Coexpression cluster:C224

Full id: C224_clear_serous_pleomorphic_choriocarcinoma_mesothelioma_amniotic_renal

Phase1 CAGE Peaks

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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 -
Id	Short description

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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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p.value	FDR	nGenes	nPathway	Name
2.78345011903363e-05	0.0176192392534829	2	23	GPCRs, 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

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GO ID	GO name	FDR corrected p-value
GO:0032841	calcitonin binding	0.0180181142069971
GO:0006587	serotonin biosynthetic process from tryptophan	0.0180181142069971
GO:0008892	guanine deaminase activity	0.0180181142069971
GO:0016724	oxidoreductase activity, oxidizing metal ions, oxygen as acceptor	0.0180181142069971
GO:0004322	ferroxidase activity	0.0180181142069971
GO:0042428	serotonin metabolic process	0.0180181142069971
GO:0004948	calcitonin receptor activity	0.0180181142069971
GO:0042427	serotonin biosynthetic process	0.0180181142069971
GO:0004510	tryptophan 5-monooxygenase activity	0.0180181142069971
GO:0042435	indole derivative biosynthetic process	0.0180181142069971
GO:0046219	indolalkylamine biosynthetic process	0.0180181142069971
GO:0016722	oxidoreductase activity, oxidizing metal ions	0.0180181142069971
GO:0006568	tryptophan metabolic process	0.0180181142069971
GO:0001573	ganglioside metabolic process	0.0180181142069971
GO:0006878	cellular copper ion homeostasis	0.0180181142069971
GO:0007154	cell communication	0.0180181142069971
GO:0017046	peptide hormone binding	0.0180181142069971
GO:0031226	intrinsic to plasma membrane	0.0180181142069971
GO:0016714	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced pteridine as one donor, and incorporation of one atom of oxygen	0.0180181142069971
GO:0006586	indolalkylamine metabolic process	0.0180181142069971
GO:0042434	indole derivative metabolic process	0.0180181142069971
GO:0055070	copper ion homeostasis	0.0180181142069971
GO:0042430	indole and derivative metabolic process	0.0180181142069971
GO:0051384	response to glucocorticoid stimulus	0.0188354560439923
GO:0031960	response to corticosteroid stimulus	0.019091255349868
GO:0005375	copper ion transmembrane transporter activity	0.019091255349868
GO:0046658	anchored to plasma membrane	0.019091255349868
GO:0016491	oxidoreductase activity	0.019091255349868
GO:0031225	anchored to membrane	0.019479793407562
GO:0042136	neurotransmitter biosynthetic process	0.0200840578765452
GO:0006687	glycosphingolipid metabolic process	0.0226127014957497
GO:0006825	copper ion transport	0.0226127014957497
GO:0016597	amino acid binding	0.0226127014957497
GO:0005886	plasma membrane	0.0226127014957497
GO:0016524	latrotoxin receptor activity	0.0244558420830832
GO:0045762	positive regulation of adenylate cyclase activity	0.0244558420830832
