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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.601697319106115,

Latest revision as of 11:15, 17 September 2013


Full id: C292_Mesenchymal_skin_umbilical_Adipocyte_mesenchymal_Chondrocyte_skeletal



Phase1 CAGE Peaks

Hg19::chr17:48261721..48261729,-p@chr17:48261721..48261729
-
Hg19::chr2:189839090..189839105,+p1@COL3A1
Hg19::chr2:189849579..189849628,+p@chr2:189849579..189849628
+
Hg19::chr2:189849915..189849949,+p@chr2:189849915..189849949
+
Hg19::chr2:189850401..189850478,+p@chr2:189850401..189850478
+
Hg19::chr2:189851773..189851845,+p4@COL3A1
Hg19::chr2:189852804..189852835,+p@chr2:189852804..189852835
+
Hg19::chr2:189855724..189855761,+p@chr2:189855724..189855761
+
Hg19::chr2:189856903..189856926,+p@chr2:189856903..189856926
+
Hg19::chr2:189857607..189857646,+p@chr2:189857607..189857646
+
Hg19::chr2:189858077..189858096,+p@chr2:189858077..189858096
+
Hg19::chr2:189858136..189858149,+p@chr2:189858136..189858149
+
Hg19::chr2:189858758..189858780,+p@chr2:189858758..189858780
+
Hg19::chr2:189858991..189859033,+p@chr2:189858991..189859033
+
Hg19::chr2:189859261..189859297,+p@chr2:189859261..189859297
+
Hg19::chr2:189859443..189859507,+p@chr2:189859443..189859507
+
Hg19::chr2:189861175..189861198,+p@chr2:189861175..189861198
+
Hg19::chr2:189864003..189864023,+p@chr2:189864003..189864023
+
Hg19::chr2:189864188..189864235,+p@chr2:189864188..189864235
+
Hg19::chr2:189864267..189864279,+p@chr2:189864267..189864279
+
Hg19::chr2:189866256..189866277,+p@chr2:189866256..189866277
+
Hg19::chr2:189867024..189867049,+p@chr2:189867024..189867049
+
Hg19::chr2:189869053..189869071,+p19@COL3A1
Hg19::chr2:189873664..189873737,+p2@COL3A1
Hg19::chr2:189873740..189873791,+p3@COL3A1
Hg19::chr2:189873796..189873815,+p12@COL3A1
Hg19::chr2:189873877..189873903,+p10@COL3A1
Hg19::chr2:189874898..189874924,+p@chr2:189874898..189874924
+
Hg19::chr2:189874955..189875006,+p@chr2:189874955..189875006
+
Hg19::chr2:189875363..189875390,+p@chr2:189875363..189875390
+
Hg19::chr2:189875404..189875442,+p@chr2:189875404..189875442
+
Hg19::chr2:189875563..189875584,+p@chr2:189875563..189875584
+
Hg19::chr2:189876360..189876377,+p4@AF130082
Hg19::chr2:189876383..189876417,+p3@AF130082
Hg19::chr2:189876466..189876506,+p1@AF130082
Hg19::chr2:189876532..189876594,+p2@AF130082
Hg19::chr2:189876664..189876675,+p10@AF130082
Hg19::chr2:189876710..189876721,+p7@AF130082
Hg19::chr2:189876741..189876752,+p9@AF130082
Hg19::chr2:189876820..189876830,+p11@AF130082
Hg19::chr2:189876888..189876899,+p12@AF130082
Hg19::chr2:189877182..189877191,+p@chr2:189877182..189877191
+
Hg19::chr2:189877298..189877309,+p@chr2:189877298..189877309
+
Hg19::chr2:189877348..189877367,+p@chr2:189877348..189877367
+


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:0005586collagen type III0.000853644177557989
GO:0005583fibrillar collagen0.00469504297656894
GO:0005581collagen0.0153655951960438
GO:0005201extracellular matrix structural constituent0.0170728835511598
GO:0044420extracellular matrix part0.0170728835511598
GO:0006817phosphate transport0.0170728835511598
GO:0003013circulatory system process0.0170728835511598
GO:0008015blood circulation0.0170728835511598
GO:0015698inorganic anion transport0.0246608317961197
GO:0006820anion transport0.027572706935123
GO:0009887organ morphogenesis0.028092653843272
GO:0005578proteinaceous extracellular matrix0.0299486832293261



