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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.66188189350471,0

Latest revision as of 12:41, 17 September 2013


Full id: C4191_Smooth_Mesenchymal_leiomyoma_Fibroblast_Preadipocyte_Adipocyte_Placental



Phase1 CAGE Peaks

Hg19::chr2:220408260..220408340,-p2@CHPF
Hg19::chr2:220408430..220408555,-p1@CHPF
Hg19::chr9:139981401..139981451,+p1@MAN1B1


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:0050510N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity0.00718206835348578
GO:0047238glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity0.00718206835348578
GO:0009311oligosaccharide metabolic process0.0157036058276523
GO:0004571mannosyl-oligosaccharide 1,2-alpha-mannosidase activity0.0157036058276523
GO:0015924mannosyl-oligosaccharide mannosidase activity0.0157036058276523
GO:0008376acetylgalactosaminyltransferase activity0.0157036058276523
GO:0015020glucuronosyltransferase activity0.0157036058276523
GO:0015923mannosidase activity0.0157036058276523
GO:0006487protein amino acid N-linked glycosylation0.0211319491565653
GO:0008194UDP-glycosyltransferase activity0.0486020383091593
GO:0006486protein amino acid glycosylation0.0486020383091593
GO:0043413biopolymer glycosylation0.0486020383091593
GO:0009101glycoprotein biosynthetic process0.0486020383091593
GO:0004553hydrolase activity, hydrolyzing O-glycosyl compounds0.0486020383091593
GO:0009100glycoprotein metabolic process0.0492197354072614
GO:0016798hydrolase activity, acting on glycosyl bonds0.0492197354072614



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><br>

Uber Anatomy
Ontology termp-valuen
organism subdivision8.86e-19264
trunk2.59e-15199
multi-tissue structure2.31e-13342
mesenchyme4.93e-13160
entire embryonic mesenchyme4.93e-13160
multilaminar epithelium6.94e-1383
skeletal muscle tissue1.94e-1162
striated muscle tissue1.94e-1162
myotome1.94e-1162
trunk mesenchyme2.37e-11122
dense mesenchyme tissue4.05e-1173
somite7.83e-1171
presomitic mesoderm7.83e-1171
presumptive segmental plate7.83e-1171
dermomyotome7.83e-1171
trunk paraxial mesoderm7.83e-1171
muscle tissue1.09e-1064
musculature1.09e-1064
musculature of body1.09e-1064
paraxial mesoderm1.12e-1072
presumptive paraxial mesoderm1.12e-1072
cell layer2.98e-10309
epithelium3.83e-10306
epithelial vesicle3.87e-1078
primordium2.08e-09160
organ component layer1.14e-0866
multi-cellular organism4.63e-08656
extraembryonic structure1.14e-0724
extraembryonic membrane1.49e-0714
membranous layer1.49e-0714
subdivision of trunk3.13e-07112
ectodermal placode3.61e-0731


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)
MA0003.12.61626
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.14.37851
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.14.88467
MA0056.10
MA0057.10.886807
MA0058.11.70328
MA0059.11.70014
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.11.55117
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.11.5295
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.23.37171
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.264678
MA0065.21.39232
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.711948
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.22.26143
MA0099.20.902716
MA0079.23.61229
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
BCL3#602223.03140186915890.002464674760842910.0138570288193191
BRCA1#672213.45615376214920.007119807716084560.0296343694428565
CCNT2#90536.336201576962630.003930750035764890.0190480513634581
CTBP2#1488241.81133355955210.0007543408259914850.00593555349398965
EGR1#195834.988179094810140.008056488137383440.0321407068482444
ELF1#199734.258097958807540.01295179875054610.0463514001202167
ELK4#2005210.8237877723120.01091284719516480.040206259858744
FOSL2#2355211.28680040304110.0100534586973120.0376820690815591
HDAC2#3066313.41562023662630.0004140761399857210.00392180085099925
HMGN3#932438.178547723350590.001827766942164210.010891205093438
IRF1#365937.63716375356390.002244692747297240.012839337632673
MAX#414936.452555509007120.003721913834265510.0186989108589982
MYC#460935.22228187160940.007020843755740150.0295212940255152
NANOG#79923219.49651898734180.003427255648501020.0174544864033646
NR2C2#7182221.74307393682720.002762207975496010.015139450997262
NRF1#4899312.21027944771090.0005492172401020010.00472135149716132
PBX3#5090214.60967512449610.006056122473217890.026848432591069
SIN3A#2594235.408884726815140.006318961977991520.0277486469335011
SP1#666735.69838137814090.005403962701712170.0247114348528446
SREBF1#6720347.00584944048839.62099323994382e-060.000255091879407589



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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