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Coexpression cluster:C224

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Full id: C224_clear_serous_pleomorphic_choriocarcinoma_mesothelioma_amniotic_renal



Phase1 CAGE Peaks

Hg19::chr10:14596140..14596159,-p17@FAM107B
Hg19::chr11:90481311..90481354,+p@chr11:90481311..90481354
+
Hg19::chr12:15088000..15088009,-p@chr12:15088000..15088009
-
Hg19::chr12:39347117..39347129,-p@chr12:39347117..39347129
-
Hg19::chr12:44976731..44976736,+p@chr12:44976731..44976736
+
Hg19::chr12:69338572..69338579,-p@chr12:69338572..69338579
-
Hg19::chr12:72425054..72425060,+p5@TPH2
Hg19::chr12:72425091..72425096,+p7@TPH2
Hg19::chr12:87855051..87855053,-p@chr12:87855051..87855053
-
Hg19::chr12:88036488..88036491,-p@chr12:88036488..88036491
-
Hg19::chr12:88064272..88064283,-p@chr12:88064272..88064283
-
Hg19::chr12:88064290..88064306,-p@chr12:88064290..88064306
-
Hg19::chr14:40235844..40235853,+p@chr14:40235844..40235853
+
Hg19::chr14:40235859..40235882,+p@chr14:40235859..40235882
+
Hg19::chr14:74297004..74297007,-p4@ENST00000555539
p4@uc001xov.1
Hg19::chr15:43580426..43580430,-p@chr15:43580426..43580430
-
Hg19::chr15:58790937..58790951,-p1@ENST00000561083
p1@uc002afb.1
Hg19::chr15:67044194..67044205,+p@chr15:67044194..67044205
+
Hg19::chr15:96607553..96607560,-p4@ENST00000558860
Hg19::chr15:96607564..96607575,-p2@ENST00000558860
Hg19::chr15:96607579..96607599,-p1@ENST00000558860
Hg19::chr16:75511082..75511090,+p@chr16:75511082..75511090
+
Hg19::chr17:65571445..65571468,-p@chr17:65571445..65571468
-
Hg19::chr19:33555780..33555801,-p1@RHPN2
Hg19::chr1:206290313..206290320,-p@chr1:206290313..206290320
-
Hg19::chr1:206290391..206290402,-p@chr1:206290391..206290402
-
Hg19::chr1:82165119..82165148,+p5@LPHN2
Hg19::chr20:18211087..18211094,-p@chr20:18211087..18211094
-
Hg19::chr20:18211099..18211106,-p@chr20:18211099..18211106
-
Hg19::chr3:148939777..148939800,-p2@CP
Hg19::chr3:148939835..148939836,-p4@CP
Hg19::chr3:70034650..70034690,+p@chr3:70034650..70034690
+
Hg19::chr4:143071426..143071431,-p@chr4:143071426..143071431
-
Hg19::chr4:143071473..143071483,-p@chr4:143071473..143071483
-
Hg19::chr4:22601437..22601444,+p@chr4:22601437..22601444
+
Hg19::chr6:136426000..136426008,+p@chr6:136426000..136426008
+
Hg19::chr6:136426009..136426018,+p@chr6:136426009..136426018
+
Hg19::chr6:18496965..18496969,+p@chr6:18496965..18496969
+
Hg19::chr6:18497065..18497066,+p@chr6:18497065..18497066
+
Hg19::chr6:18497083..18497107,+p@chr6:18497083..18497107
+
Hg19::chr6:75178491..75178498,+p@chr6:75178491..75178498
+
Hg19::chr6:75178505..75178516,+p@chr6:75178505..75178516
+
Hg19::chr7:20257327..20257374,-p6@MACC1
Hg19::chr7:20257434..20257446,-p7@MACC1
Hg19::chr7:20257461..20257472,-p9@MACC1
Hg19::chr7:20369383..20369396,+p@chr7:20369383..20369396
+
Hg19::chr7:20370263..20370280,+p11@ITGB8
Hg19::chr7:27160553..27160560,+p1@ENST00000523364
p1@uc010kux.1
Hg19::chr7:27164585..27164612,-p@chr7:27164585..27164612
-
Hg19::chr7:27164759..27164766,-p@chr7:27164759..27164766
-
Hg19::chr7:27164806..27164816,-p@chr7:27164806..27164816
-
Hg19::chr7:76911218..76911223,+p17@CCDC146
Hg19::chr7:76911238..76911250,+p9@CCDC146
Hg19::chr7:76911322..76911329,+p15@CCDC146
Hg19::chr7:76911438..76911446,+p12@CCDC146
Hg19::chr7:76911622..76911634,+p7@CCDC146
Hg19::chr7:93204033..93204043,-p1@CALCR
Hg19::chr7:93204048..93204059,-p2@CALCR
Hg19::chr7:93520223..93520231,+p2@ENST00000435257
Hg19::chr7:93520249..93520264,+p1@ENST00000435257
Hg19::chr8:133566176..133566183,+p@chr8:133566176..133566183
+
Hg19::chr9:132472047..132472078,+p@chr9:132472047..132472078
+
Hg19::chr9:74729520..74729525,+p10@GDA


