Coexpression cluster:C226

Full id: C226_Corneal_Keratinocyte_Esophageal_Urothelial_Mammary_Bronchial_Tracheal

Phase1 CAGE Peaks

Hg19::chr11:120008848..120008862,-	p4@TRIM29
Hg19::chr11:66673490..66673527,-	p@chr11:66673490..66673527 -
Hg19::chr11:66673538..66673570,-	p@chr11:66673538..66673570 -
Hg19::chr11:72432950..72432974,-	p9@ARAP1
Hg19::chr12:120105914..120105973,+	p2@PRKAB1
Hg19::chr12:52887143..52887158,-	p8@KRT6A
Hg19::chr12:52887160..52887186,-	p3@KRT6A
Hg19::chr16:68679173..68679184,+	p2@CDH3
Hg19::chr16:68679193..68679253,+	p1@CDH3
Hg19::chr16:68679261..68679268,+	p3@CDH3
Hg19::chr16:68716248..68716260,-	p@chr16:68716248..68716260 -
Hg19::chr17:39925803..39925824,-	p@chr17:39925803..39925824 -
Hg19::chr17:39942208..39942219,-	p7@JUP
Hg19::chr17:39942220..39942242,-	p2@JUP
Hg19::chr17:39942245..39942256,-	p9@JUP
Hg19::chr17:39942268..39942282,-	p6@JUP
Hg19::chr17:39942286..39942313,-	p3@JUP
Hg19::chr17:39942940..39942970,-	p1@JUP
Hg19::chr17:73717531..73717550,+	p2@ITGB4
Hg19::chr17:73717551..73717609,+	p1@ITGB4
Hg19::chr17:73717624..73717635,+	p3@ITGB4
Hg19::chr17:7493405..7493419,-	p1@SOX15
Hg19::chr17:8006982..8007017,-	p@chr17:8006982..8007017 -
Hg19::chr1:153585571..153585629,-	p2@S100A16
Hg19::chr1:153585634..153585651,-	p7@S100A16
Hg19::chr1:153588789..153588808,-	p1@S100A14
Hg19::chr1:200864020..200864063,+	p1@C1orf106
Hg19::chr1:200864071..200864088,+	p3@C1orf106
Hg19::chr1:201368430..201368460,-	p1@LAD1
Hg19::chr1:201368476..201368498,-	p4@LAD1
Hg19::chr1:207206059..207206084,-	p3@C1orf116
Hg19::chr1:209825762..209825779,-	p1@LAMB3
Hg19::chr1:209825932..209825936,-	p10@LAMB3
Hg19::chr1:209826381..209826392,-	p@chr1:209826381..209826392 -
Hg19::chr1:209979411..209979433,-	p2@IRF6
Hg19::chr1:209979449..209979460,-	p3@IRF6
Hg19::chr1:27189631..27189648,+	p1@SFN
Hg19::chr1:27190343..27190365,-	p4@uc010ofi.1
Hg19::chr1:27190373..27190427,-	p1@uc010ofi.1
Hg19::chr1:27190643..27190678,-	p2@uc010ofi.1
Hg19::chr1:31886034..31886099,+	p1@SERINC2
Hg19::chr1:35220613..35220718,+	p1@GJB5
Hg19::chr1:35220725..35220754,+	p2@GJB5
Hg19::chr1:35247024..35247046,+	p4@GJB3
Hg19::chr1:35247057..35247079,+	p3@GJB3
Hg19::chr1:35247081..35247102,+	p6@GJB3
Hg19::chr1:44399399..44399444,+	p1@ARTN
Hg19::chr1:44399451..44399461,+	p6@ARTN
Hg19::chr1:44399466..44399482,+	p3@ARTN
Hg19::chr1:44401579..44401643,+	p2@ARTN
Hg19::chr1:6479968..6479986,-	p1@HES2
Hg19::chr20:60953877..60953897,-	p@chr20:60953877..60953897 -
Hg19::chr22:38302285..38302361,+	p1@MICALL1
Hg19::chr2:20424783..20424794,-	p4@SDC1
Hg19::chr2:74669009..74669077,-	p1@RTKN
Hg19::chr3:12800751..12800777,-	p1@TMEM40
Hg19::chr6:30850697..30850739,+	p2@DDR1
Hg19::chr6:35360450..35360509,+	p@chr6:35360450..35360509 +
Hg19::chr7:150811705..150811763,+	p4@AGAP3
Hg19::chr8:144815895..144815912,-	p4@FAM83H
Hg19::chr8:144815914..144815961,-	p1@FAM83H
Hg19::chr8:144815966..144815986,-	p2@FAM83H
Hg19::chrX:54501038..54501075,-	p@chrX:54501038..54501075 -

