Coexpression cluster:C2899

Full id: C2899_epidermoid_oral_cervical_Small_large_placenta_mucinous

Phase1 CAGE Peaks

Hg19::chr7:55086703..55086717,+	p1@EGFR
Hg19::chr7:55086735..55086738,+	p3@EGFR
Hg19::chr7:55086794..55086803,+	p2@EGFR
Hg19::chr7:55087162..55087197,+	p1@BC057802

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:0004710	MAP/ERK kinase kinase activity	0.00323796067349582
GO:0043006	calcium-dependent phospholipase A2 activation	0.00323796067349582
GO:0032430	positive regulation of phospholipase A2 activity	0.00323796067349582
GO:0032429	regulation of phospholipase A2 activity	0.00323796067349582
GO:0005006	epidermal growth factor receptor activity	0.00323796067349582
GO:0032431	activation of phospholipase A2	0.00323796067349582
GO:0030235	nitric-oxide synthase regulator activity	0.00323796067349582
GO:0030128	clathrin coat of endocytic vesicle	0.00323796067349582
GO:0030669	clathrin-coated endocytic vesicle membrane	0.00323796067349582
GO:0030122	AP-2 adaptor complex	0.00323796067349582
GO:0030666	endocytic vesicle membrane	0.00348703457145704
GO:0050999	regulation of nitric-oxide synthase activity	0.00348703457145704
GO:0045334	clathrin-coated endocytic vesicle	0.00348703457145704
GO:0045429	positive regulation of nitric oxide biosynthetic process	0.00370052648399522
GO:0051205	protein insertion into membrane	0.00388555280819498
GO:0045428	regulation of nitric oxide biosynthetic process	0.00404745084186977
GO:0051341	regulation of oxidoreductase activity	0.0044308935532048
GO:0030132	clathrin coat of coated pit	0.0044308935532048
GO:0051668	localization within membrane	0.0044308935532048
GO:0007202	phospholipase C activation	0.00480471583809057
GO:0030335	positive regulation of cell migration	0.00480471583809057
GO:0050679	positive regulation of epithelial cell proliferation	0.00480471583809057
GO:0004709	MAP kinase kinase kinase activity	0.00480471583809057
GO:0051272	positive regulation of cell motility	0.00480471583809057
GO:0040017	positive regulation of locomotion	0.00480471583809057
GO:0046209	nitric oxide metabolic process	0.00480471583809057
GO:0030125	clathrin vesicle coat	0.00480471583809057
GO:0030139	endocytic vesicle	0.00480471583809057
GO:0006809	nitric oxide biosynthetic process	0.00480471583809057
GO:0042327	positive regulation of phosphorylation	0.00480471583809057
GO:0030665	clathrin coated vesicle membrane	0.00480471583809057
GO:0045937	positive regulation of phosphate metabolic process	0.00505931355233722
GO:0050730	regulation of peptidyl-tyrosine phosphorylation	0.005494721142902
GO:0050678	regulation of epithelial cell proliferation	0.00571404824734557
GO:0007173	epidermal growth factor receptor signaling pathway	0.00593626123474233
GO:0050673	epithelial cell proliferation	0.00593626123474233
GO:0019722	calcium-mediated signaling	0.00647592134699164
GO:0051015	actin filament binding	0.00664634032980721
GO:0018108	peptidyl-tyrosine phosphorylation	0.00677028140821853
GO:0005905	coated pit	0.00677028140821853
GO:0018212	peptidyl-tyrosine modification	0.00677028140821853
GO:0001932	regulation of protein amino acid phosphorylation	0.00677028140821853
GO:0033238	regulation of amine metabolic process	0.00677028140821853
GO:0006521	regulation of amino acid metabolic process	0.00677028140821853
GO:0030120	vesicle coat	0.00717982584122986
GO:0030662	coated vesicle membrane	0.00717982584122986
GO:0030131	clathrin adaptor complex	0.00728541151536559
GO:0030119	AP-type membrane coat adaptor complex	0.00728541151536559
GO:0030334	regulation of cell migration	0.00792969960856119
GO:0042325	regulation of phosphorylation	0.00809490168373955
GO:0043406	positive regulation of MAP kinase activity	0.00809490168373955
GO:0030118	clathrin coat	0.00809490168373955
GO:0051174	regulation of phosphorus metabolic process	0.00809490168373955
GO:0019220	regulation of phosphate metabolic process	0.00809490168373955
GO:0051270	regulation of cell motility	0.00809490168373955
GO:0009891	positive regulation of biosynthetic process	0.00809490168373955
GO:0040012	regulation of locomotion	0.00815072859190327
GO:0040011	locomotion	0.00815072859190327
GO:0051345	positive regulation of hydrolase activity	0.00831076572863927
GO:0004702	receptor signaling protein serine/threonine kinase activity	0.00831076572863927
GO:0001503	ossification	0.00904573140532166
GO:0007200	G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)	0.00904573140532166
GO:0031214	biomineral formation	0.00904573140532166
GO:0043405	regulation of MAP kinase activity	0.00941032320734723
GO:0046849	bone remodeling	0.00956443768171072