GO:0031281	positive regulation of cyclase activity	0.0244558420830832
GO:0051349	positive regulation of lyase activity	0.0244558420830832
GO:0042562	hormone binding	0.0244558420830832
GO:0007568	aging	0.0244558420830832
GO:0042221	response to chemical stimulus	0.0259718531222645
GO:0006664	glycolipid metabolic process	0.0259718531222645
GO:0046915	transition metal ion transmembrane transporter activity	0.0262402933491107
GO:0042133	neurotransmitter metabolic process	0.0267409396897012
GO:0006672	ceramide metabolic process	0.0267409396897012
GO:0042401	biogenic amine biosynthetic process	0.0277896834696146
GO:0046519	sphingoid metabolic process	0.0279958952000989
GO:0007189	G-protein signaling, adenylate cyclase activating pathway	0.02801430006676
GO:0048545	response to steroid hormone stimulus	0.02801430006676
GO:0001633	secretin-like receptor activity	0.02801430006676
GO:0045761	regulation of adenylate cyclase activity	0.02801430006676
GO:0007584	response to nutrient	0.02801430006676
GO:0031279	regulation of cyclase activity	0.02801430006676
GO:0042398	amino acid derivative biosynthetic process	0.02801430006676
GO:0051339	regulation of lyase activity	0.02801430006676
GO:0044459	plasma membrane part	0.02801430006676
GO:0042446	hormone biosynthetic process	0.02801430006676
GO:0043176	amine binding	0.02801430006676
GO:0019239	deaminase activity	0.02801430006676
GO:0009072	aromatic amino acid family metabolic process	0.029417834829284
GO:0016814	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines	0.0301615508818891
GO:0007166	cell surface receptor linked signal transduction	0.0304408096550909
GO:0015082	di-, tri-valent inorganic cation transmembrane transporter activity	0.0318392749054169
GO:0008305	integrin complex	0.0318392749054169
GO:0055072	iron ion homeostasis	0.0318392749054169
GO:0006879	cellular iron ion homeostasis	0.0318392749054169
GO:0031667	response to nutrient levels	0.0335924896810473
GO:0007165	signal transduction	0.0336211191108662
GO:0009991	response to extracellular stimulus	0.0358616776243445
GO:0006665	sphingolipid metabolic process	0.0364141327106336
GO:0006576	biogenic amine metabolic process	0.039048333144058
GO:0009725	response to hormone stimulus	0.0395397183492577
GO:0001505	regulation of neurotransmitter levels	0.0400172800283473
GO:0007188	G-protein signaling, coupled to cAMP nucleotide second messenger	0.042490656764607
GO:0007229	integrin-mediated signaling pathway	0.04276461186658
GO:0019933	cAMP-mediated signaling	0.04276461186658
GO:0042445	hormone metabolic process	0.04276461186658
GO:0006575	amino acid derivative metabolic process	0.0431681912286786
GO:0004872	receptor activity	0.0459792440025895
GO:0007160	cell-matrix adhesion	0.046261134576347
GO:0000041	transition metal ion transport	0.0469397938229353
GO:0031589	cell-substrate adhesion	0.0469397938229353
GO:0043235	receptor complex	0.0494953267747032

