Coexpression cluster:C515

Full id: C515_Small_Urothelial_Sebocyte_Prostate_Bronchial_Mallassezderived_Esophageal

Phase1 CAGE Peaks

Hg19::chr12:47661665..47661671,+	p@chr12:47661665..47661671 +
Hg19::chr21:45020673..45020684,-	p@chr21:45020673..45020684 -
Hg19::chr21:45020688..45020711,-	p@chr21:45020688..45020711 -
Hg19::chr21:45020721..45020728,-	p@chr21:45020721..45020728 -
Hg19::chr4:188228506..188228525,+	p@chr4:188228506..188228525 +
Hg19::chr5:146263947..146263959,-	p@chr5:146263947..146263959 -
Hg19::chr5:149979871..149979915,+	p@chr5:149979871..149979915 +
Hg19::chr5:61213098..61213119,-	p@chr5:61213098..61213119 -
Hg19::chr5:61213127..61213133,-	p@chr5:61213127..61213133 -
Hg19::chr5:61213156..61213165,-	p@chr5:61213156..61213165 -
Hg19::chr5:61213166..61213177,-	p@chr5:61213166..61213177 -
Hg19::chr5:61213179..61213189,-	p@chr5:61213179..61213189 -
Hg19::chr6:12314459..12314482,-	p3@EDN1
Hg19::chr7:150813498..150813509,+	p30@AGAP3
Hg19::chr8:123132065..123132067,+	p@chr8:123132065..123132067 +
Hg19::chr8:143814087..143814102,-	p@chr8:143814087..143814102 -
Hg19::chr9:113802868..113802878,-	p@chr9:113802868..113802878 -
Hg19::chrX:102977640..102977644,-	p@chrX:102977640..102977644 -

