Coexpression cluster:C268

Full id: C268_Mallassezderived_Urothelial_Gingival_Small_Bronchial_Tracheal_Prostate

Phase1 CAGE Peaks

Hg19::chr12:28125659..28125672,-	p1@PTHLH
Hg19::chr14:51955987..51955996,+	p31@FRMD6
Hg19::chr14:51956090..51956101,+	p32@FRMD6
Hg19::chr18:26736784..26736799,+	p@chr18:26736784..26736799 +
Hg19::chr18:26736800..26736811,+	p@chr18:26736800..26736811 +
Hg19::chr18:26736814..26736831,+	p@chr18:26736814..26736831 +
Hg19::chr18:67715323..67715368,-	p2@RTTN
Hg19::chr1:183155389..183155406,+	p1@LAMC2
Hg19::chr1:183189986..183190012,+	p@chr1:183189986..183190012 +
Hg19::chr1:183192299..183192310,+	p@chr1:183192299..183192310 +
Hg19::chr1:183192330..183192349,+	p@chr1:183192330..183192349 +
Hg19::chr1:183195929..183195945,+	p@chr1:183195929..183195945 +
Hg19::chr1:183196792..183196807,+	p@chr1:183196792..183196807 +
Hg19::chr1:183197647..183197676,+	p@chr1:183197647..183197676 +
Hg19::chr1:183201372..183201407,+	p@chr1:183201372..183201407 +
Hg19::chr1:183203526..183203539,+	p@chr1:183203526..183203539 +
Hg19::chr1:183204745..183204775,+	p@chr1:183204745..183204775 +
Hg19::chr1:183204785..183204796,+	p@chr1:183204785..183204796 +
Hg19::chr1:183204800..183204830,+	p@chr1:183204800..183204830 +
Hg19::chr1:183204832..183204840,+	p@chr1:183204832..183204840 +
Hg19::chr1:183205642..183205677,+	p@chr1:183205642..183205677 +
Hg19::chr1:183205712..183205723,+	p@chr1:183205712..183205723 +
Hg19::chr1:183206514..183206566,+	p@chr1:183206514..183206566 +
Hg19::chr1:183206565..183206612,-	p@chr1:183206565..183206612 -
Hg19::chr1:183206616..183206643,-	p@chr1:183206616..183206643 -
Hg19::chr1:183207431..183207488,+	p@chr1:183207431..183207488 +
Hg19::chr1:183207499..183207519,+	p@chr1:183207499..183207519 +
Hg19::chr1:183208494..183208511,+	p9@LAMC2
Hg19::chr1:183208516..183208541,+	p6@LAMC2
Hg19::chr1:183208540..183208573,-	p@chr1:183208540..183208573 -
Hg19::chr1:183208543..183208558,+	p8@LAMC2
Hg19::chr1:183208607..183208635,+	p4@LAMC2
Hg19::chr1:183208643..183208654,+	p10@LAMC2
Hg19::chr1:183208657..183208675,+	p3@LAMC2
Hg19::chr1:183209165..183209207,+	p@chr1:183209165..183209207 +
Hg19::chr1:183209229..183209250,+	p@chr1:183209229..183209250 +
Hg19::chr1:183209265..183209312,-	p@chr1:183209265..183209312 -
Hg19::chr1:183209335..183209346,-	p@chr1:183209335..183209346 -
Hg19::chr1:183211988..183211991,+	p@chr1:183211988..183211991 +
Hg19::chr1:183212294..183212340,+	p2@LAMC2
Hg19::chr1:183212409..183212419,+	p12@LAMC2
Hg19::chr1:183212478..183212492,+	p7@LAMC2
Hg19::chr1:183212689..183212705,+	p@chr1:183212689..183212705 +
Hg19::chr1:183212941..183212952,+	p@chr1:183212941..183212952 +
Hg19::chr1:183212991..183213014,+	p@chr1:183212991..183213014 +
Hg19::chr1:183213130..183213176,+	p@chr1:183213130..183213176 +
Hg19::chr1:209790842..209790854,-	p@chr1:209790842..209790854 -
Hg19::chr1:209826169..209826182,-	p4@LAMB3
Hg19::chr3:184018352..184018374,+	p3@PSMD2

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
0.000130420068097775	0.0256875006414391	2	85	ECM-receptor interaction (KEGG):04512
0.000319242834381215	0.0336801190272182	2	133	Toxoplasmosis (KEGG):05145
0.000202902848668555	0.0256875006414391	2	106	Amoebiasis (KEGG):05146
0.000130420068097775	0.0256875006414391	2	85	Small cell lung cancer (KEGG):05222
8.58329659590162e-05	0.0256875006414391	2	69	Alpha6-Beta4 Integrin Signaling Pathway (Wikipathways):WP244
0.000169903235631845	0.0256875006414391	2	97	Cell junction organization (Reactome):REACT_20676

