Personal tools

Coexpression cluster:C770: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(4 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Coexpression_clusters
{
|full_id=C770_Mesenchymal_chorionic_tubular_ovary_Smooth_mesenchymal_granulosa
|

Latest revision as of 11:30, 17 September 2013


Full id: C770_Mesenchymal_chorionic_tubular_ovary_Smooth_mesenchymal_granulosa



Phase1 CAGE Peaks

Hg19::chr3:138665669..138665685,-p11@FOXL2
Hg19::chr3:138665702..138665729,-p7@FOXL2
Hg19::chr3:138665760..138665772,-p3@FOXL2
Hg19::chr3:138665774..138665786,-p5@FOXL2
Hg19::chr3:138665790..138665809,-p4@FOXL2
Hg19::chr3:138666029..138666038,-p8@FOXL2
Hg19::chr3:138666052..138666066,+p2@C3orf72
Hg19::chr3:138666175..138666186,+p5@C3orf72
Hg19::chr3:138666329..138666339,-p10@FOXL2
Hg19::chr3:138666453..138666470,+p4@C3orf72
Hg19::chr8:102344320..102344363,-p@chr8:102344320..102344363
-


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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
female reproductive organ1.51e-1037
female reproductive system1.51e-1037
embryonic uterus2.46e-0922
female organism2.47e-0941
reproductive organ2.60e-0948
reproductive structure1.07e-0859
reproductive system1.07e-0859
uterus2.65e-0721
internal female genitalia6.09e-0722
Disease
Ontology termp-valuen
cell type benign neoplasm3.81e-073
leiomyoma3.81e-073


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)
MA0003.11.92888
MA0004.10.349539
MA0006.10.605586
MA0007.12.41122
MA0009.10.79061
MA0014.11.37711
MA0017.10.24363
MA0019.10.486183
MA0024.11.64584
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.10.0494179
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.10.00989454
MA0056.10
MA0057.13.20993
MA0058.10.265212
MA0059.10.2641
MA0060.10.119532
MA0061.10.100525
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.0758327
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.304769
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.11.34305
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.0234479
MA0089.10
MA0090.10.792817
MA0091.10.351901
MA0092.10.318032
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.587485
MA0105.11.91523
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.12.26737
MA0113.10.498009
MA0114.10.908082
MA0115.11.02805
MA0116.10.159642
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.12.79395
MA0140.10.405425
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.10.142196
MA0145.10.515404
MA0146.11.91914
MA0147.10.162359
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.20.404774
MA0039.23.21617
MA0138.20.534556
MA0002.20.111226
MA0137.20.229531
MA0104.20.118985
MA0047.20.47109
MA0112.20.487949
MA0065.21.6488
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.11.89039
MA0155.10.0230394
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.17.34279
MA0160.10.386031
MA0161.10
MA0162.10.324348
MA0163.10.122012
MA0164.10.509774
MA0080.20.21336
MA0018.20.483823
MA0099.20.411824
MA0079.212.3862
MA0102.21.32663
MA0258.10.135061
MA0259.10.168926
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#90595.184164926605792.45776684955985e-068.6835829499723e-05
CEBPB#105185.797198273327147.09770251647579e-060.000204772638982932
E2F1#186994.015136630355812.22155664174121e-050.000486205268455176
E2F6#187683.648840532143550.0002292448799299190.00252847249075941
EGR1#195894.081237441208291.93184303045374e-050.00043586034620341
ELF1#199783.096798515496390.0007580113527617290.00595815064883587
HEY1#2346282.938262576804150.001105997388051380.00768626971058677
HMGN3#932496.691539046377762.65773098024031e-071.36936736973516e-05
NRF1#489988.880203234698842.65835991535536e-071.36901603155719e-05
SMARCB1#6598914.93404018458332.20335696545219e-102.26492517829588e-08
SPI1#668885.966780733471075.69573958039735e-060.000171428629981879
TAF1#687282.431306389632940.004204244189139110.020019471065039
TBP#690893.032812380351590.0002388258630576910.00260091077287614
USF1#739184.626544928878523.91779279463149e-050.000731837527595274
YY1#752883.571760545348260.0002682005866906720.00286524151732683
ZBTB7A#5134185.346843133000651.31319566009782e-050.000320891065851558



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C770&oldid=3067887"