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:0031705	bombesin receptor binding	0.000917422190823815
GO:0031583	G-protein signaling, phospholipase D activating pathway	0.000917422190823815
GO:0043179	rhythmic excitation	0.000917422190823815
GO:0031708	endothelin B receptor binding	0.000917422190823815
GO:0031707	endothelin A receptor binding	0.000917422190823815
GO:0060024	rhythmic synaptic transmission	0.000917422190823815
GO:0030815	negative regulation of cAMP metabolic process	0.00137613328623572
GO:0030818	negative regulation of cAMP biosynthetic process	0.00137613328623572
GO:0030809	negative regulation of nucleotide biosynthetic process	0.00137613328623572
GO:0030803	negative regulation of cyclic nucleotide biosynthetic process	0.00137613328623572
GO:0042474	middle ear morphogenesis	0.00137613328623572
GO:0030800	negative regulation of cyclic nucleotide metabolic process	0.00137613328623572
GO:0030147	natriuresis	0.00157272375569797
GO:0030817	regulation of cAMP biosynthetic process	0.00157272375569797
GO:0003091	renal water homeostasis	0.00157272375569797
GO:0030146	diuresis	0.00157272375569797
GO:0030802	regulation of cyclic nucleotide biosynthetic process	0.00157272375569797
GO:0030808	regulation of nucleotide biosynthetic process	0.00157272375569797
GO:0051482	elevation of cytosolic calcium ion concentration during G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)	0.00157272375569797
GO:0045980	negative regulation of nucleotide metabolic process	0.00157272375569797
GO:0030814	regulation of cAMP metabolic process	0.00157272375569797
GO:0030799	regulation of cyclic nucleotide metabolic process	0.00167529269628697
GO:0030104	water homeostasis	0.00167529269628697
GO:0018987	osmoregulation	0.00183484438164763
GO:0003014	renal system process	0.00183484438164763
GO:0019229	regulation of vasoconstriction	0.00183484438164763
GO:0051899	membrane depolarization	0.00183484438164763
GO:0006140	regulation of nucleotide metabolic process	0.00196590469462246
GO:0001569	patterning of blood vessels	0.00201832881981239
GO:0046888	negative regulation of hormone secretion	0.00201832881981239
GO:0009405	pathogenesis	0.0023083526091696
GO:0014032	neural crest cell development	0.00233525648573335
GO:0014033	neural crest cell differentiation	0.00233525648573335
GO:0042310	vasoconstriction	0.00251635800911675
GO:0050804	regulation of synaptic transmission	0.00251635800911675
GO:0051048	negative regulation of secretion	0.00259936287400081
GO:0051969	regulation of transmission of nerve impulse	0.00260741043707821
GO:0007589	fluid secretion	0.00260741043707821
GO:0046883	regulation of hormone secretion	0.00261465324384787
GO:0006171	cAMP biosynthetic process	0.00261465324384787
GO:0046058	cAMP metabolic process	0.00295365193143277
GO:0048762	mesenchymal cell differentiation	0.00307229756927045
GO:0014031	mesenchymal cell development	0.00307229756927045
GO:0031644	regulation of neurological process	0.00312757565053574
GO:0009880	embryonic pattern specification	0.00314544751139594
GO:0048754	branching morphogenesis of a tube	0.00314544751139594
GO:0009953	dorsal/ventral pattern formation	0.00314544751139594
GO:0007585	respiratory gaseous exchange	0.00314544751139594
GO:0015758	glucose transport	0.00314544751139594
GO:0042471	ear morphogenesis	0.00314544751139594
GO:0042391	regulation of membrane potential	0.00314544751139594
GO:0001763	morphogenesis of a branching structure	0.00314544751139594
GO:0008645	hexose transport	0.00314544751139594
GO:0044403	symbiosis, encompassing mutualism through parasitism	0.00314544751139594
GO:0044419	interspecies interaction between organisms	0.00314544751139594
GO:0015749	monosaccharide transport	0.00314544751139594
GO:0006885	regulation of pH	0.00318683497865115
GO:0046879	hormone secretion	0.00322679529186308
GO:0051216	cartilage development	0.00335869819013465
GO:0007205	protein kinase C activation	0.0034862043251305
GO:0009190	cyclic nucleotide biosynthetic process	0.00355677526288618
GO:0007588	excretion	0.00355677526288618
GO:0035150	regulation of tube size	0.00355677526288618
GO:0050880	regulation of blood vessel size	0.00355677526288618
GO:0043583	ear development	0.00355677526288618
GO:0003018	vascular process in circulatory system	0.00358628674594764
GO:0001666	response to hypoxia	0.00394354613369043
GO:0009187	cyclic nucleotide metabolic process	0.00398879213401659
GO:0001701	in utero embryonic development	0.00398879213401659
GO:0009890	negative regulation of biosynthetic process	0.00401044557702982
GO:0008217	regulation of blood pressure	0.00426407497143464
GO:0051046	regulation of secretion	0.00451065910488376
GO:0051480	cytosolic calcium ion homeostasis	0.00506996473876319
GO:0003001	generation of a signal involved in cell-cell signaling	0.00506996473876319
GO:0007204	elevation of cytosolic calcium ion concentration	0.00506996473876319
GO:0032147	activation of protein kinase activity	0.00506996473876319