GO:0048771	tissue remodeling	0.00994190742002941
GO:0046982	protein heterodimerization activity	0.00994190742002941
GO:0030659	cytoplasmic vesicle membrane	0.00994190742002941
GO:0044433	cytoplasmic vesicle part	0.00994190742002941
GO:0003690	double-stranded DNA binding	0.00994190742002941
GO:0004714	transmembrane receptor protein tyrosine kinase activity	0.00994190742002941
GO:0012506	vesicle membrane	0.0100160916833471
GO:0030136	clathrin-coated vesicle	0.0100160916833471
GO:0030117	membrane coat	0.0100160916833471
GO:0048475	coated membrane	0.0100160916833471
GO:0018193	peptidyl-amino acid modification	0.010310348460342
GO:0019199	transmembrane receptor protein kinase activity	0.0106810650788044
GO:0048015	phosphoinositide-mediated signaling	0.0107101776123323
GO:0045860	positive regulation of protein kinase activity	0.0114694028675635
GO:0033674	positive regulation of kinase activity	0.0114694028675635
GO:0044271	nitrogen compound biosynthetic process	0.0114694028675635
GO:0030135	coated vesicle	0.0114694028675635
GO:0051347	positive regulation of transferase activity	0.0114694028675635
GO:0043566	structure-specific DNA binding	0.0122579939782342
GO:0005057	receptor signaling protein activity	0.0134851538637355
GO:0005768	endosome	0.0145331723252254
GO:0001501	skeletal development	0.0154539032144119
GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	0.0154539032144119
GO:0009889	regulation of biosynthetic process	0.0157896059808673
GO:0045786	negative regulation of progression through cell cycle	0.0161898033674791
GO:0016477	cell migration	0.0164009747157506
GO:0008284	positive regulation of cell proliferation	0.0164009747157506
GO:0045859	regulation of protein kinase activity	0.0165031544003981
GO:0043549	regulation of kinase activity	0.0166720528294891
GO:0051338	regulation of transferase activity	0.0168373955021783
GO:0043085	positive regulation of catalytic activity	0.0172691235919777
GO:0019932	second-messenger-mediated signaling	0.0178922362989047
GO:0016044	membrane organization and biogenesis	0.0187669557402615
GO:0007167	enzyme linked receptor protein signaling pathway	0.0194912534659454
GO:0009888	tissue development	0.0194912534659454
GO:0004713	protein-tyrosine kinase activity	0.0194912534659454
GO:0051336	regulation of hydrolase activity	0.0194912534659454
GO:0016337	cell-cell adhesion	0.0215471564818085
GO:0016023	cytoplasmic membrane-bound vesicle	0.0215471564818085
GO:0031988	membrane-bound vesicle	0.0215471564818085
GO:0000074	regulation of progression through cell cycle	0.0215471564818085
GO:0051726	regulation of cell cycle	0.0215471564818085
GO:0042802	identical protein binding	0.0215471564818085
GO:0031325	positive regulation of cellular metabolic process	0.0215471564818085
GO:0046983	protein dimerization activity	0.0215471564818085
GO:0006928	cell motility	0.0221453381776589
GO:0051674	localization of cell	0.0221453381776589
GO:0009893	positive regulation of metabolic process	0.0224078340413604
GO:0051246	regulation of protein metabolic process	0.0239327528040995
GO:0031410	cytoplasmic vesicle	0.0239327528040995
GO:0031982	vesicle	0.0241172243267275
GO:0003779	actin binding	0.0242431927348918
GO:0042127	regulation of cell proliferation	0.0257390433198227
GO:0006520	amino acid metabolic process	0.0257948463737314
GO:0005615	extracellular space	0.0284940539267632
GO:0006519	amino acid and derivative metabolic process	0.0293289661004249
GO:0008092	cytoskeletal protein binding	0.0318531090644711
GO:0050790	regulation of catalytic activity	0.0318531090644711
GO:0022402	cell cycle process	0.032640732595724
GO:0009308	amine metabolic process	0.0329494878134935
GO:0065009	regulation of a molecular function	0.0344868509827888
GO:0006807	nitrogen compound metabolic process	0.0345722415217349
GO:0004674	protein serine/threonine kinase activity	0.0353646017308371
GO:0008283	cell proliferation	0.0373997008023936
GO:0019752	carboxylic acid metabolic process	0.0394487422511399
GO:0006082	organic acid metabolic process	0.0394487422511399
GO:0007049	cell cycle	0.0411613485615605
GO:0044421	extracellular region part	0.044308935532048
GO:0045184	establishment of protein localization	0.0445582050890022
GO:0048522	positive regulation of cellular process	0.0450968145975287
GO:0022610	biological adhesion	0.0450968145975287
GO:0007155	cell adhesion	0.0450968145975287
GO:0008104	protein localization	0.0450968145975287
GO:0033036	macromolecule localization	0.0471484345550758
GO:0012505	endomembrane system	0.0475517653193386
GO:0048518	positive regulation of biological process	0.0487760884432987