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
7.90940612888754e-05	0.0166888469319527	3	85	ECM-receptor interaction (KEGG):04512
6.12511642504549e-07	0.000387719869705379	4	69	Alpha6-Beta4 Integrin Signaling Pathway (Wikipathways):WP244
2.40906544721509e-06	0.000762469214043575	4	97	Cell junction organization (Reactome):REACT_20676
0.000171638888981101	0.0271618541812592	4	288	{ACTB,297} (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:0009888	tissue development	0.000467859320844482
GO:0007398	ectoderm development	0.000467859320844482
GO:0014704	intercalated disc	0.000494265234320962
GO:0048731	system development	0.00501723215290283
GO:0007275	multicellular organismal development	0.00501723215290283
GO:0048513	organ development	0.00501723215290283
GO:0008544	epidermis development	0.0050388845571958
GO:0005922	connexon complex	0.00705063890640088
GO:0032502	developmental process	0.00733551717943004
GO:0005911	intercellular junction	0.00733551717943004
GO:0005921	gap junction	0.00749484253179777
GO:0048856	anatomical structure development	0.00749484253179777
GO:0022610	biological adhesion	0.00964929591541734
GO:0007155	cell adhesion	0.00964929591541734
GO:0032501	multicellular organismal process	0.0122266281545092
GO:0005604	basement membrane	0.0247177030320746
GO:0005610	laminin-5 complex	0.0273908549258614
GO:0008426	protein kinase C inhibitor activity	0.038791147396166
GO:0005515	protein binding	0.0448481256440162
GO:0043403	skeletal muscle regeneration	0.0465343065901034
GO:0030054	cell junction	0.0468426097393087
GO:0017049	GTP-Rho binding	0.0468426097393087
GO:0005916	fascia adherens	0.0468426097393087
GO:0005243	gap junction channel activity	0.0468426097393087
GO:0044459	plasma membrane part	0.0468426097393087
GO:0044420	extracellular matrix part	0.0468426097393087
GO:0022829	wide pore channel activity	0.0481077772224277
GO:0043588	skin development	0.0481077772224277
GO:0009898	internal side of plasma membrane	0.0481077772224277

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	9.61e-43	253
endo-epithelial cell	4.58e-31	42
endodermal cell	2.07e-22	58
epithelial cell of alimentary canal	1.41e-16	20
respiratory epithelial cell	9.45e-14	13
kidney tubule cell	1.30e-09	10
nephron tubule epithelial cell	1.30e-09	10
epithelial cell of tracheobronchial tree	3.17e-09	9
epithelial cell of lower respiratory tract	3.17e-09	9
general ecto-epithelial cell	8.82e-09	14
acinar cell	4.50e-07	5
epithelial cell of nephron	4.83e-07	15

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	4.98e-32	160
endoderm	4.98e-32	160
presumptive endoderm	4.98e-32	160
respiratory system	3.41e-24	74
digestive system	1.35e-23	145
digestive tract	1.35e-23	145
primitive gut	1.35e-23	145
subdivision of digestive tract	1.02e-20	118
respiratory tract	8.60e-18	54
urinary system structure	5.00e-16	47
renal system	1.77e-15	48
foregut	2.15e-14	87
orifice	4.42e-14	36
respiratory primordium	2.96e-13	38
endoderm of foregut	2.96e-13	38
segment of respiratory tract	7.71e-13	47
anatomical space	1.40e-12	95
epithelial bud	3.20e-12	37
endo-epithelium	3.43e-11	82
oral opening	7.38e-11	22
organ part	1.57e-10	218
epithelial fold	2.54e-10	47
organ	3.28e-10	503
extraembryonic membrane	5.31e-10	14
membranous layer	5.31e-10	14
thoracic cavity element	8.73e-10	34
thoracic cavity	8.73e-10	34
immaterial anatomical entity	1.11e-09	117
nephron tubule epithelium	1.30e-09	10
organism subdivision	1.89e-09	264
thoracic segment organ	2.51e-09	35
trunk region element	3.04e-09	101
mouth	2.73e-08	29
stomodeum	2.73e-08	29
reproductive structure	3.98e-08	59
reproductive system	3.98e-08	59
mucosa	5.48e-08	20
surface structure	7.03e-08	99
multi-cellular organism	1.05e-07	656
chorion	1.18e-07	7
excretory tube	1.24e-07	16
kidney epithelium	1.24e-07	16
urothelium	1.58e-07	5
embryo	2.08e-07	592
anterior region of body	2.64e-07	62
craniocervical region	2.64e-07	62
tracheobronchial tree	3.18e-07	15
lower respiratory tract	3.18e-07	15
upper respiratory tract	4.19e-07	19
nephron epithelium	4.83e-07	15
renal tubule	4.83e-07	15
nephron tubule	4.83e-07	15
nephron	4.83e-07	15
uriniferous tubule	4.83e-07	15
nephrogenic mesenchyme	4.83e-07	15
thoracic segment of trunk	6.16e-07	52
male organism	6.55e-07	22
male reproductive system	6.55e-07	22
respiratory system epithelium	7.76e-07	28

Disease

Ontology term	p-value	n
carcinoma	5.95e-21	106
squamous cell carcinoma	2.76e-13	14
cell type cancer	9.42e-13	143
adenocarcinoma	1.01e-10	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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
CTCF#10664	21	1.78675212435834	0.00395645447998033	0.0189928364329227
E2F1#1869	23	1.79158653876547	0.00225427379515551	0.012804378141744
MYC#4609	22	1.82365398691122	0.00234023697568195	0.0132673981925549
POLR2A#5430	59	2.01110694312581	1.33117697459636e-15	2.46939239875433e-13
SMARCC1#6599	6	4.15841517329824	0.00320606301401661	0.0168167352278078
STAT3#6774	15	2.50463452313196	0.000678719432485891	0.00547457358737983
TFAP2A#7020	10	2.62200545603888	0.00439187349915724	0.0208132714574137
TFAP2C#7022	17	2.91677597408927	4.14543338165909e-05	0.00075229351337462
ZEB1#6935	20	5.36140698969646	3.10677472077757e-10	3.12891461006065e-08

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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