GO:0035239	tube morphogenesis	0.00600494524902861
GO:0007423	sensory organ development	0.00605498645943718
GO:0003002	regionalization	0.00605498645943718
GO:0007200	G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)	0.00605498645943718
GO:0048598	embryonic morphogenesis	0.00622536486630446
GO:0007507	heart development	0.00622536486630446
GO:0009792	embryonic development ending in birth or egg hatching	0.00622536486630446
GO:0043009	chordate embryonic development	0.00622536486630446
GO:0001664	G-protein-coupled receptor binding	0.0067349582008713
GO:0008643	carbohydrate transport	0.00710468812893792
GO:0006874	cellular calcium ion homeostasis	0.00723629638155414
GO:0055074	calcium ion homeostasis	0.00723629638155414
GO:0035295	tube development	0.00723629638155414
GO:0006875	cellular metal ion homeostasis	0.00739856605503077
GO:0055065	metal ion homeostasis	0.00739856605503077
GO:0007389	pattern specification process	0.00739856605503077
GO:0050878	regulation of body fluid levels	0.00739856605503077
GO:0048015	phosphoinositide-mediated signaling	0.00747457658629087
GO:0001525	angiogenesis	0.00747457658629087
GO:0045860	positive regulation of protein kinase activity	0.00808478305663487
GO:0033674	positive regulation of kinase activity	0.00817167807084306
GO:0051347	positive regulation of transferase activity	0.00817339770006672
GO:0048514	blood vessel morphogenesis	0.00817339770006672
GO:0048646	anatomical structure formation	0.00842193571176262
GO:0008015	blood circulation	0.00863456179598885
GO:0003013	circulatory system process	0.00863456179598885
GO:0001568	blood vessel development	0.00876449937641393
GO:0001944	vasculature development	0.00878608175058193
GO:0030005	cellular di-, tri-valent inorganic cation homeostasis	0.00943634253418782
GO:0055066	di-, tri-valent inorganic cation homeostasis	0.00950310910872217
GO:0030003	cellular cation homeostasis	0.0102888469998933
GO:0055080	cation homeostasis	0.010346483596513
GO:0001501	skeletal development	0.0105545635531474
GO:0005179	hormone activity	0.0107611143464199
GO:0009889	regulation of biosynthetic process	0.0107611143464199
GO:0008284	positive regulation of cell proliferation	0.0111502081653971
GO:0005625	soluble fraction	0.0111502081653971
GO:0009790	embryonic development	0.0111502081653971
GO:0045859	regulation of protein kinase activity	0.0111502081653971
GO:0055082	cellular chemical homeostasis	0.0111502081653971
GO:0006873	cellular ion homeostasis	0.0111502081653971
GO:0043549	regulation of kinase activity	0.0112889578057303
GO:0051338	regulation of transferase activity	0.0114253755193352
GO:0009165	nucleotide biosynthetic process	0.0116459544223585
GO:0043085	positive regulation of catalytic activity	0.0116459544223585
GO:0050801	ion homeostasis	0.0119936169336967
GO:0019932	second-messenger-mediated signaling	0.0119936169336967
GO:0051239	regulation of multicellular organismal process	0.0122964167834611
GO:0007268	synaptic transmission	0.0127705168962675
GO:0048878	chemical homeostasis	0.0131934048394663
GO:0009888	tissue development	0.0132195481039967
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0137183286971624
GO:0019226	transmission of nerve impulse	0.0140813638591562
GO:0051704	multi-organism process	0.0141000733635845
GO:0009117	nucleotide metabolic process	0.0142865745746609
GO:0009887	organ morphogenesis	0.0150957651399192
GO:0055086	nucleobase, nucleoside and nucleotide metabolic process	0.015189200482662
GO:0019725	cellular homeostasis	0.0153311441666558
GO:0007243	protein kinase cascade	0.0153311441666558
GO:0031324	negative regulation of cellular metabolic process	0.0154207877075238
GO:0046903	secretion	0.0154287644354604
GO:0009892	negative regulation of metabolic process	0.0173911337043123
GO:0042127	regulation of cell proliferation	0.0185728492444476
GO:0042592	homeostatic process	0.0188726850683756
GO:0005615	extracellular space	0.0206127198619138
GO:0050790	regulation of catalytic activity	0.0234524123428905
GO:0007267	cell-cell signaling	0.0246356728165276
GO:0065009	regulation of a molecular function	0.0256495954184492
GO:0008283	cell proliferation	0.0282819116757411
GO:0000267	cell fraction	0.034007458196839
GO:0044421	extracellular region part	0.034075681373456
GO:0065008	regulation of biological quality	0.0352437893978223
GO:0048522	positive regulation of cellular process	0.0352437893978223
GO:0005102	receptor binding	0.0380546724753719
GO:0009653	anatomical structure morphogenesis	0.0381671933957299
GO:0048518	positive regulation of biological process	0.0384593039469036
GO:0048523	negative regulation of cellular process	0.040783586482986
GO:0048513	organ development	0.040783586482986
GO:0048519	negative regulation of biological process	0.0419765043698226
GO:0006950	response to stress	0.0431188429687193
GO:0048468	cell development	0.0435454150701852
GO:0050877	neurological system process	0.0442104592464084

