Coexpression cluster:C511

Full id: C511_Placental_Alveolar_Bronchial_amniotic_Gingival_Corneal_Mammary

Phase1 CAGE Peaks

Hg19::chr11:394157..394180,+	p3@PKP3
Hg19::chr11:394196..394258,+	p1@PKP3
Hg19::chr11:394263..394275,+	p5@PKP3
Hg19::chr11:66824276..66824298,+	p2@RHOD
Hg19::chr11:66824303..66824343,+	p1@RHOD
Hg19::chr11:66824346..66824359,+	p3@RHOD
Hg19::chr14:105330834..105330858,+	p@chr14:105330834..105330858 +
Hg19::chr17:7284402..7284414,+	p1@TNK1
Hg19::chr19:45843994..45844015,+	p1@KLC3
Hg19::chr1:35246775..35246797,+	p2@GJB3
Hg19::chr1:35246802..35246823,+	p1@GJB3
Hg19::chr1:35247135..35247151,+	p9@GJB3
Hg19::chr1:35247162..35247173,+	p7@GJB3
Hg19::chr1:35247859..35247901,+	p5@GJB3
Hg19::chr5:175843524..175843547,-	p1@CLTB
Hg19::chr6:41604725..41604741,+	p4@MDFI
Hg19::chr6:41604747..41604796,+	p1@MDFI
Hg19::chr9:140506925..140506963,+	p3@ARRDC1

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:0014704	intercalated disc	0.00971357311575209
GO:0005911	intercellular junction	0.0328503730566494
GO:0009950	dorsal/ventral axis specification	0.0328503730566494
GO:0005243	gap junction channel activity	0.0328503730566494
GO:0022829	wide pore channel activity	0.0328503730566494
GO:0043392	negative regulation of DNA binding	0.0328503730566494
GO:0051100	negative regulation of binding	0.0328503730566494
GO:0042994	cytoplasmic sequestering of transcription factor	0.0328503730566494
GO:0030057	desmosome	0.0328503730566494
GO:0051220	cytoplasmic sequestering of protein	0.0328503730566494
GO:0042308	negative regulation of protein import into nucleus	0.0328503730566494
GO:0042992	negative regulation of transcription factor import into nucleus	0.0328503730566494
GO:0051101	regulation of DNA binding	0.0328503730566494
GO:0046823	negative regulation of nucleocytoplasmic transport	0.0328503730566494
GO:0051224	negative regulation of protein transport	0.0328503730566494
GO:0030132	clathrin coat of coated pit	0.0328503730566494
GO:0001890	placenta development	0.0328503730566494
GO:0030054	cell junction	0.0328503730566494
GO:0030130	clathrin coat of trans-Golgi network vesicle	0.0328503730566494
GO:0012510	trans-Golgi network transport vesicle membrane	0.0328503730566494
GO:0009798	axis specification	0.0328503730566494
GO:0030178	negative regulation of Wnt receptor signaling pathway	0.0328503730566494
GO:0005886	plasma membrane	0.0328503730566494
GO:0007257	activation of JNK activity	0.0328503730566494
GO:0042990	regulation of transcription factor import into nucleus	0.0328503730566494
GO:0042991	transcription factor import into nucleus	0.0328503730566494
GO:0030125	clathrin vesicle coat	0.0328503730566494
GO:0042306	regulation of protein import into nucleus	0.0328503730566494
GO:0033157	regulation of intracellular protein transport	0.0328503730566494
GO:0043507	positive regulation of JNK activity	0.0328503730566494
GO:0030665	clathrin coated vesicle membrane	0.0328503730566494
GO:0006886	intracellular protein transport	0.0328503730566494
GO:0032507	maintenance of cellular protein localization	0.0328503730566494
GO:0043506	regulation of JNK activity	0.0328503730566494
GO:0051651	maintenance of cellular localization	0.0328503730566494
GO:0032386	regulation of intracellular transport	0.0328503730566494
GO:0045185	maintenance of protein localization	0.0328503730566494
GO:0030111	regulation of Wnt receptor signaling pathway	0.0328503730566494
GO:0051223	regulation of protein transport	0.0328503730566494
GO:0009953	dorsal/ventral pattern formation	0.0328503730566494
GO:0005922	connexon complex	0.0328503730566494
GO:0051098	regulation of binding	0.0328503730566494
GO:0005871	kinesin complex	0.0328503730566494
GO:0046822	regulation of nucleocytoplasmic transport	0.0328503730566494
GO:0030140	trans-Golgi network transport vesicle	0.0328503730566494
GO:0051051	negative regulation of transport	0.0336156853620909
GO:0030658	transport vesicle membrane	0.0336156853620909
GO:0030660	Golgi-associated vesicle membrane	0.0339741446877352
GO:0005921	gap junction	0.0353546012067987
GO:0004715	non-membrane spanning protein tyrosine kinase activity	0.0407401896373074
GO:0051235	maintenance of localization	0.040936282410428
GO:0044459	plasma membrane part	0.0413010282697245
GO:0005905	coated pit	0.0413057609230136
GO:0046777	protein amino acid autophosphorylation	0.0414799877126929
GO:0016540	protein autoprocessing	0.0425694626794528
GO:0030120	vesicle coat	0.0454288408777507
GO:0030662	coated vesicle membrane	0.0455204621896562
GO:0000187	activation of MAPK activity	0.049972168624338

