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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.552682694606051,

Latest revision as of 11:26, 17 September 2013


Full id: C609_Smooth_mesenchymal_Preadipocyte_Cardiac_Fibroblast_Osteoblast_tenocyte



Phase1 CAGE Peaks

Hg19::chrX:47441825..47441846,+p1@TIMP1
Hg19::chrX:47442857..47442871,+p5@TIMP1
Hg19::chrX:47442876..47442906,+p3@TIMP1
Hg19::chrX:47444329..47444370,+p4@TIMP1
Hg19::chrX:47444375..47444387,-p@chrX:47444375..47444387
-
Hg19::chrX:47444394..47444423,-p@chrX:47444394..47444423
-
Hg19::chrX:47444675..47444713,-p@chrX:47444675..47444713
-
Hg19::chrX:47444716..47444731,-p@chrX:47444716..47444731
-
Hg19::chrX:47445998..47446031,+p@chrX:47445998..47446031
+
Hg19::chrX:47446039..47446094,+p@chrX:47446039..47446094
+
Hg19::chrX:47446043..47446074,-p4@CU674427
Hg19::chrX:47446081..47446133,-p1@CU674427
Hg19::chrX:47446099..47446146,+p@chrX:47446099..47446146
+
Hg19::chrX:47446141..47446157,-p7@CU674427
Hg19::chrX:47446158..47446174,-p3@CU674427


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:0051045negative regulation of membrane protein ectodomain proteolysis0.000809490168373955
GO:0051043regulation of membrane protein ectodomain proteolysis0.000809490168373955
GO:0043249erythrocyte maturation0.00202372542093489
GO:0045861negative regulation of proteolysis0.00202372542093489
GO:0048821erythrocyte development0.00226657247144707
GO:0033619membrane protein proteolysis0.00300667776824612
GO:0006509membrane protein ectodomain proteolysis0.00300667776824612
GO:0030162regulation of proteolysis0.00305807396941272
GO:0008191metalloendopeptidase inhibitor activity0.00305807396941272
GO:0030218erythrocyte differentiation0.0053426351112681
GO:0048469cell maturation0.00662310137760508
GO:0021700developmental maturation0.00715049648730327
GO:0030099myeloid cell differentiation0.00958934507150685
GO:0051248negative regulation of protein metabolic process0.0120267110729845
GO:0030097hemopoiesis0.0173326130169482
GO:0048534hemopoietic or lymphoid organ development0.0173326130169482
GO:0002520immune system development0.0173326130169482
GO:0008284positive regulation of cell proliferation0.0209568010256813
GO:0004866endopeptidase inhibitor activity0.0214727918347617
GO:0030414protease inhibitor activity0.0215324384787472
GO:0031324negative regulation of cellular metabolic process0.0282350170728835
GO:0004857enzyme inhibitor activity0.0282350170728835
GO:0005578proteinaceous extracellular matrix0.0282350170728835
GO:0051246regulation of protein metabolic process0.0282350170728835
GO:0009892negative regulation of metabolic process0.0282350170728835
GO:0042127regulation of cell proliferation0.0292039145359527
GO:0008283cell proliferation0.0446718648473034



