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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.0724992894770213,

Latest revision as of 11:55, 17 September 2013


Full id: C1920_ovary_granulosa_chorionic_Mesenchymal_Fibroblast_tubular_leiomyoma



Phase1 CAGE Peaks

Hg19::chr3:138665921..138665932,-p6@FOXL2
Hg19::chr3:138665937..138665968,-p1@FOXL2
Hg19::chr3:138665969..138665993,-p2@FOXL2
Hg19::chr3:138666070..138666100,+p1@C3orf72
Hg19::chr3:138666102..138666138,+p3@C3orf72


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

No results for this coexpression

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:0018993somatic sex determination0.000718238549393618
GO:0019101female somatic sex determination0.000718238549393618
GO:0002074extraocular skeletal muscle development0.000718238549393618
GO:0030237female sex determination0.000718238549393618
GO:0042703menstruation0.000718238549393618
GO:0060014granulosa cell differentiation0.00119706424898936
GO:0048048embryonic eye morphogenesis0.00205211014112462
GO:0048562embryonic organ morphogenesis0.00448899093371011
GO:0006309DNA fragmentation during apoptosis0.00495926617438451
GO:0001541ovarian follicle development0.00495926617438451
GO:0048568embryonic organ development0.00495926617438451
GO:0007530sex determination0.00495926617438451
GO:0043028caspase regulator activity0.00495926617438451
GO:0006921cell structure disassembly during apoptosis0.00495926617438451
GO:0030262apoptotic nuclear changes0.00495926617438451
GO:0022601menstrual cycle phase0.00495926617438451
GO:0022602menstrual cycle process0.00495926617438451
GO:0048592eye morphogenesis0.00495926617438451
GO:0008585female gonad development0.00495926617438451
GO:0046545development of primary female sexual characteristics0.00495926617438451
GO:0046660female sex differentiation0.00495926617438451
GO:0042698menstrual cycle0.00523715608932846
GO:0043010camera-type eye development0.00523715608932846
GO:0006308DNA catabolic process0.00523715608932846
GO:0006997nuclear organization and biogenesis0.0054586129753915
GO:0001654eye development0.00622473409474469
GO:0022411cellular component disassembly0.00622473409474469
GO:0043280positive regulation of caspase activity0.00622473409474469
GO:0008406gonad development0.00622473409474469
GO:0048608reproductive structure development0.00622473409474469
GO:0045137development of primary sexual characteristics0.0064430222813251
GO:0043281regulation of caspase activity0.0064430222813251
GO:0048609reproductive process in a multicellular organism0.0064430222813251
GO:0032504multicellular organism reproduction0.0064430222813251
GO:0007519skeletal muscle development0.00687456897276748
GO:0051345positive regulation of hydrolase activity0.00758140691026597
GO:0007548sex differentiation0.00779551596293073
GO:0007423sensory organ development0.00779551596293073
GO:0003006reproductive developmental process0.00779551596293073
GO:0014706striated muscle development0.00779551596293073
GO:0008632apoptotic program0.00779551596293073
GO:0048598embryonic morphogenesis0.00795192679685792
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0116087393448503
GO:0007517muscle development0.0140382989199662
GO:0006917induction of apoptosis0.0166287838066131
GO:0012502induction of programmed cell death0.0166287838066131
GO:0045893positive regulation of transcription, DNA-dependent0.0170390634590188
GO:0009790embryonic development0.0175818811570313
GO:0043085positive regulation of catalytic activity0.018167210367015
GO:0043065positive regulation of apoptosis0.018167210367015
GO:0043068positive regulation of programmed cell death0.018167210367015
GO:0045941positive regulation of transcription0.0192681303154634
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0195821642240336
GO:0022414reproductive process0.0200453849694401
GO:0051336regulation of hydrolase activity0.0200453849694401
GO:0009887organ morphogenesis0.0229962342569009
GO:0031325positive regulation of cellular metabolic process0.0229962342569009
GO:0009893positive regulation of metabolic process0.0242095924838711
GO:0006357regulation of transcription from RNA polymerase II promoter0.0257470259655509
GO:0043285biopolymer catabolic process0.0271733584520586
GO:0042981regulation of apoptosis0.0333633390686068
GO:0043067regulation of programmed cell death0.0333633390686068
GO:0050790regulation of catalytic activity0.0344868509827888
GO:0009057macromolecule catabolic process0.0350702416696102
GO:0006366transcription from RNA polymerase II promoter0.0353594362778397
GO:0065009regulation of a molecular function0.0365104595941756
GO:0044248cellular catabolic process0.043362312422346
GO:0006915apoptosis0.0447360010765168
GO:0012501programmed cell death0.0447360010765168
GO:0043565sequence-specific DNA binding0.0447360010765168
GO:0016265death0.0452889307534309
GO:0008219cell death0.0452889307534309
GO:0048522positive regulation of cellular process0.0469314778165419
GO:0009056catabolic process0.0472193316594588



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
skin fibroblast6.53e-1623
epithelial cell2.72e-07253
Uber Anatomy
Ontology termp-valuen
skin of body1.58e-1641
integument1.69e-1346
integumental system1.69e-1346
surface structure1.93e-1099
larynx5.49e-099
organ6.31e-08503
organ part1.20e-07218
dermis1.71e-079
dermatome1.71e-079
future dermis1.71e-079
female reproductive organ2.42e-0737
female reproductive system2.42e-0737
reproductive structure3.13e-0759
reproductive system3.13e-0759
Disease
Ontology termp-valuen
disease of cellular proliferation3.00e-09239
cancer2.30e-07235


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)
MA0003.10.481059
MA0004.10.626788
MA0006.11.14863
MA0007.16.24161
MA0009.11.11255
MA0014.10.660087
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.11.66737
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.362215
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.11.2972
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.12.39477
MA0113.10.797251
MA0114.10.973423
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.11.39016
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.10.333008
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.22.8814
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.839774
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.14.71524
MA0160.10.669748
MA0161.10
MA0162.10.21472
MA0163.10.382496
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.25.7251
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
CCNT2#90556.336201576962639.78880505817628e-050.00139149722535848
CEBPB#105157.971147625824823.10621793420244e-050.000628945899244219
E2F1#186954.907389214879320.0003512818099256460.00353342203089902
E2F6#187655.017155731697390.0003144978599297790.0032312682728191
EGR1#195854.988179094810140.0003237398000590710.00330994233757899
ELF1#199754.258097958807540.0007142416939776840.0057362879327388
HEY1#2346254.040111043105710.0009288852205177990.00674771117379554
HMGN3#932458.178547723350592.73180911341838e-050.000582616728601801
NRF1#4899512.21027944771093.68220991173981e-060.000120780879702322
SMARCB1#6598518.25271578115744.93125075403021e-072.3167561740898e-05
SPI1#668858.204323508522732.68916109982495e-050.000575165464068437
TAF1#687253.343046285745290.002394600090870310.0135491190210426
TBP#690853.706770687096390.001428755106721120.00919791373918802
USF1#739156.361499277207969.59569864925045e-050.00137038858365796
YY1#752854.911170749853860.00034993140821360.00352935647922937
ZBTB7A#5134157.35190930787594.65425347594289e-050.000816401711074906



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

This analysis result is provided for C0 - C305 clusters.

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