544	epidermis development	0.0353904821731165
GO:0030594	neurotransmitter receptor activity	0.0353904821731165
GO:0050794	regulation of cellular process	0.0353904821731165
GO:0042165	neurotransmitter binding	0.0353904821731165
GO:0007398	ectoderm development	0.0353904821731165
GO:0001653	peptide receptor activity	0.0353904821731165
GO:0008528	peptide receptor activity, G-protein coupled	0.0353904821731165
GO:0006913	nucleocytoplasmic transport	0.0362248593712815
GO:0051169	nuclear transport	0.0362248593712815
GO:0001558	regulation of cell growth	0.0370784581505363
GO:0048856	anatomical structure development	0.0372283652565221
GO:0004888	transmembrane receptor activity	0.0373534571022978
GO:0050789	regulation of biological process	0.038333343120518
GO:0016049	cell growth	0.0429041116610036
GO:0040008	regulation of growth	0.0429041116610036
GO:0008361	regulation of cell size	0.0432464846577091
GO:0042277	peptide binding	0.0432464846577091
GO:0006605	protein targeting	0.0447321235486876
GO:0016021	integral to membrane	0.0449080317908855
GO:0008285	negative regulation of cell proliferation	0.0449080317908855
GO:0031224	intrinsic to membrane	0.0449080317908855

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><br>uberon_data<br>disease_data<br>

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Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	7.92e-16	169
endoderm	7.92e-16	169
presumptive endoderm	7.92e-16	169
digestive system	2.87e-14	155
digestive tract	2.87e-14	155
primitive gut	2.87e-14	155
mixed endoderm/mesoderm-derived structure	8.18e-11	130
subdivision of digestive tract	1.16e-10	129
endodermal part of digestive tract	1.16e-10	129
multi-tissue structure	2.22e-10	347
multi-cellular organism	4.49e-09	659
adult organism	2.48e-08	115
hindgut	2.85e-08	19
organ	1.34e-07	511
embryo	2.47e-07	612
mesenchyme	4.37e-07	238
entire embryonic mesenchyme	4.37e-07	238
gastrointestinal system	5.52e-07	35

Disease

Ontology term	p-value	n
carcinoma	7.75e-08	106

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
FOXA1#3169	6	3.91108932331251	0.00277869454389008	0.0152218242575052
FOXA2#3170	5	7.24425404490154	0.00045226648015411	0.0042057037593104
MAFF#23764	3	9.9380040864609	0.00315701286110089	0.0165719373844248
NR3C1#2908	5	4.40383039152148	0.00416198804232154	0.0198318217516206
RXRA#6256	4	4.72343932685489	0.00868395261593973	0.0330001574521024
SETDB1#9869	4	9.48706498306129	0.00069418209031199	0.00559497479009831
SMC3#9126	7	6.19497234791352	6.13164858570721e-05	0.00100531121921927
TBP#6908	10	2.18045334535082	0.00564921492164463	0.0255145458052951
TCF7L2#6934	8	5.06831838265287	6.20084288736012e-05	0.00101585855735373

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.