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>

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Cell Type

Ontology term	p-value	n
serous secreting cell	2.55e-98	1
seromucus secreting cell	4.52e-50	2

Uber Anatomy

Ontology term	p-value	n
epithelium of female gonad	2.55e-98	1
epithelium of gonad	4.52e-50	2
female gonad	5.70e-09	13

Disease

Ontology term	p-value	n
ovary epithelial cancer	2.55e-98	1
clear cell adenocarcinoma	2.74e-50	2
adenocarcinoma	4.64e-17	25
female reproductive organ cancer	6.71e-16	27
reproductive organ cancer	6.74e-15	29
ovarian cancer	2.00e-08	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	1.15531e-09
MA0004.1	0.0692917
MA0006.1	0.0119561
MA0007.1	0.318244
MA0009.1	0.196219
MA0014.1	0.000168144
MA0017.1	0.448072
MA0019.1	0.404253
MA0024.1	0.136013
MA0025.1	0.285416
MA0027.1	1.64023
MA0028.1	0.0150707
MA0029.1	0.146371
MA0030.1	1.3779
MA0031.1	0.709629
MA0038.1	0.934456
MA0040.1	0.893513
MA0041.1	0.651315
MA0042.1	1.55643
MA0043.1	0.57133
MA0046.1	1.05697
MA0048.1	0.205415
MA0050.1	0.0625073
MA0051.1	0.136921
MA0052.1	0.151713
MA0055.1	0.0238642
MA0056.1	0
MA0057.1	0.0228816
MA0058.1	0.0277371
MA0059.1	0.0826709
MA0060.1	0.151401
MA0061.1	0.526253
MA0063.1	0
MA0066.1	0.140731
MA0067.1	0.426099
MA0068.1	0.443875
MA0069.1	0.187175
MA0070.1	0.180428
MA0071.1	0.799731
MA0072.1	0.177746
MA0073.1	3.24791e-08
MA0074.1	0.582101
MA0076.1	0.00607824
MA0077.1	1.57436
MA0078.1	1.29026
MA0081.1	0.527155
MA0083.1	1.10194
MA0084.1	2.43655
MA0087.1	3.01884
MA0088.1	0.0663195
MA0089.1	0
MA0090.1	1.24341
MA0091.1	0.184212
MA0092.1	0.140498
MA0093.1	0.00192412
MA0095.1	0
MA0098.1	0
MA0100.1	0.152048
MA0101.1	0.206844
MA0103.1	1.53126
MA0105.1	0.201142
MA0106.1	0.176444
MA0107.1	0.279781
MA0108.2	0.106251
MA0109.1	0
MA0111.1	0.123492
MA0113.1	1.14665
MA0114.1	0.264975
MA0115.1	0.365583
MA0116.1	0.0436546
MA0117.1	0.22006
MA0119.1	0.700896
MA0122.1	0.667475
MA0124.1	0.887885
MA0125.1	0.749804
MA0130.1	0
MA0131.1	0.0709376
MA0132.1	0
MA0133.1	0
MA0135.1	1.15841
MA0136.1	0.146254
MA0139.1	0.137704
MA0140.1	0.492673
MA0141.1	0.520719
MA0142.1	0.641851
MA0143.1	1.6134
MA0144.1	1.75041
MA0145.1	0.00446344
MA0146.1	5.62407e-05
MA0147.1	0.00423696
MA0148.1	2.27337
MA0149.1	0.101583
MA0062.2	0.000441011
MA0035.2	0.490997
MA0039.2	1.69899e-05
MA0138.2	0.0646653
MA0002.2	0.127342
MA0137.2	0.841841
MA0104.2	0.00521186
MA0047.2	0.670694
MA0112.2	0.0775751
MA0065.2	0.0391677
MA0150.1	0.222744
MA0151.1	0
MA0152.1	0.273429
MA0153.1	0.260996
MA0154.1	0.362938
MA0155.1	0.000299618
MA0156.1	0.0552371
MA0157.1	2.02331
MA0158.1	0
MA0159.1	0.0464478
MA0160.1	0.720618
MA0161.1	0
MA0162.1	0.000349637
MA0163.1	0.00053335
MA0164.1	1.194
MA0080.2	0.0426084
MA0018.2	0.399835
MA0099.2	1.60754
MA0079.2	4.7011e-14
MA0102.2	0.616902
MA0258.1	0.116491
MA0259.1	0.201419
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
ESR1#2099	15	7.32585792765583	1.30709378936389e-09	1.17885637536593e-07
FOXA1#3169	17	2.9902243768183	3.01975007822677e-05	0.00062070395280442
GATA3#2625	7	3.02627959524511	0.00822411243133383	0.0324573207201025
NR3C1#2908	19	4.51567370305219	1.60437133710146e-08	1.16928777442805e-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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FF samples	Score

FF samples	Score
clear cell carcinoma cell line:TEN CNhs11930	0.96
serous cystadenocarcinoma cell line:HTOA CNhs11827	0.05
Adipocyte - breast, donor1 CNhs11051	0.00
Adipocyte - breast, donor2 CNhs11969	0.00
Adipocyte - omental, donor1 CNhs11054	0.00
Adipocyte - omental, donor2 CNhs12067	0.00
Adipocyte - omental, donor3 CNhs12068	0.00
Adipocyte - perirenal, donor1 CNhs12069	0.00
Adipocyte - subcutaneous, donor1 CNhs12494	0.00
Adipocyte - subcutaneous, donor2 CNhs11371	0.00

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