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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:02, 17 September 2013


Full id: C233_uterus_cervix_ovary_epididymis_colon_rectum_MCF7



Phase1 CAGE Peaks

Hg19::chr11:100935059..100935062,-p9@PGR
Hg19::chr11:100978593..100978596,-p@chr11:100978593..100978596
-
Hg19::chr11:100996790..100996823,-p10@PGR
Hg19::chr11:100999679..100999686,-p11@PGR
Hg19::chr11:100999697..100999708,-p7@PGR
Hg19::chr11:100999775..100999800,-p2@PGR
Hg19::chr11:100999802..100999819,-p4@PGR
Hg19::chr11:100999848..100999858,-p6@PGR
Hg19::chr11:101000445..101000465,-p5@PGR
Hg19::chr11:101000524..101000535,-p3@PGR
Hg19::chr11:101000537..101000553,-p1@PGR
Hg19::chr11:106475101..106475144,-p@chr11:106475101..106475144
-
Hg19::chr12:11586047..11586051,-p@chr12:11586047..11586051
-
Hg19::chr14:52066633..52066647,-p1@ENST00000557625
Hg19::chr14:52066650..52066658,-p6@ENST00000556617
Hg19::chr14:52066664..52066674,-p3@ENST00000556617
Hg19::chr14:52066684..52066693,-p4@ENST00000556617
Hg19::chr14:52066704..52066710,-p5@ENST00000556617
Hg19::chr14:52066714..52066739,-p1@ENST00000556617
Hg19::chr14:52066745..52066774,-p2@ENST00000556617
Hg19::chr14:52164820..52164841,+p25@FRMD6
Hg19::chr14:68353962..68353975,+p@chr14:68353962..68353975
+
Hg19::chr19:24140667..24140676,-p2@uc002nrp.1
Hg19::chr19:6076501..6076505,-p@chr19:6076501..6076505
-
Hg19::chr1:192761703..192761710,-p@chr1:192761703..192761710
-
Hg19::chr1:202485611..202485613,-p@chr1:202485611..202485613
-
Hg19::chr1:202508608..202508633,+p@chr1:202508608..202508633
+
Hg19::chr1:226129114..226129123,-p3@LEFTY2
Hg19::chr1:226129194..226129232,-p2@LEFTY2
Hg19::chr21:17553654..17553663,+p@chr21:17553654..17553663
+
Hg19::chr21:17553669..17553705,+p@chr21:17553669..17553705
+
Hg19::chr21:18500690..18500701,-p@chr21:18500690..18500701
-
Hg19::chr21:33745128..33745131,-p@chr21:33745128..33745131
-
Hg19::chr2:177627285..177627294,-p1@ENST00000430460
Hg19::chr2:178016016..178016026,-p@chr2:178016016..178016026
-
Hg19::chr2:232135672..232135717,+p5@ARMC9
Hg19::chr2:27371866..27371878,+p3@TCF23
Hg19::chr2:27371879..27371907,+p1@TCF23
Hg19::chr2:27371919..27371935,+p2@TCF23
Hg19::chr2:48706616..48706634,+p@chr2:48706616..48706634
+
Hg19::chr3:64479939..64479946,-p@chr3:64479939..64479946
-
Hg19::chr3:69795884..69795894,+p@chr3:69795884..69795894
+
Hg19::chr5:35230771..35230780,-p17@PRLR
Hg19::chr6:111839306..111839347,-p@chr6:111839306..111839347
-
Hg19::chr6:152126688..152126695,+p22@ESR1
Hg19::chr6:152126790..152126828,+p3@ESR1
Hg19::chr6:152126830..152126847,+p4@ESR1
Hg19::chr6:152128325..152128339,+p10@ESR1
Hg19::chr6:152128371..152128382,+p14@ESR1
Hg19::chr6:152128782..152128803,+p5@ESR1
Hg19::chr6:152128810..152128827,+p2@ESR1
Hg19::chr6:33864685..33864698,-p1@ENST00000533304
Hg19::chr6:56362490..56362515,-p60@DST
Hg19::chr7:38042854..38042870,+p@chr7:38042854..38042870
+
Hg19::chr7:38042894..38042903,+p@chr7:38042894..38042903
+
Hg19::chr9:15846687..15846709,+p@chr9:15846687..15846709
+
Hg19::chr9:15846755..15846764,+p@chr9:15846755..15846764
+
Hg19::chr9:16575347..16575359,-p12@BNC2
Hg19::chr9:16575389..16575395,-p49@BNC2
Hg19::chrX:9165216..9165223,-p@chrX:9165216..9165223
-
Hg19::chrX:9165234..9165241,-p@chrX:9165234..9165241
-