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	1.45e-16	253
endo-epithelial cell	9.18e-12	42
endodermal cell	4.25e-11	58
embryonic cell	2.49e-09	250
mesothelial cell	1.24e-07	19
fibroblast	1.97e-07	76

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	2.82e-23	160
endoderm	2.82e-23	160
presumptive endoderm	2.82e-23	160
multi-tissue structure	9.01e-19	342
digestive system	1.30e-17	145
digestive tract	1.30e-17	145
primitive gut	1.30e-17	145
organism subdivision	2.23e-16	264
respiratory system	5.09e-14	74
surface structure	3.07e-13	99
organ part	2.49e-12	218
anatomical system	4.40e-12	624
anatomical group	7.79e-12	625
anatomical cluster	5.21e-11	373
organ	1.02e-10	503
subdivision of digestive tract	1.07e-10	118
multi-cellular organism	1.59e-10	656
primordium	2.08e-10	160
head	4.34e-10	56
mouth	1.28e-09	29
stomodeum	1.28e-09	29
subdivision of head	1.53e-09	49
orifice	1.73e-09	36
organ component layer	1.85e-09	66
anterior region of body	2.91e-09	62
craniocervical region	2.91e-09	62
respiratory tract	3.14e-09	54
trunk	1.97e-08	199
foregut	4.25e-08	87
oral opening	5.01e-08	22
mouth mucosa	9.73e-08	13
embryo	1.22e-07	592
developing anatomical structure	2.02e-07	581
immaterial anatomical entity	2.22e-07	117
endo-epithelium	2.27e-07	82
cell layer	2.59e-07	309
respiratory primordium	3.11e-07	38
endoderm of foregut	3.11e-07	38
mucosa	3.11e-07	20
epithelium	5.06e-07	306
segment of respiratory tract	5.65e-07	47
embryonic structure	5.68e-07	564
organ system subdivision	8.77e-07	223