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

p.valueFDRnGenesnPathwayName
2.78345011903363e-050.0176192392534829223GPCRs, Class B Secretin-like (Wikipathways):WP334



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

GO IDGO nameFDR corrected p-value
GO:0032841calcitonin binding0.0180181142069971
GO:0006587serotonin biosynthetic process from tryptophan0.0180181142069971
GO:0008892guanine deaminase activity0.0180181142069971
GO:0016724oxidoreductase activity, oxidizing metal ions, oxygen as acceptor0.0180181142069971
GO:0004322ferroxidase activity0.0180181142069971
GO:0042428serotonin metabolic process0.0180181142069971
GO:0004948calcitonin receptor activity0.0180181142069971
GO:0042427serotonin biosynthetic process0.0180181142069971
GO:0004510tryptophan 5-monooxygenase activity0.0180181142069971
GO:0042435indole derivative biosynthetic process0.0180181142069971
GO:0046219indolalkylamine biosynthetic process0.0180181142069971
GO:0016722oxidoreductase activity, oxidizing metal ions0.0180181142069971
GO:0006568tryptophan metabolic process0.0180181142069971
GO:0001573ganglioside metabolic process0.0180181142069971
GO:0006878cellular copper ion homeostasis0.0180181142069971
GO:0007154cell communication0.0180181142069971
GO:0017046peptide hormone binding0.0180181142069971
GO:0031226intrinsic to plasma membrane0.0180181142069971
GO:0016714oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced pteridine as one donor, and incorporation of one atom of oxygen0.0180181142069971
GO:0006586indolalkylamine metabolic process0.0180181142069971
GO:0042434indole derivative metabolic process0.0180181142069971
GO:0055070copper ion homeostasis0.0180181142069971
GO:0042430indole and derivative metabolic process0.0180181142069971
GO:0051384response to glucocorticoid stimulus0.0188354560439923
GO:0031960response to corticosteroid stimulus0.019091255349868
GO:0005375copper ion transmembrane transporter activity0.019091255349868
GO:0046658anchored to plasma membrane0.019091255349868
GO:0016491oxidoreductase activity0.019091255349868
GO:0031225anchored to membrane0.019479793407562
GO:0042136neurotransmitter biosynthetic process0.0200840578765452
GO:0006687glycosphingolipid metabolic process0.0226127014957497
GO:0006825copper ion transport0.0226127014957497
GO:0016597amino acid binding0.0226127014957497
GO:0005886plasma membrane0.0226127014957497
GO:0016524latrotoxin receptor activity0.0244558420830832
GO:0045762positive regulation of adenylate cyclase activity0.0244558420830832
GO:0031281positive regulation of cyclase activity0.0244558420830832
GO:0051349positive regulation of lyase activity0.0244558420830832
GO:0042562hormone binding0.0244558420830832
GO:0007568aging0.0244558420830832
GO:0042221response to chemical stimulus0.0259718531222645
GO:0006664glycolipid metabolic process0.0259718531222645
GO:0046915transition metal ion transmembrane transporter activity0.0262402933491107
GO:0042133neurotransmitter metabolic process0.0267409396897012
GO:0006672ceramide metabolic process0.0267409396897012
GO:0042401biogenic amine biosynthetic process0.0277896834696146
GO:0046519sphingoid metabolic process0.0279958952000989
GO:0007189G-protein signaling, adenylate cyclase activating pathway0.02801430006676
GO:0048545response to steroid hormone stimulus0.02801430006676
GO:0001633secretin-like receptor activity0.02801430006676
GO:0045761regulation of adenylate cyclase activity0.02801430006676
GO:0007584response to nutrient0.02801430006676
GO:0031279regulation of cyclase activity0.02801430006676
GO:0042398amino acid derivative biosynthetic process0.02801430006676
GO:0051339regulation of lyase activity0.02801430006676
GO:0044459plasma membrane part0.02801430006676
GO:0042446hormone biosynthetic process0.02801430006676
GO:0043176amine binding0.02801430006676
GO:0019239deaminase activity0.02801430006676
GO:0009072aromatic amino acid family metabolic process0.029417834829284
GO:0016814hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines0.0301615508818891
GO:0007166cell surface receptor linked signal transduction0.0304408096550909
GO:0015082di-, tri-valent inorganic cation transmembrane transporter activity0.0318392749054169
GO:0008305integrin complex0.0318392749054169
GO:0055072iron ion homeostasis0.0318392749054169
GO:0006879cellular iron ion homeostasis0.0318392749054169
GO:0031667response to nutrient levels0.0335924896810473
GO:0007165signal transduction0.0336211191108662
GO:0009991response to extracellular stimulus0.0358616776243445
GO:0006665sphingolipid metabolic process0.0364141327106336
GO:0006576biogenic amine metabolic process0.039048333144058
GO:0009725response to hormone stimulus0.0395397183492577
GO:0001505regulation of neurotransmitter levels0.0400172800283473
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.042490656764607
GO:0007229integrin-mediated signaling pathway0.04276461186658
GO:0019933cAMP-mediated signaling0.04276461186658
GO:0042445hormone metabolic process0.04276461186658
GO:0006575amino acid derivative metabolic process0.0431681912286786
GO:0004872receptor activity0.0459792440025895
GO:0007160cell-matrix adhesion0.046261134576347
GO:0000041transition metal ion transport0.0469397938229353
GO:0031589cell-substrate adhesion0.0469397938229353
GO:0043235receptor complex0.0494953267747032