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
6.17526981842456e-050.0195447289753137238Nuclear Receptors (Wikipathways):WP170
4.08931644966022e-050.0195447289753137231Ovarian Infertility Genes (Wikipathways):WP34



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:0047485protein N-terminus binding0.00862299819090196
GO:0005496steroid binding0.00862299819090196
GO:0042977tyrosine phosphorylation of JAK2 protein0.00862299819090196
GO:0042978ornithine decarboxylase activator activity0.00862299819090196
GO:0004925prolactin receptor activity0.00862299819090196
GO:0042976activation of JAK protein0.00862299819090196
GO:0065007biological regulation0.00862299819090196
GO:0003707steroid hormone receptor activity0.00987327936311198
GO:0007308oocyte construction0.00987327936311198
GO:0007309oocyte axis determination0.00987327936311198
GO:0030284estrogen receptor activity0.00987327936311198
GO:0004879ligand-dependent nuclear receptor activity0.0120644998964412
GO:0007171transmembrane receptor protein tyrosine kinase activation (dimerization)0.0120644998964412
GO:0006916anti-apoptosis0.0120644998964412
GO:0043195terminal button0.0120644998964412
GO:0030235nitric-oxide synthase regulator activity0.0120644998964412
GO:0033267axon part0.0120644998964412
GO:0043526neuroprotection0.0120644998964412
GO:0050794regulation of cellular process0.0127404926994134
GO:0043204perikaryon0.0129247279452068
GO:0030315T-tubule0.0129247279452068
GO:0043066negative regulation of apoptosis0.0136009037720845
GO:0048599oocyte development0.0136009037720845
GO:0043069negative regulation of programmed cell death0.0136009037720845
GO:0050789regulation of biological process0.0140702788789496
GO:0009994oocyte differentiation0.0140702788789496
GO:0042979ornithine decarboxylase regulator activity0.0140702788789496
GO:0045885positive regulation of survival gene product activity0.0155041960416895
GO:0007167enzyme linked receptor protein signaling pathway0.0184473339640376
GO:0048523negative regulation of cellular process0.0184473339640376
GO:0030520estrogen receptor signaling pathway0.0186468984701006
GO:0005160transforming growth factor beta receptor binding0.0186468984701006
GO:0048519negative regulation of biological process0.01872935275268
GO:0048468cell development0.0209223442115531
GO:0045104intermediate filament cytoskeleton organization and biogenesis0.0216905469581283
GO:0045103intermediate filament-based process0.0225916600030853
GO:0045884regulation of survival gene product activity0.0228267795774616
GO:0042383sarcolemma0.0228267795774616
GO:0007566embryo implantation0.023038068441521
GO:0048477oogenesis0.023038068441521
GO:0009798axis specification0.0237954903388163
GO:0007281germ cell development0.0245165410777021
GO:0007595lactation0.0264608312544518
GO:0043523regulation of neuron apoptosis0.0307705672403622
GO:0042562hormone binding0.031286565321858
GO:0051402neuron apoptosis0.0352984815400051
GO:0030424axon0.037782476750978
GO:0007292female gamete generation0.037782476750978
GO:0043025cell soma0.037782476750978
GO:0042981regulation of apoptosis0.037782476750978
GO:0043067regulation of programmed cell death0.037782476750978
GO:0008289lipid binding0.037782476750978
GO:0048869cellular developmental process0.037782476750978
GO:0030154cell differentiation0.037782476750978
GO:0007259JAK-STAT cascade0.038338450462916
GO:0045449regulation of transcription0.0388811799911008
GO:0016585chromatin remodeling complex0.0388811799911008
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0403349002062704
GO:0007267cell-cell signaling0.0406006327953373
GO:0044463cell projection part0.0417295745523015
GO:0006350transcription0.0417295745523015
GO:0010468regulation of gene expression0.0422068599713276
GO:0007179transforming growth factor beta receptor signaling pathway0.0428548548408523
GO:0030518steroid hormone receptor signaling pathway0.0430238910265278
GO:0031323regulation of cellular metabolic process0.0440653693060164
GO:0030522intracellular receptor-mediated signaling pathway0.0449711386481836
GO:0048609reproductive process in a multicellular organism0.0483759551790002
GO:0032504multicellular organism reproduction0.0483759551790002