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
muscle tissue3.39e-1664
musculature3.39e-1664
musculature of body3.39e-1664
skeletal muscle tissue8.20e-1662
striated muscle tissue8.20e-1662
myotome8.20e-1662
dense mesenchyme tissue3.33e-1573
somite4.04e-1571
presomitic mesoderm4.04e-1571
presumptive segmental plate4.04e-1571
dermomyotome4.04e-1571
trunk paraxial mesoderm4.04e-1571
paraxial mesoderm1.14e-1472
presumptive paraxial mesoderm1.14e-1472
mesenchyme1.51e-12160
entire embryonic mesenchyme1.51e-12160
epithelial vesicle3.07e-1278
multilaminar epithelium5.24e-1283
trunk mesenchyme6.52e-11122
mesoderm1.48e-10315
mesoderm-derived structure1.48e-10315
presumptive mesoderm1.48e-10315
extraembryonic structure4.94e-0924
splanchnic layer of lateral plate mesoderm1.83e-0883
heart4.16e-0824
primitive heart tube4.16e-0824
primary heart field4.16e-0824
anterior lateral plate mesoderm4.16e-0824
heart tube4.16e-0824
heart primordium4.16e-0824
cardiac mesoderm4.16e-0824
cardiogenic plate4.16e-0824
heart rudiment4.16e-0824
adipose tissue2.56e-0714
primary circulatory organ3.08e-0727
trunk4.32e-07199
organ component layer5.21e-0766
Disease
Ontology termp-valuen
ovarian cancer3.53e-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)
MA0003.15.69884e-10
MA0004.10.374044
MA0006.10.133821
MA0007.10.147035
MA0009.10.295212
MA0014.17.15747e-09
MA0017.10.182593
MA0019.12.24352
MA0024.10.221542
MA0025.10.398381
MA0027.11.79461
MA0028.10.0116229
MA0029.16.4265
MA0030.11.87191
MA0031.11.039
MA0038.10.576398
MA0040.10.670844
MA0041.11.56295
MA0042.12.41007
MA0043.10.295444
MA0046.13.03491
MA0048.10.000576826
MA0050.10.351617
MA0051.10.268697
MA0052.10.677023
MA0055.10.00713467
MA0056.10
MA0057.14.62234e-05
MA0058.11.3913
MA0059.11.38385
MA0060.10.00986038
MA0061.10.0220854
MA0063.10
MA0066.10.577301
MA0067.10.553259
MA0068.10.0101776
MA0069.10.284408
MA0070.11.38745
MA0071.10.229527
MA0072.10.273057
MA0073.14.35394e-14
MA0074.11.43136
MA0076.10.0224905
MA0077.10.267535
MA0078.10.394373
MA0081.10.216071
MA0083.10.300765
MA0084.10.721137
MA0087.11.36911
MA0088.10.00385533
MA0089.10
MA0090.10.263616
MA0091.11.0453
MA0092.10.570619
MA0093.10.482121
MA0095.10
MA0098.10
MA0100.10.0858032
MA0101.10.0103659
MA0103.10.0439436
MA0105.10.0056559
MA0106.10.0982452
MA0107.10.00369115
MA0108.21.03138
MA0109.10
MA0111.10.0287033
MA0113.10.106097
MA0114.10.272528
MA0115.10.487485
MA0116.10.00390545
MA0117.10.32334
MA0119.10.074899
MA0122.10.343167
MA0124.12.00293
MA0125.10.384032
MA0130.10
MA0131.10.419238
MA0132.10
MA0133.10
MA0135.10.317863
MA0136.10.282045
MA0139.10.000582754
MA0140.10.226615
MA0141.10.410305
MA0142.10.96059
MA0143.10.34524
MA0144.10.596821
MA0145.10.00597318
MA0146.12.11855e-09
MA0147.10.0239147
MA0148.12.6918
MA0149.10.0597142
MA0062.20.00069578
MA0035.20.844007
MA0039.23.56719e-12
MA0138.20.396038
MA0002.20.0288361
MA0137.20.0602547
MA0104.20.0343269
MA0047.21.57612
MA0112.20.00467289
MA0065.28.69169e-05
MA0150.10.0242915
MA0151.10
MA0152.10.504329
MA0153.10.370648
MA0154.10.0146552
MA0155.10.00111729
MA0156.10.326838
MA0157.10.894256
MA0158.10
MA0159.10.490945
MA0160.10.0556436
MA0161.10
MA0162.15.83157e-09
MA0163.18.3779e-07
MA0164.10.3612
MA0080.20.0499414
MA0018.20.0988962
MA0099.20.234232
MA0079.20
MA0102.20.755388
MA0258.10.216927
MA0259.10.00470836
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

No analysis results for this cluster

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

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