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
multi fate stem cell1.24e-22427
somatic stem cell2.39e-21433
stem cell1.54e-19441
somatic cell7.03e-19588
fibroblast1.15e-1876
muscle precursor cell3.67e-1858
myoblast3.67e-1858
multi-potent skeletal muscle stem cell3.67e-1858
contractile cell4.46e-1759
muscle cell5.54e-1755
smooth muscle cell4.89e-1443
smooth muscle myoblast4.89e-1443
electrically responsive cell6.33e-1461
electrically active cell6.33e-1461
non-terminally differentiated cell4.03e-13106
animal cell5.73e-13679
eukaryotic cell5.73e-13679
vascular associated smooth muscle cell2.08e-1132
connective tissue cell4.59e-11361
mesodermal cell2.05e-10121
mesenchymal cell8.59e-10354
cardiocyte3.31e-0816
classical monocyte7.24e-0842
CD14-positive, CD16-negative classical monocyte7.24e-0842
preadipocyte8.30e-0812
motile cell1.10e-07386
defensive cell1.77e-0748
phagocyte1.77e-0748
Uber Anatomy
Ontology termp-valuen
mesoderm9.54e-24315
mesoderm-derived structure9.54e-24315
presumptive mesoderm9.54e-24315
musculoskeletal system1.05e-19167
somite1.37e-1771
presomitic mesoderm1.37e-1771
presumptive segmental plate1.37e-1771
dermomyotome1.37e-1771
trunk paraxial mesoderm1.37e-1771
epithelial vesicle1.66e-1778
dense mesenchyme tissue2.09e-1773
paraxial mesoderm7.00e-1772
presumptive paraxial mesoderm7.00e-1772
skeletal muscle tissue2.70e-1662
striated muscle tissue2.70e-1662
myotome2.70e-1662
muscle tissue1.25e-1564
musculature1.25e-1564
musculature of body1.25e-1564
multilaminar epithelium6.70e-1483
trunk mesenchyme2.00e-13122
mesenchyme2.55e-12160
entire embryonic mesenchyme2.55e-12160
splanchnic layer of lateral plate mesoderm1.49e-1183
lateral plate mesoderm1.72e-11203
connective tissue4.62e-11371
artery7.59e-1042
arterial blood vessel7.59e-1042
arterial system7.59e-1042
epithelial tube2.48e-09117
unilaminar epithelium2.55e-09148
circulatory system3.03e-09112
cardiovascular system3.27e-09109
trunk3.86e-09199
vasculature6.34e-0978
vascular system6.34e-0978
multi-cellular organism9.65e-09656
systemic artery1.06e-0833
systemic arterial system1.06e-0833
heart1.19e-0824
primitive heart tube1.19e-0824
primary heart field1.19e-0824
anterior lateral plate mesoderm1.19e-0824
heart tube1.19e-0824
heart primordium1.19e-0824
cardiac mesoderm1.19e-0824
cardiogenic plate1.19e-0824
heart rudiment1.19e-0824
primary circulatory organ2.86e-0827
epithelial tube open at both ends9.78e-0859
blood vessel9.78e-0859
blood vasculature9.78e-0859
vascular cord9.78e-0859
anatomical group1.97e-07625
vessel2.50e-0768
anatomical system2.53e-07624
adipose tissue4.16e-0714
organism subdivision5.51e-07264
Disease
Ontology termp-valuen
ovarian cancer6.47e-0714


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)
MA0003.10.0972587
MA0004.10.256222
MA0006.10.137644
MA0007.10.67744
MA0009.10.669377
MA0014.10.000336449
MA0017.10.16476
MA0019.10.38027
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.454219
MA0029.10.588958
MA0030.10.578277
MA0031.10.518602
MA0038.10.34128
MA0040.10.594421
MA0041.10.27117
MA0042.10.245557
MA0043.10.669676
MA0046.10.659066
MA0048.10.23222
MA0050.10.246257
MA0051.10.337676
MA0052.10.598036
MA0055.10.0510304
MA0056.10
MA0057.10.0873069
MA0058.10.182945
MA0059.10.182001
MA0060.10.877206
MA0061.10.198509
MA0063.10
MA0066.10.341645
MA0067.10.975379
MA0068.10.147451
MA0069.10.655419
MA0070.11.55511
MA0071.10.308534
MA0072.10.640598
MA0073.10.062487
MA0074.10.337035
MA0076.11.07748
MA0077.10.633326
MA0078.11.90704
MA0081.10.536866
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.10.244241
MA0089.10
MA0090.10.205547
MA0091.10.258318
MA0092.11.88087
MA0093.10.139688
MA0095.10
MA0098.10
MA0100.10.353174
MA0101.10.141917
MA0103.10.815939
MA0105.10.376193
MA0106.10.37688
MA0107.10.0950422
MA0108.21.28312
MA0109.10
MA0111.11.16023
MA0113.10.39123
MA0114.10.0920489
MA0115.10.900969
MA0116.10.0971018
MA0117.10.705104
MA0119.10.97973
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.10.406749
MA0140.10.826015
MA0141.10.180729
MA0142.10.489543
MA0143.10.391385
MA0144.10.596391
MA0145.10.00981909
MA0146.10.62917
MA0147.10.0991954
MA0148.10.276339
MA0149.11.46736
MA0062.20.191053
MA0035.20.305721
MA0039.20.395398
MA0138.20.425279
MA0002.20.82964
MA0137.20.465392
MA0104.20.0667907
MA0047.20.366327
MA0112.20.258654
MA0065.20.140846
MA0150.10.201098
MA0151.10
MA0152.10.311809
MA0153.10.763487
MA0154.10.367546
MA0155.10.0077078
MA0156.10.154615
MA0157.10.46471
MA0158.10
MA0159.10.0995776
MA0160.10.288813
MA0161.10
MA0162.10.551213
MA0163.11.00044
MA0164.11.03839
MA0080.20.432036
MA0018.20.378086
MA0099.20.839067
MA0079.20.34639
MA0102.21.1957
MA0258.10.569952
MA0259.10.104286
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
ZNF263#1012784.384982206405690.0001387797216824230.00181197841640088



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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