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Coexpression cluster:C1528: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.333388,0.436508,0.58616,0.393082,0.584466,0.662701,0.742622,0.736703,1.41135,0.553339,0.707204,1.85338,0.650887,0.391663,0.415981,0.889639,0.336106,0.236034,1.30166,0.436569,0.0880431,0.576478,0.387783,0.483957,0.730467,1.10781,1.40695,0.396295,0.547818,0.530785,0.92701,0.302275,0.225641,0.35719,3.42097,0.35388,0.585658,4.2891,1.28576,0.355745,0.513952,0.0979105,0.390088,1.41477,0.468392,0.66382,0.542147,0.630853,1.02586,0.745008,0.675919,2.05902,1.00488,1.15929,0.653901,0.400834,0.62023,0.547548,0.619193,3.64737,0.666252,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.45007,1.15727,0.218784,2.48597,1.07049,0.84426,0.913168,2.08653,0.240887,0.86037,0.684313,0.272514,1.10535,0.406668,0.398737,3.89396,1.81827,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,0.234532,0.987239,0.776336,0.498077,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,1.56033,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.210279,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,3.87911,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,3.0089,4.45611,0.57483,1.31259,2.17352,1.7705,1.27501,1.58249,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,1.49651,0.8388,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.79772,0.661335,0.152397
|tfbs_overrepresentation_jaspar=MA0003.1;0.00461978,MA0004.1;0.558729,MA0006.1;1.01439,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;3.10532,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;0.408079,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;3.56533,MA0050.1;1.34656,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;1.22849,MA0056.1;0,MA0057.1;4.31533,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;3.80179,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.578694,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;1.87192,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;1.61871,MA0089.1;0,MA0090.1;0.490736,MA0091.1;0.561458,MA0092.1;1.29635,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.134725,MA0106.1;0.70837,MA0107.1;0.320267,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;0.314898,MA0115.1;1.28169,MA0116.1;0.323925,MA0117.1;1.07516,MA0119.1;0.440684,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;0.226048,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.707171,MA0146.1;0.0213085,MA0147.1;2.3862,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;0.00570825,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;2.08061,MA0047.2;0.695777,MA0112.2;0.101413,MA0065.2;0.718489,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.132326,MA0155.1;0.0961854,MA0156.1;0.417278,MA0157.1;1.89858,MA0158.1;0,MA0159.1;2.38949,MA0160.1;0.600559,MA0161.1;0,MA0162.1;0.62636,MA0163.1;0.273773,MA0164.1;0.738243,MA0080.2;1.02158,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;7.0058,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:59, 22 January 2013


Full id: C1528_Mesenchymal_Pericytes_mesodermal_Adipocyte_Fibroblast_Multipotent_Hair



Phase1 CAGE Peaks

Hg19::chr5:149535244..149535282,-p4@PDGFRB
Hg19::chr5:149535298..149535305,-p6@PDGFRB
Hg19::chr5:149535335..149535359,-p3@PDGFRB
Hg19::chr5:149535378..149535385,-p5@PDGFRB
Hg19::chr5:149535392..149535417,-p1@PDGFRB
Hg19::chr5:149535421..149535441,-p2@PDGFRB


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

No GOStat results

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>

Cell Type
Ontology termp-valuen
fibroblast9.78e-2576
contractile cell1.12e-1059
skin fibroblast4.82e-1023
muscle cell1.98e-0955
muscle precursor cell2.72e-0958
myoblast2.72e-0958
multi-potent skeletal muscle stem cell2.72e-0958
non-terminally differentiated cell8.37e-09106
fat cell3.24e-0815
electrically responsive cell1.16e-0761
electrically active cell1.16e-0761
preadipocyte3.16e-0712
Uber Anatomy
Ontology termp-valuen
dense mesenchyme tissue1.56e-1373
structure with developmental contribution from neural crest1.86e-13132
multi-tissue structure2.87e-13342
paraxial mesoderm4.91e-1372
presumptive paraxial mesoderm4.91e-1372
somite4.94e-1371
presomitic mesoderm4.94e-1371
presumptive segmental plate4.94e-1371
dermomyotome4.94e-1371
trunk paraxial mesoderm4.94e-1371
epithelial vesicle1.91e-1278
adult organism1.47e-11114
muscle tissue1.02e-1064
musculature1.02e-1064
musculature of body1.02e-1064
mesenchyme1.32e-10160
entire embryonic mesenchyme1.32e-10160
skeletal muscle tissue1.92e-1062
striated muscle tissue1.92e-1062
myotome1.92e-1062
integument1.06e-0946
integumental system1.06e-0946
tissue1.78e-09773
surface structure2.34e-0999
multilaminar epithelium4.71e-0983
trunk mesenchyme4.79e-09122
adipose tissue9.37e-0914
multi-cellular organism3.84e-08656
organism subdivision4.12e-08264
skin of body1.15e-0741
neural plate1.45e-0782
presumptive neural plate1.45e-0782
ectoderm-derived structure1.77e-07171
ectoderm1.77e-07171
presumptive ectoderm1.77e-07171
neurectoderm3.79e-0786


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)
MA0003.10.00461978
MA0004.10.558729
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.13.10532
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.13.56533
MA0050.11.34656
MA0051.10.661179
MA0052.10.959373
MA0055.11.22849
MA0056.10
MA0057.14.31533
MA0058.10.458909
MA0059.10.457555
MA0060.13.80179
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.578694
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.11.87192
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.11.61871
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.11.29635
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.707171
MA0146.10.0213085
MA0147.12.3862
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.00570825
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.22.08061
MA0047.20.695777
MA0112.20.101413
MA0065.20.718489
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.10.417278
MA0157.11.89858
MA0158.10
MA0159.12.38949
MA0160.10.600559
MA0161.10
MA0162.10.62636
MA0163.10.273773
MA0164.10.738243
MA0080.21.02158
MA0018.20.709805
MA0099.20.629739
MA0079.27.0058
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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
CTCF#1066465.360256373075034.21437267579784e-050.000756132739886017
EP300#203366.77394172622321.03454107484288e-050.000269913653049002
POLR2A#543062.147453176558070.01019570676818780.0380717730044966
RAD21#5885610.35503389545638.10515055094479e-073.54478148404574e-05
TAF1#687263.343046285745290.0007162474284635620.0057373957034289
YY1#752864.911170749853867.12445972864136e-050.00112431467150132



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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