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><br>

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Cell Type

Ontology term	p-value	n
respiratory epithelial cell	8.03e-42	13
endo-epithelial cell	4.19e-39	42
endodermal cell	3.05e-27	58
general ecto-epithelial cell	1.05e-24	14
transitional epithelial cell	2.91e-24	4
urothelial cell	2.91e-24	4
epithelial cell of tracheobronchial tree	5.84e-22	9
epithelial cell of lower respiratory tract	5.84e-22	9
epithelial cell	4.88e-21	253
bronchial epithelial cell	1.29e-17	3
epithelial cell of Malassez	1.61e-17	3
gingival epithelial cell	1.70e-17	3
mammary gland epithelial cell	4.46e-13	4
sebum secreting cell	1.67e-12	2
epithelial cell of sweat gland	1.67e-12	2
epithelial cell of skin gland	1.67e-12	2
acinar cell of sebaceous gland	1.67e-12	2
epidermal cell	1.83e-10	9
embryonic cell	1.29e-09	250
ecto-epithelial cell	1.82e-09	34
epithelial cell of alimentary canal	2.20e-09	20
stratified squamous epithelial cell	4.77e-09	6
keratin accumulating cell	4.77e-09	6
stratified epithelial cell	4.77e-09	6
keratinizing barrier epithelial cell	4.77e-09	6
epithelial fate stem cell	4.77e-09	6
stratified epithelial stem cell	4.77e-09	6
surface ectodermal cell	4.77e-09	6
duct epithelial cell	1.43e-08	3
branched duct epithelial cell	1.43e-08	3
tracheal epithelial cell	1.43e-08	3
tracheoblast	1.43e-08	3
epithelial cell of prostate	2.91e-08	3
epithelial cell of esophagus	7.15e-07	1

Uber Anatomy

Ontology term	p-value	n
urothelium	1.91e-19	5
lower respiratory tract epithelium	1.29e-17	3
epithelium of bronchus	1.29e-17	3
gingival epithelium	1.70e-17	3
transitional epithelium	3.15e-16	6
jaw skeleton	2.82e-13	4
splanchnocranium	2.82e-13	4
mammary gland	4.46e-13	4
mammary bud	4.46e-13	4
mammary ridge	4.46e-13	4
mammary placode	4.46e-13	4
tracheobronchial tree	5.78e-13	15
lower respiratory tract	5.78e-13	15
skin gland	1.67e-12	2
epidermis gland	1.67e-12	2
gland of integumental system	1.67e-12	2
sebaceous gland	1.67e-12	2
skin sebaceous gland	1.67e-12	2
sweat gland	1.67e-12	2
sweat gland placode	1.67e-12	2
sebaceous gland placode	1.67e-12	2
endoderm-derived structure	3.06e-12	160
endoderm	3.06e-12	160
presumptive endoderm	3.06e-12	160
bronchus	8.86e-11	5
primary subdivision of cranial skeletal system	1.01e-10	5
epithelial bud	1.27e-10	37
respiratory system	2.99e-10	74
epithelial fold	6.06e-10	47
endo-epithelium	4.78e-09	82
protuberance	5.18e-09	6
pharyngeal arch	5.18e-09	6
embryonic head	5.18e-09	6
respiratory system epithelium	6.43e-09	28
respiratory tract	1.06e-08	54
surface structure	3.57e-08	99
thoracic cavity element	3.30e-07	34
thoracic cavity	3.30e-07	34
mouth mucosa	5.32e-07	13
thoracic segment organ	5.62e-07	35
epithelium of mucosa	7.42e-07	8
gingiva	7.42e-07	8
external ectoderm	9.08e-07	8