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>

Cell Type
Ontology termp-valuen
epithelial cell4.48e-23254
endodermal cell1.30e-1059
endo-epithelial cell3.53e-0743
Uber Anatomy
Ontology termp-valuen
multi-tissue structure2.39e-18347
immaterial anatomical entity3.01e-17126
organ6.66e-17511
anatomical conduit1.22e-16241
organism subdivision2.65e-15365
trunk region element4.25e-15107
subdivision of trunk4.33e-14113
tube8.58e-14194
subdivision of digestive tract1.24e-13129
endodermal part of digestive tract1.24e-13129
endoderm-derived structure1.24e-13169
endoderm1.24e-13169
presumptive endoderm1.24e-13169
digestive system1.58e-13155
digestive tract1.58e-13155
primitive gut1.58e-13155
anatomical cluster2.09e-13286
organ part2.12e-13219
multi-cellular organism1.24e-12659
anatomical space2.09e-12104
abdomen element4.31e-1255
abdominal segment element4.31e-1255
mixed endoderm/mesoderm-derived structure6.42e-12130
embryo1.11e-11612
epithelium1.43e-11309
abdominal segment of trunk1.98e-1161
abdomen1.98e-1161
cell layer2.87e-11312
endo-epithelium9.10e-1182
anatomical cavity1.33e-1070
anatomical group1.52e-10626
anatomical system1.75e-10625
primordium2.02e-10168
embryonic structure8.17e-10605
developing anatomical structure8.17e-10605
central nervous system1.35e-0982
germ layer1.77e-09604
embryonic tissue1.77e-09604
presumptive structure1.77e-09604
epiblast (generic)1.77e-09604
body cavity precursor1.78e-0963
foregut2.42e-0998
mesenchyme2.85e-09238
entire embryonic mesenchyme2.85e-09238
cavitated compound organ7.93e-0932
adult organism9.29e-09115
trunk1.11e-08216
neural plate1.41e-0886
presumptive neural plate1.41e-0886
regional part of nervous system2.22e-0894
nervous system2.22e-0894
reproductive structure2.60e-0859
reproductive system2.60e-0859
neural tube2.90e-0857
neural rod2.90e-0857
future spinal cord2.90e-0857
neural keel2.90e-0857
neurectoderm6.40e-0890
ectoderm-derived structure1.09e-07169
gut epithelium1.17e-0754
epithelium of foregut-midgut junction1.53e-0725
anatomical boundary1.53e-0725
hepatobiliary system1.53e-0725
foregut-midgut junction1.53e-0725
septum transversum1.53e-0725
reproductive organ1.60e-0748
renal system1.68e-0745
sac2.61e-0726
ectoderm2.62e-07173
presumptive ectoderm2.62e-07173
urinary system structure2.79e-0744
duct3.03e-0726
head3.10e-07123
kidney3.62e-0727
kidney mesenchyme3.62e-0727
kidney rudiment3.62e-0727
kidney field3.62e-0727
epithelial sac4.25e-0725
intermediate mesoderm5.68e-0737
anterior region of body7.43e-07129
craniocervical region7.43e-07129
brain8.99e-0769
future brain8.99e-0769
Disease
Ontology termp-valuen
carcinoma1.82e-25106
cell type cancer5.45e-22143
adenocarcinoma8.65e-1125
cancer7.39e-10235
disease of cellular proliferation6.73e-09239


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

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

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

TF#promotersEnrichmentp-valueq-value
ESR1#2099157.325857927655831.30709378936389e-091.17885637536593e-07
FOXA1#3169172.99022437681833.01975007822677e-050.00062070395280442
GATA3#262573.026279595245110.008224112431333830.0324573207201025
NR3C1#2908194.515673703052191.60437133710146e-081.16928777442805e-06



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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