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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:00, 17 September 2013


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
serous secreting cell2.55e-981
seromucus secreting cell4.52e-502
Uber Anatomy
Ontology termp-valuen
epithelium of female gonad2.55e-981
epithelium of gonad4.52e-502
female gonad5.70e-0913
Disease
Ontology termp-valuen
ovary epithelial cancer2.55e-981
clear cell adenocarcinoma2.74e-502
adenocarcinoma4.64e-1725
female reproductive organ cancer6.71e-1627
reproductive organ cancer6.74e-1529
ovarian cancer2.00e-0814


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)
MA0003.11.15531e-09
MA0004.10.0692917
MA0006.10.0119561
MA0007.10.318244
MA0009.10.196219
MA0014.10.000168144
MA0017.10.448072
MA0019.10.404253
MA0024.10.136013
MA0025.10.285416
MA0027.11.64023
MA0028.10.0150707
MA0029.10.146371
MA0030.11.3779
MA0031.10.709629
MA0038.10.934456
MA0040.10.893513
MA0041.10.651315
MA0042.11.55643
MA0043.10.57133
MA0046.11.05697
MA0048.10.205415
MA0050.10.0625073
MA0051.10.136921
MA0052.10.151713
MA0055.10.0238642
MA0056.10
MA0057.10.0228816
MA0058.10.0277371
MA0059.10.0826709
MA0060.10.151401
MA0061.10.526253
MA0063.10
MA0066.10.140731
MA0067.10.426099
MA0068.10.443875
MA0069.10.187175
MA0070.10.180428
MA0071.10.799731
MA0072.10.177746
MA0073.13.24791e-08
MA0074.10.582101
MA0076.10.00607824
MA0077.11.57436
MA0078.11.29026
MA0081.10.527155
MA0083.11.10194
MA0084.12.43655
MA0087.13.01884
MA0088.10.0663195
MA0089.10
MA0090.11.24341
MA0091.10.184212
MA0092.10.140498
MA0093.10.00192412
MA0095.10
MA0098.10
MA0100.10.152048
MA0101.10.206844
MA0103.11.53126
MA0105.10.201142
MA0106.10.176444
MA0107.10.279781
MA0108.20.106251
MA0109.10
MA0111.10.123492
MA0113.11.14665
MA0114.10.264975
MA0115.10.365583
MA0116.10.0436546
MA0117.10.22006
MA0119.10.700896
MA0122.10.667475
MA0124.10.887885
MA0125.10.749804
MA0130.10
MA0131.10.0709376
MA0132.10
MA0133.10
MA0135.11.15841
MA0136.10.146254
MA0139.10.137704
MA0140.10.492673
MA0141.10.520719
MA0142.10.641851
MA0143.11.6134
MA0144.11.75041
MA0145.10.00446344
MA0146.15.62407e-05
MA0147.10.00423696
MA0148.12.27337
MA0149.10.101583
MA0062.20.000441011
MA0035.20.490997
MA0039.21.69899e-05
MA0138.20.0646653
MA0002.20.127342
MA0137.20.841841
MA0104.20.00521186
MA0047.20.670694
MA0112.20.0775751
MA0065.20.0391677
MA0150.10.222744
MA0151.10
MA0152.10.273429
MA0153.10.260996
MA0154.10.362938
MA0155.10.000299618
MA0156.10.0552371
MA0157.12.02331
MA0158.10
MA0159.10.0464478
MA0160.10.720618
MA0161.10
MA0162.10.000349637
MA0163.10.00053335
MA0164.11.194
MA0080.20.0426084
MA0018.20.399835
MA0099.21.60754
MA0079.24.7011e-14
MA0102.20.616902
MA0258.10.116491
MA0259.10.201419
MA0442.10



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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