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	3.50e-50	254
endo-epithelial cell	1.43e-17	43
endodermal cell	5.51e-16	59
embryonic cell	3.54e-15	248
squamous epithelial cell	2.50e-11	62
epithelial cell of alimentary canal	3.42e-09	21
respiratory epithelial cell	1.73e-07	13

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	1.30e-26	169
endoderm	1.30e-26	169
presumptive endoderm	1.30e-26	169
digestive system	1.62e-20	155
digestive tract	1.62e-20	155
primitive gut	1.62e-20	155
mesenchyme	6.04e-18	238
entire embryonic mesenchyme	6.04e-18	238
multi-tissue structure	9.16e-18	347
mixed endoderm/mesoderm-derived structure	3.55e-17	130
multi-cellular organism	5.11e-17	659
subdivision of digestive tract	2.81e-16	129
endodermal part of digestive tract	2.81e-16	129
immaterial anatomical entity	2.75e-15	126
respiratory system	3.25e-15	72
anatomical space	1.71e-14	104
trunk	1.61e-13	216
primordium	2.94e-13	168
organ part	3.94e-12	219
anatomical system	5.07e-12	625
foregut	8.25e-12	98
anatomical group	8.89e-12	626
organism subdivision	1.22e-11	365
subdivision of trunk	1.47e-11	113
embryo	1.62e-11	612
respiratory tract	1.00e-10	53
embryonic structure	1.83e-10	605
developing anatomical structure	1.83e-10	605
germ layer	3.25e-10	604
embryonic tissue	3.25e-10	604
presumptive structure	3.25e-10	604
epiblast (generic)	3.25e-10	604
orifice	6.81e-10	35
organ	1.14e-09	511
organ segment	1.67e-09	97
endo-epithelium	1.85e-09	82
anatomical cluster	2.16e-09	286
thoracic segment of trunk	3.52e-09	52
intermediate mesoderm	3.86e-09	37
respiratory primordium	6.29e-09	38
endoderm of foregut	6.29e-09	38
trunk region element	7.03e-09	107
epithelium	7.34e-09	309
segment of respiratory tract	9.99e-09	46
anatomical cavity	1.12e-08	70
cell layer	1.17e-08	312
reproductive structure	1.61e-08	59
reproductive system	1.61e-08	59
trunk mesenchyme	3.81e-08	143
epithelial fold	4.80e-08	51
oral opening	1.05e-07	21
extraembryonic membrane	1.13e-07	14
membranous layer	1.13e-07	14
subdivision of head	1.14e-07	48
anatomical conduit	1.97e-07	241
renal system	2.76e-07	45
urinary system structure	3.64e-07	44
epithelial bud	4.82e-07	37
female organism	5.12e-07	41
mesoderm	5.49e-07	448
mesoderm-derived structure	5.49e-07	448
presumptive mesoderm	5.49e-07	448
thoracic cavity element	6.11e-07	34
thoracic cavity	6.11e-07	34
mouth	6.65e-07	28
stomodeum	6.65e-07	28
reproductive organ	7.03e-07	48

Disease

Ontology term	p-value	n
carcinoma	5.51e-19	106
cell type cancer	1.60e-12	143
adenocarcinoma	6.25e-09	25
squamous cell carcinoma	2.45e-08	14

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	9	2.45369460743966	0.00484908095192365	0.0227252934950843
GABPB1#2553	8	3.14119281608097	0.00185447627799343	0.0109435895579928
NR3C1#2908	6	4.99100777705768	0.000815683005575803	0.0062150082016
POLR2A#5430	18	2.14745317655807	1.059158074972e-06	4.41410256153236e-05
SMARCC1#6599	3	7.27722655327191	0.00757158057464432	0.0312075576634942

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.