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Coexpression cluster:C2899

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Full id: C2899_epidermoid_oral_cervical_Small_large_placenta_mucinous



Phase1 CAGE Peaks

  Short description
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 clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0004710MAP/ERK kinase kinase activity0.00323796067349582
GO:0043006calcium-dependent phospholipase A2 activation0.00323796067349582
GO:0032430positive regulation of phospholipase A2 activity0.00323796067349582
GO:0032429regulation of phospholipase A2 activity0.00323796067349582
GO:0005006epidermal growth factor receptor activity0.00323796067349582
GO:0032431activation of phospholipase A20.00323796067349582
GO:0030235nitric-oxide synthase regulator activity0.00323796067349582
GO:0030128clathrin coat of endocytic vesicle0.00323796067349582
GO:0030669clathrin-coated endocytic vesicle membrane0.00323796067349582
GO:0030122AP-2 adaptor complex0.00323796067349582
GO:0030666endocytic vesicle membrane0.00348703457145704
GO:0050999regulation of nitric-oxide synthase activity0.00348703457145704
GO:0045334clathrin-coated endocytic vesicle0.00348703457145704
GO:0045429positive regulation of nitric oxide biosynthetic process0.00370052648399522
GO:0051205protein insertion into membrane0.00388555280819498
GO:0045428regulation of nitric oxide biosynthetic process0.00404745084186977
GO:0051341regulation of oxidoreductase activity0.0044308935532048
GO:0030132clathrin coat of coated pit0.0044308935532048
GO:0051668localization within membrane0.0044308935532048
GO:0007202phospholipase C activation0.00480471583809057
GO:0030335positive regulation of cell migration0.00480471583809057
GO:0050679positive regulation of epithelial cell proliferation0.00480471583809057
GO:0004709MAP kinase kinase kinase activity0.00480471583809057
GO:0051272positive regulation of cell motility0.00480471583809057
GO:0040017positive regulation of locomotion0.00480471583809057
GO:0046209nitric oxide metabolic process0.00480471583809057
GO:0030125clathrin vesicle coat0.00480471583809057
GO:0030139endocytic vesicle0.00480471583809057
GO:0006809nitric oxide biosynthetic process0.00480471583809057
GO:0042327positive regulation of phosphorylation0.00480471583809057
GO:0030665clathrin coated vesicle membrane0.00480471583809057
GO:0045937positive regulation of phosphate metabolic process0.00505931355233722
GO:0050730regulation of peptidyl-tyrosine phosphorylation0.005494721142902
GO:0050678regulation of epithelial cell proliferation0.00571404824734557
GO:0007173epidermal growth factor receptor signaling pathway0.00593626123474233
GO:0050673epithelial cell proliferation0.00593626123474233
GO:0019722calcium-mediated signaling0.00647592134699164
GO:0051015actin filament binding0.00664634032980721
GO:0018108peptidyl-tyrosine phosphorylation0.00677028140821853
GO:0005905coated pit0.00677028140821853
GO:0018212peptidyl-tyrosine modification0.00677028140821853
GO:0001932regulation of protein amino acid phosphorylation0.00677028140821853
GO:0033238regulation of amine metabolic process0.00677028140821853
GO:0006521regulation of amino acid metabolic process0.00677028140821853
GO:0030120vesicle coat0.00717982584122986
GO:0030662coated vesicle membrane0.00717982584122986
GO:0030131clathrin adaptor complex0.00728541151536559
GO:0030119AP-type membrane coat adaptor complex0.00728541151536559
GO:0030334regulation of cell migration0.00792969960856119
GO:0042325regulation of phosphorylation0.00809490168373955
GO:0043406positive regulation of MAP kinase activity0.00809490168373955
GO:0030118clathrin coat0.00809490168373955
GO:0051174regulation of phosphorus metabolic process0.00809490168373955
GO:0019220regulation of phosphate metabolic process0.00809490168373955
GO:0051270regulation of cell motility0.00809490168373955
GO:0009891positive regulation of biosynthetic process0.00809490168373955
GO:0040012regulation of locomotion0.00815072859190327
GO:0040011locomotion0.00815072859190327
GO:0051345positive regulation of hydrolase activity0.00831076572863927
GO:0004702receptor signaling protein serine/threonine kinase activity0.00831076572863927
GO:0001503ossification0.00904573140532166
GO:0007200G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.00904573140532166
GO:0031214biomineral formation0.00904573140532166
GO:0043405regulation of MAP kinase activity0.00941032320734723