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
male genital duct3.11e-273
internal male genitalia3.11e-273
uterus or analog1.53e-211
seminal vesicle3.45e-211
seminal fluid secreting gland3.45e-211
epididymis6.31e-211
duct of male reproductive system1.05e-204
male reproductive organ9.29e-1711
reproductive structure2.97e-1659
reproductive system2.97e-1659
reproductive organ7.75e-1548
male organism1.06e-1422
male reproductive system1.06e-1422
internal genitalia3.66e-1325
intermediate mesoderm1.27e-1128
urinary bladder4.52e-112
lower urinary tract4.52e-112
testis7.67e-118
adult organism9.07e-11114
mesonephros9.24e-109
pronephros9.24e-109
nephrogenic cord9.24e-109
pronephric mesoderm9.24e-109
rostral part of nephrogenic cord9.24e-109
presumptive pronephric mesoderm9.24e-109
body cavity precursor3.09e-0954
gonad4.08e-0921
indifferent external genitalia4.08e-0921
indifferent gonad4.08e-0921
gonad primordium4.08e-0921
embryonic uterus6.84e-0922
external genitalia9.94e-0922
anatomical cavity3.47e-0861
urogenital ridge3.76e-0811
sex gland1.47e-0712
male reproductive gland1.47e-0712
intraembryonic coelom1.52e-0712
body cavity3.35e-0746
urinary system structure4.71e-0747
renal system6.52e-0748
body cavity or lining8.91e-0749


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)
MA0003.12.41423e-10
MA0004.10.380155
MA0006.10.110912
MA0007.10.0652326
MA0009.10.204394
MA0014.11.691e-06
MA0017.10.00401388
MA0019.10.747187
MA0024.10.439917
MA0025.10.294989
MA0027.11.65408
MA0028.10.00282582
MA0029.10.153483
MA0030.14.3166
MA0031.11.76703
MA0038.11.87051
MA0040.12.11967
MA0041.10.420877
MA0042.11.22994
MA0043.10.204593
MA0046.10.197569
MA0048.10.103447
MA0050.10.179546
MA0051.10.146796
MA0052.12.13663
MA0055.10.010617
MA0056.10
MA0057.10.0285587
MA0058.10.200382
MA0059.10.0915374
MA0060.10.00143531
MA0061.10.0033336
MA0063.10
MA0066.10.34801
MA0067.10.43712
MA0068.10.000188404
MA0069.10.195175
MA0070.10.551797
MA0071.10.839892
MA0072.10.185556
MA0073.19.24404e-13
MA0074.11.37138
MA0076.10.00696909
MA0077.10.533912
MA0078.10.519908
MA0081.10.564043
MA0083.12.50764
MA0084.10.596203
MA0087.12.32634
MA0088.10.0299519
MA0089.10
MA0090.10.251839
MA0091.10.0169584
MA0092.10.793933
MA0093.10.560492
MA0095.10
MA0098.10
MA0100.10.162525
MA0101.10.0502056
MA0103.10.0413974
MA0105.10.000323139
MA0106.10.0502319
MA0107.10.017504
MA0108.20.112274
MA0109.10
MA0111.10.730006
MA0113.10.0555453
MA0114.10.0160225
MA0115.10.376065
MA0116.10.00476488
MA0117.10.22866
MA0119.10.0256525
MA0122.10.245976
MA0124.10.910486
MA0125.10.282149
MA0130.10
MA0131.10.0757356
MA0132.10
MA0133.10
MA0135.11.85638
MA0136.10.0401427
MA0139.10.00236754
MA0140.10.281206
MA0141.10.812031
MA0142.12.88661
MA0143.14.85142
MA0144.10.0789837
MA0145.10.00603849
MA0146.10.0109574
MA0147.10.203982
MA0148.10.708648
MA0149.10.109875
MA0062.20.00288527
MA0035.20.519158
MA0039.27.51973e-06
MA0138.20.243696
MA0002.20.883687
MA0137.20.0604977
MA0104.20.169395
MA0047.20.703125
MA0112.20.00449384
MA0065.20.180134
MA0150.10.422215
MA0151.10
MA0152.10.537017
MA0153.10.744058
MA0154.10.017493
MA0155.10.0154457
MA0156.10.0194723
MA0157.12.08726
MA0158.10
MA0159.10.927809
MA0160.10.249928
MA0161.10
MA0162.10.0012736
MA0163.16.97256e-07
MA0164.10.216326
MA0080.20.0145081
MA0018.20.0506682
MA0099.20.122327
MA0079.24.48318e-05
MA0102.20.629093
MA0258.10.13198
MA0259.10.124551
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

No analysis results for this cluster

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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