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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.665915502040858,0.

Latest revision as of 11:29, 17 September 2013


Full id: C720_Smooth_Fibroblast_Preadipocyte_Sertoli_Ewing_hepatic_Synoviocyte



Phase1 CAGE Peaks

Hg19::chr10:135201174..135201177,+p@chr10:135201174..135201177
+
Hg19::chr15:48937840..48937844,-p3@FBN1
Hg19::chr15:48937853..48937881,-p2@FBN1
Hg19::chr15:48937884..48937933,-p1@FBN1
Hg19::chr15:48937982..48937988,-p9@FBN1
Hg19::chr3:112359244..112359263,-p11@CCDC80
Hg19::chr4:55095975..55095998,+p9@PDGFRA
Hg19::chr4:55096011..55096052,+p5@PDGFRA
Hg19::chr4:55098129..55098159,+p@chr4:55098129..55098159
+
Hg19::chr7:128379449..128379463,+p2@CALU
Hg19::chr7:128410336..128410348,+p@chr7:128410336..128410348
+


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:0005018platelet-derived growth factor alpha-receptor activity0.00688802543270929
GO:0048407platelet-derived growth factor binding0.00688802543270929
GO:0005017platelet-derived growth factor receptor activity0.0137748343177302
GO:0001527microfibril0.0236046189169336
GO:0030539male genitalia development0.0236046189169336
GO:0043205fibril0.0236046189169336
GO:0048806genitalia development0.0236046189169336
GO:0042475odontogenesis of dentine-containing teeth0.0325256475399368
GO:0005021vascular endothelial growth factor receptor activity0.0325256475399368
GO:0042476odontogenesis0.0325256475399368
GO:0046546development of primary male sexual characteristics0.0325256475399368
GO:0046661male sex differentiation0.0366858802823338
GO:0030324lung development0.0421626850121848
GO:0030323respiratory tube development0.0421626850121848
GO:0030198extracellular matrix organization and biogenesis0.0421626850121848
GO:0048513organ development0.0469735600688954
GO:0045137development of primary sexual characteristics0.0469735600688954
GO:0005788endoplasmic reticulum lumen0.0469735600688954
GO:0005604basement membrane0.0469735600688954
GO:0007548sex differentiation0.0469735600688954
GO:0048770pigment granule0.0469735600688954
GO:0042470melanosome0.0469735600688954
GO:0043062extracellular structure organization and biogenesis0.0469735600688954
GO:0003006reproductive developmental process0.0469735600688954
GO:0005509calcium ion binding0.0469735600688954
GO:0019838growth factor binding0.0469735600688954
GO:0007507heart development0.0477644719140857



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>

Uber Anatomy
Ontology termp-valuen
dense mesenchyme tissue1.66e-2273
somite1.71e-2271
presomitic mesoderm1.71e-2271
presumptive segmental plate1.71e-2271
dermomyotome1.71e-2271
trunk paraxial mesoderm1.71e-2271
paraxial mesoderm7.61e-2272
presumptive paraxial mesoderm7.61e-2272
muscle tissue7.98e-2264
musculature7.98e-2264
musculature of body7.98e-2264
skeletal muscle tissue1.02e-2162
striated muscle tissue1.02e-2162
myotome1.02e-2162
epithelial vesicle4.36e-1978
multilaminar epithelium9.82e-1983
splanchnic layer of lateral plate mesoderm1.52e-1383
trunk mesenchyme7.65e-13122
mesenchyme1.78e-12160
entire embryonic mesenchyme1.78e-12160
systemic artery1.34e-1133
systemic arterial system1.34e-1133
artery1.11e-1042
arterial blood vessel1.11e-1042
arterial system1.11e-1042
integument9.19e-1046
integumental system9.19e-1046
heart2.67e-0924
primitive heart tube2.67e-0924
primary heart field2.67e-0924
anterior lateral plate mesoderm2.67e-0924
heart tube2.67e-0924
heart primordium2.67e-0924
cardiac mesoderm2.67e-0924
cardiogenic plate2.67e-0924
heart rudiment2.67e-0924
unilaminar epithelium6.15e-09148
mesoderm1.36e-08315
mesoderm-derived structure1.36e-08315
presumptive mesoderm1.36e-08315
adipose tissue1.47e-0814
organ component layer1.69e-0866
primary circulatory organ3.51e-0827
cardiovascular system3.63e-08109
skin of body4.30e-0841
circulatory system7.22e-08112
vasculature7.70e-0878
vascular system7.70e-0878
trunk1.55e-07199
surface structure1.71e-0799
epithelial tube open at both ends2.15e-0759
blood vessel2.15e-0759
blood vasculature2.15e-0759
vascular cord2.15e-0759
organism subdivision2.37e-07264
connective tissue3.66e-07371
smooth muscle tissue3.96e-0715
Disease
Ontology termp-valuen
ovarian cancer6.50e-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)
MA0003.10.0370565
MA0004.10.349539
MA0006.10.605586
MA0007.10.332734
MA0009.10.79061
MA0014.10.36818
MA0017.10.24363
MA0019.10.486183
MA0024.10.688373
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
MA0048.11.57917
MA0050.11.61016
MA0051.10.439895
MA0052.11.70446
MA0055.10.136684
MA0056.10
MA0057.10.703296
MA0058.10.265212
MA0059.10.2641
MA0060.10.38025
MA0061.10.100525
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.12.54939
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.17.60126
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.11.79102
MA0088.11.51073
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.10.852371
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.203171
MA0105.10.0403209
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.153042
MA0115.11.02805
MA0116.10.159642
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.11.3572
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.0922451
MA0140.10.405425
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.10.438224
MA0145.10.115359
MA0146.10.951488
MA0147.10.162359
MA0148.10.972544
MA0149.11.02604
MA0062.20.0969238
MA0035.21.04409
MA0039.20.267159
MA0138.20.534556
MA0002.20.725804
MA0137.20.229531
MA0104.20.118985
MA0047.20.47109
MA0112.20.106997
MA0065.20.839576
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.153348
MA0155.11.09568
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.489747
MA0160.10.386031
MA0161.10
MA0162.10.0809571
MA0163.11.42599
MA0164.10.509774
MA0080.20.21336
MA0018.20.483823
MA0099.20.411824
MA0079.22.16409
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
BRCA1#67247.339720233899550.001499531755796010.0095803264845892
CHD2#110654.701828560962210.002363882154558910.0133949046899234
REST#597854.38637668914910.003222672881545890.0166992177164858
YY1#752862.678820409011190.01273933791341470.0459357724188343
ZBTB33#10009411.51444546544770.0002743430759209510.00292487918600533
ZEB1#693546.141248006379590.002893399946065070.0156450322012472



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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