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)
MA0003.1	5.5441e-05
MA0004.1	0.207008
MA0006.1	0.334079
MA0007.1	0.193512
MA0009.1	0.600198
MA0014.1	8.02757e-05
MA0017.1	0.125342
MA0019.1	0.322194
MA0024.1	0.50459
MA0025.1	0.725013
MA0027.1	2.18072
MA0028.1	0.111328
MA0029.1	0.522011
MA0030.1	2.19952
MA0031.1	0.454061
MA0038.1	0.285594
MA0040.1	0.527306
MA0041.1	0.628965
MA0042.1	0.197306
MA0043.1	0.60049
MA0046.1	0.590147
MA0048.1	0.0114521
MA0050.1	0.197941
MA0051.1	0.282227
MA0052.1	0.530811
MA0055.1	0.0063545
MA0056.1	0
MA0057.1	0.0104156
MA0058.1	0.141262
MA0059.1	0.140431
MA0060.1	0.0444001
MA0061.1	1.32241
MA0063.1	0
MA0066.1	1.42268
MA0067.1	0.900956
MA0068.1	0.0222576
MA0069.1	0.586593
MA0070.1	0.576293
MA0071.1	0.255111
MA0072.1	0.572162
MA0073.1	1.60413e-05
MA0074.1	0.281628
MA0076.1	0.151641
MA0077.1	0.565087
MA0078.1	0.363755
MA0081.1	0.434032
MA0083.1	0.607144
MA0084.1	1.08294
MA0087.1	0.569916
MA0088.1	0.0658118
MA0089.1	0
MA0090.1	0.485893
MA0091.1	0.601165
MA0092.1	0.181853
MA0093.1	0.103729
MA0095.1	0
MA0098.1	0
MA0100.1	0.296726
MA0101.1	1.69535
MA0103.1	0.658605
MA0105.1	0.970472
MA0106.1	0.854542
MA0107.1	1.31477
MA0108.2	1.1451
MA0109.1	0
MA0111.1	0.170509
MA0113.1	0.332535
MA0114.1	0.228885
MA0115.1	0.827474
MA0116.1	0.0681676
MA0117.1	0.635078
MA0119.1	0.130226
MA0122.1	0.659244
MA0124.1	0.787807
MA0125.1	0.708116
MA0130.1	0
MA0131.1	0.379172
MA0132.1	0
MA0133.1	0
MA0135.1	0.628343
MA0136.1	0.291242
MA0139.1	0.0300305
MA0140.1	0.253051
MA0141.1	0.139313
MA0142.1	0.426146
MA0143.1	0.332682
MA0144.1	0.459643
MA0145.1	0.175315
MA0146.1	0.00856874
MA0147.1	0.0698742
MA0148.1	0.225411
MA0149.1	0.245595
MA0062.2	0.0323736
MA0035.2	0.252505
MA0039.2	9.54563e-05
MA0138.2	0.364793
MA0002.2	0.999186
MA0137.2	3.85561
MA0104.2	0.0440964
MA0047.2	0.309071
MA0112.2	0.00394022
MA0065.2	0.0827578
MA0150.1	0.157331
MA0151.1	0
MA0152.1	0.258148
MA0153.1	1.65387
MA0154.1	0.117204
MA0155.1	0.146881
MA0156.1	0.372479
MA0157.1	0.402372
MA0158.1	0
MA0159.1	0.0701863
MA0160.1	0.666979
MA0161.1	0
MA0162.1	0.0280426
MA0163.1	0.00430547
MA0164.1	0.342871
MA0080.2	1.67871
MA0018.2	0.320136
MA0099.2	0.716923
MA0079.2	6.62378e-11
MA0102.2	1.11935
MA0258.1	0.053266
MA0259.1	0.257452
MA0442.1	0

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
STAT3#6774	7	4.09090305444887	0.000864707674329911	0.0064538844278812

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.