Disease

Ontology term	p-value	n
squamous cell carcinoma	2.45e-07	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)
MA0003.1	2.92335
MA0004.1	0.71247
MA0006.1	0.532262
MA0007.1	1.65296
MA0009.1	1.20602
MA0014.1	3.08565
MA0017.1	0.577281
MA0019.1	0.873355
MA0024.1	1.09684
MA0025.1	1.34373
MA0027.1	2.83281
MA0028.1	0.550763
MA0029.1	1.11704
MA0030.1	1.10506
MA0031.1	1.03735
MA0038.1	0.824639
MA0040.1	1.12314
MA0041.1	0.732902
MA0042.1	0.697662
MA0043.1	1.20635
MA0046.1	1.19471
MA0048.1	0.709734
MA0050.1	0.69864
MA0051.1	0.820063
MA0052.1	1.12718
MA0055.1	1.28887
MA0056.1	0
MA0057.1	0.248209
MA0058.1	0.605914
MA0059.1	0.604454
MA0060.1	0.393285
MA0061.1	2.54366
MA0063.1	0
MA0066.1	0.825101
MA0067.1	1.53181
MA0068.1	0.841508
MA0069.1	1.19071
MA0070.1	1.17908
MA0071.1	0.782546
MA0072.1	1.1744
MA0073.1	0.100363
MA0074.1	0.819248
MA0076.1	0.623864
MA0077.1	1.16637
MA0078.1	0.926725
MA0081.1	0.604638
MA0083.1	1.21381
MA0084.1	1.72172
MA0087.1	1.17185
MA0088.1	1.02755
MA0089.1	0
MA0090.1	0.640115
MA0091.1	0.715356
MA0092.1	0.673508
MA0093.1	0.535768
MA0095.1	0
MA0098.1	0
MA0100.1	0.83965
MA0101.1	1.33363
MA0103.1	0.521546
MA0105.1	2.66951
MA0106.1	3.33935
MA0107.1	0.453492
MA0108.2	1.03412
MA0109.1	0
MA0111.1	0.655276
MA0113.1	2.05499
MA0114.1	1.13665
MA0115.1	1.45393
MA0116.1	0.457606
MA0117.1	1.24497
MA0119.1	0.586221
MA0122.1	1.27173
MA0124.1	1.41151
MA0125.1	1.32534
MA0130.1	0
MA0131.1	0.94608
MA0132.1	0
MA0133.1	0
MA0135.1	1.23748
MA0136.1	0.832277
MA0139.1	0.344952
MA0140.1	0.779643
MA0141.1	0.602484
MA0142.1	1.00381
MA0143.1	0.887001
MA0144.1	0.430413
MA0145.1	0.569905
MA0146.1	0.481
MA0147.1	0.46175
MA0148.1	0.739888
MA0149.1	0.769072
MA0062.2	0.353589
MA0035.2	0.778873
MA0039.2	0.483275
MA0138.2	0.928035
MA0002.2	0.379056
MA0137.2	0.558189
MA0104.2	0.392359
MA0047.2	0.856092
MA0112.2	0.187982
MA0065.2	0.199162
MA0150.1	0.633493
MA0151.1	0
MA0152.1	0.78681
MA0153.1	1.30799
MA0154.1	0.229241
MA0155.1	0.533581
MA0156.1	0.560797
MA0157.1	0.97481
MA0158.1	0
MA0159.1	1.1691
MA0160.1	0.756582
MA0161.1	0
MA0162.1	1.06783
MA0163.1	0.918944
MA0164.1	0.90014
MA0080.2	0.535868
MA0018.2	0.870662
MA0099.2	0.7872
MA0079.2	6.45898
MA0102.2	1.75932
MA0258.1	0.418966
MA0259.1	0.471671
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
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106806958702401
TFAP2A#7020	3	12.3889757797837	0.00084694130358843	0.00638286208727609
TFAP2C#7022	3	8.10692145739517	0.00294701173986644	0.0157216610869853
ZNF263#10127	4	8.22184163701068	0.000218787118095832	0.00249998991540597

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.