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:0005610	laminin-5 complex	2.23558022420707e-06
GO:0008544	epidermis development	3.68581257411776e-05
GO:0007398	ectoderm development	3.68581257411776e-05
GO:0043256	laminin complex	3.68581257411776e-05
GO:0009888	tissue development	0.000241622122118908
GO:0005605	basal lamina	0.00028975954818347
GO:0005604	basement membrane	0.000857750512404879
GO:0044420	extracellular matrix part	0.00235550148606838
GO:0007275	multicellular organismal development	0.00268383219890349
GO:0044421	extracellular region part	0.00310151907770258
GO:0048513	organ development	0.00547554905699508
GO:0032502	developmental process	0.00858513447901359
GO:0048731	system development	0.0119522547386036
GO:0032501	multicellular organismal process	0.0119522547386036
GO:0005838	proteasome regulatory particle (sensu Eukaryota)	0.0119522547386036
GO:0005578	proteinaceous extracellular matrix	0.0119522547386036
GO:0048856	anatomical structure development	0.0175600804050097
GO:0007595	lactation	0.0175600804050097
GO:0046058	cAMP metabolic process	0.0175600804050097
GO:0007189	G-protein signaling, adenylate cyclase activating pathway	0.0280252688159154
GO:0009187	cyclic nucleotide metabolic process	0.036034072684621
GO:0043234	protein complex	0.0366964549910522
GO:0048609	reproductive process in a multicellular organism	0.0366964549910522
GO:0032504	multicellular organism reproduction	0.0366964549910522
GO:0022610	biological adhesion	0.0366964549910522
GO:0007155	cell adhesion	0.0366964549910522
GO:0000502	proteasome complex (sensu Eukaryota)	0.0410003388770995
GO:0008201	heparin binding	0.0410003388770995
GO:0007565	female pregnancy	0.042175394935033
GO:0007188	G-protein signaling, coupled to cAMP nucleotide second messenger	0.0422702018209267
GO:0019933	cAMP-mediated signaling	0.0423582494144555

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
endo-epithelial cell	2.47e-36	42
epithelial cell	8.98e-36	253
respiratory epithelial cell	1.75e-25	13
endodermal cell	2.41e-24	58
general ecto-epithelial cell	1.38e-19	14
epithelial cell of alimentary canal	1.86e-17	20
epithelial cell of tracheobronchial tree	6.62e-15	9
epithelial cell of lower respiratory tract	6.62e-15	9
transitional epithelial cell	5.28e-13	4
urothelial cell	5.28e-13	4
squamous epithelial cell	3.93e-12	63
ecto-epithelial cell	1.60e-11	34
gingival epithelial cell	5.15e-10	3
epithelial cell of Malassez	5.31e-10	3
bronchial epithelial cell	1.69e-09	3
duct epithelial cell	2.01e-09	3
branched duct epithelial cell	2.01e-09	3
tracheal epithelial cell	2.01e-09	3
tracheoblast	2.01e-09	3
acinar cell	3.00e-09	5
embryonic cell	1.40e-08	250
stratified squamous epithelial cell	2.77e-08	6
keratin accumulating cell	2.77e-08	6
stratified epithelial cell	2.77e-08	6
keratinizing barrier epithelial cell	2.77e-08	6
epithelial fate stem cell	2.77e-08	6
stratified epithelial stem cell	2.77e-08	6
surface ectodermal cell	2.77e-08	6
epidermal cell	3.34e-08	9
protein secreting cell	1.05e-07	6
mammary gland epithelial cell	3.05e-07	4
animal cell	3.90e-07	679
eukaryotic cell	3.90e-07	679
sebum secreting cell	5.08e-07	2
epithelial cell of sweat gland	5.08e-07	2
epithelial cell of skin gland	5.08e-07	2
acinar cell of sebaceous gland	5.08e-07	2

Uber Anatomy

Ontology term	p-value	n
urothelium	5.19e-15	5
endoderm-derived structure	3.06e-14	160
endoderm	3.06e-14	160
presumptive endoderm	3.06e-14	160
mouth mucosa	1.10e-12	13
respiratory system	1.23e-12	74
transitional epithelium	1.94e-12	6
mucosa of oral region	1.27e-10	4
respiratory system mucosa	1.27e-10	4
gingival epithelium	5.15e-10	3
mucosa	1.25e-09	20
lower respiratory tract epithelium	1.69e-09	3
epithelium of bronchus	1.69e-09	3
surface structure	2.66e-09	99
endo-epithelium	1.13e-08	82
extraembryonic membrane	1.56e-08	14
membranous layer	1.56e-08	14
oral opening	1.56e-08	22
tracheobronchial tree	1.72e-08	15
lower respiratory tract	1.72e-08	15
orifice	1.77e-08	36
head	8.52e-08	56
mouth	1.29e-07	29
stomodeum	1.29e-07	29
jaw skeleton	1.41e-07	4
splanchnocranium	1.41e-07	4
digestive system	1.62e-07	145
digestive tract	1.62e-07	145
primitive gut	1.62e-07	145
mammary gland	3.05e-07	4
mammary bud	3.05e-07	4
mammary ridge	3.05e-07	4
mammary placode	3.05e-07	4
epithelial fold	3.16e-07	47
respiratory tract	4.69e-07	54
skin gland	5.08e-07	2
epidermis gland	5.08e-07	2
gland of integumental system	5.08e-07	2
sebaceous gland	5.08e-07	2
skin sebaceous gland	5.08e-07	2
sweat gland	5.08e-07	2
sweat gland placode	5.08e-07	2
sebaceous gland placode	5.08e-07	2
epithelial bud	5.65e-07	37
organ component layer	9.22e-07	66

Disease

Ontology term	p-value	n
squamous cell carcinoma	1.29e-16	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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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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