GO:0046849bone remodeling0.00956443768171072
GO:0048771tissue remodeling0.00994190742002941
GO:0046982protein heterodimerization activity0.00994190742002941
GO:0030659cytoplasmic vesicle membrane0.00994190742002941
GO:0044433cytoplasmic vesicle part0.00994190742002941
GO:0003690double-stranded DNA binding0.00994190742002941
GO:0004714transmembrane receptor protein tyrosine kinase activity0.00994190742002941
GO:0012506vesicle membrane0.0100160916833471
GO:0030136clathrin-coated vesicle0.0100160916833471
GO:0030117membrane coat0.0100160916833471
GO:0048475coated membrane0.0100160916833471
GO:0018193peptidyl-amino acid modification0.010310348460342
GO:0019199transmembrane receptor protein kinase activity0.0106810650788044
GO:0048015phosphoinositide-mediated signaling0.0107101776123323
GO:0045860positive regulation of protein kinase activity0.0114694028675635
GO:0033674positive regulation of kinase activity0.0114694028675635
GO:0044271nitrogen compound biosynthetic process0.0114694028675635
GO:0030135coated vesicle0.0114694028675635
GO:0051347positive regulation of transferase activity0.0114694028675635
GO:0043566structure-specific DNA binding0.0122579939782342
GO:0005057receptor signaling protein activity0.0134851538637355
GO:0005768endosome0.0145331723252254
GO:0001501skeletal development0.0154539032144119
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0154539032144119
GO:0009889regulation of biosynthetic process0.0157896059808673
GO:0045786negative regulation of progression through cell cycle0.0161898033674791
GO:0016477cell migration0.0164009747157506
GO:0008284positive regulation of cell proliferation0.0164009747157506
GO:0045859regulation of protein kinase activity0.0165031544003981
GO:0043549regulation of kinase activity0.0166720528294891
GO:0051338regulation of transferase activity0.0168373955021783
GO:0043085positive regulation of catalytic activity0.0172691235919777
GO:0019932second-messenger-mediated signaling0.0178922362989047
GO:0016044membrane organization and biogenesis0.0187669557402615
GO:0007167enzyme linked receptor protein signaling pathway0.0194912534659454
GO:0009888tissue development0.0194912534659454
GO:0004713protein-tyrosine kinase activity0.0194912534659454
GO:0051336regulation of hydrolase activity0.0194912534659454
GO:0016337cell-cell adhesion0.0215471564818085
GO:0016023cytoplasmic membrane-bound vesicle0.0215471564818085
GO:0031988membrane-bound vesicle0.0215471564818085
GO:0000074regulation of progression through cell cycle0.0215471564818085
GO:0051726regulation of cell cycle0.0215471564818085
GO:0042802identical protein binding0.0215471564818085
GO:0031325positive regulation of cellular metabolic process0.0215471564818085
GO:0046983protein dimerization activity0.0215471564818085
GO:0006928cell motility0.0221453381776589
GO:0051674localization of cell0.0221453381776589
GO:0009893positive regulation of metabolic process0.0224078340413604
GO:0051246regulation of protein metabolic process0.0239327528040995
GO:0031410cytoplasmic vesicle0.0239327528040995
GO:0031982vesicle0.0241172243267275
GO:0003779actin binding0.0242431927348918
GO:0042127regulation of cell proliferation0.0257390433198227
GO:0006520amino acid metabolic process0.0257948463737314
GO:0005615extracellular space0.0284940539267632
GO:0006519amino acid and derivative metabolic process0.0293289661004249
GO:0008092cytoskeletal protein binding0.0318531090644711
GO:0050790regulation of catalytic activity0.0318531090644711
GO:0022402cell cycle process0.032640732595724
GO:0009308amine metabolic process0.0329494878134935
GO:0065009regulation of a molecular function0.0344868509827888
GO:0006807nitrogen compound metabolic process0.0345722415217349
GO:0004674protein serine/threonine kinase activity0.0353646017308371
GO:0008283cell proliferation0.0373997008023936
GO:0019752carboxylic acid metabolic process0.0394487422511399
GO:0006082organic acid metabolic process0.0394487422511399
GO:0007049cell cycle0.0411613485615605
GO:0044421extracellular region part0.044308935532048
GO:0045184establishment of protein localization0.0445582050890022
GO:0048522positive regulation of cellular process0.0450968145975287
GO:0022610biological adhesion0.0450968145975287
GO:0007155cell adhesion0.0450968145975287
GO:0008104protein localization0.0450968145975287
GO:0033036macromolecule localization0.0471484345550758
GO:0012505endomembrane system0.0475517653193386
GO:0048518positive regulation of biological process0.0487760884432987



Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data
disease_data


Cell Type
Ontology termp-valuen
epithelial cell1.45e-16253
endo-epithelial cell9.18e-1242
endodermal cell4.25e-1158
embryonic cell2.49e-09250
mesothelial cell1.24e-0719
fibroblast1.97e-0776
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.82e-23160
endoderm2.82e-23160
presumptive endoderm2.82e-23160
multi-tissue structure9.01e-19342
digestive system1.30e-17145
digestive tract1.30e-17145
primitive gut1.30e-17145
organism subdivision2.23e-16264
respiratory system5.09e-1474
surface structure3.07e-1399
organ part2.49e-12218
anatomical system4.40e-12624
anatomical group7.79e-12625
anatomical cluster5.21e-11373
organ1.02e-10503
subdivision of digestive tract1.07e-10118
multi-cellular organism1.59e-10656
primordium2.08e-10160
head4.34e-1056
mouth1.28e-0929
stomodeum1.28e-0929
subdivision of head1.53e-0949
orifice1.73e-0936
organ component layer1.85e-0966
anterior region of body2.91e-0962
craniocervical region2.91e-0962
respiratory tract3.14e-0954
trunk1.97e-08199
foregut4.25e-0887
oral opening5.01e-0822
mouth mucosa9.73e-0813
embryo1.22e-07592
developing anatomical structure2.02e-07581
immaterial anatomical entity2.22e-07117
endo-epithelium2.27e-0782
cell layer2.59e-07309
respiratory primordium3.11e-0738
endoderm of foregut3.11e-0738
mucosa3.11e-0720
epithelium5.06e-07306
segment of respiratory tract5.65e-0747
embryonic structure5.68e-07564
organ system subdivision8.77e-07223
Disease
Ontology termp-valuen
squamous cell carcinoma2.45e-0714


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.12.92335
MA0004.10.71247
MA0006.10.532262
MA0007.11.65296
MA0009.11.20602
MA0014.13.08565
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.11.28887
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.12.54366
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.100363
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.10.521546
MA0105.12.66951
MA0106.13.33935
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.12.05499
MA0114.11.13665
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.483275
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.11.06783
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.26.45898
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
E2F1#186944.907389214879320.001724022357361790.0106806958702401
TFAP2A#7020312.38897577978370.000846941303588430.00638286208727609
TFAP2C#702238.106921457395170.002947011739866440.0157216610869853
ZNF263#1012748.221841637010680.0002187871180958320.00249998991540597



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.