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Coexpression cluster:C1353: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.12961,0.946942,0.436508,0.58616,0.393082,0.584466,1.59238,0.742622,0.267027,1.41135,0.553339,0.707204,1.85338,0.650887,0.391663,0.415981,0.889639,0.336106,0.236034,0.127969,0.436569,1.53265,1.41165,0.387783,0.483957,0.730467,1.10781,0.574247,0.396295,0.186644,0.530785,0.92701,0.816912,0.225641,0.35719,0.0334022,0.35388,0.585658,0.329602,0.69481,0.355745,0.513952,0.664116,0.390088,0.992846,0.468392,0.66382,0.542147,0.630853,0.396429,0.745008,0.675919,0.455399,1.00488,1.15929,1.57403,0.400834,0.62023,1.65059,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,1.25018,0.275507,2.73856,1.15727,1.17153,1.12235,0.562953,0.84426,0.913168,0.477584,1.25579,0.86037,0.684313,0.272514,1.10535,2.07207,0.794988,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,1.80351,0.864356,0.234532,0.987239,0.776336,0.498077,0.881389,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,1.21459,1.74379,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,2.24955,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.520084,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,1.9604,2.15723,1.07915,1.32317,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,5.8228
|tfbs_overrepresentation_jaspar=MA0003.1;3.55314,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;4.33274,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;0.906394,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.808182,MA0056.1;0,MA0057.1;0.450439,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.199491,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;4.94062,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,MA0083.1;2.3765,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;2.86388,MA0089.1;0,MA0090.1;0.490736,MA0091.1;0.561458,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.830067,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;5.28787,MA0117.1;1.07516,MA0119.1;1.12205,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;0.641617,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;3.7317,MA0146.1;2.91645,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;6.1078,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;1.06611,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;1.65732,MA0065.2;0.354331,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;1.3291,MA0155.1;0.318517,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;4.25353,MA0163.1;8.07551,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;6.53042,MA0102.2;1.58513,MA0258.1;0.788656,MA0259.1;0.893594,MA0442.1;0
}}
}}

Revision as of 19:52, 22 January 2013


Full id: C1353_Mesenchymal_Preadipocyte_basal_Adipocyte_Fibroblast_Smooth_leiomyoma



Phase1 CAGE Peaks

Hg19::chr11:844406..844448,+p4@TSPAN4
Hg19::chr19:42463447..42463513,-p1@RABAC1
Hg19::chr20:35169885..35169911,+p2@MYL9
Hg19::chr22:31503490..31503584,-p1@SELM
Hg19::chr22:43045336..43045416,-p1@CYB5R3
Hg19::chr22:43045417..43045424,-p6@CYB5R3


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>

Uber Anatomy
Ontology termp-valuen
epithelial vesicle1.55e-2378
mesenchyme2.47e-21160
entire embryonic mesenchyme2.47e-21160
dense mesenchyme tissue3.48e-2173
somite4.38e-2171
presomitic mesoderm4.38e-2171
presumptive segmental plate4.38e-2171
dermomyotome4.38e-2171
trunk paraxial mesoderm4.38e-2171
paraxial mesoderm1.18e-2072
presumptive paraxial mesoderm1.18e-2072
splanchnic layer of lateral plate mesoderm1.45e-2083
vasculature4.01e-2078
vascular system4.01e-2078
multilaminar epithelium7.54e-2083
skeletal muscle tissue7.65e-2062
striated muscle tissue7.65e-2062
myotome7.65e-2062
muscle tissue9.62e-2064
musculature9.62e-2064
musculature of body9.62e-2064
trunk mesenchyme4.40e-19122
epithelial tube6.53e-18117
vessel1.25e-1768
epithelial tube open at both ends8.64e-1759
blood vessel8.64e-1759
blood vasculature8.64e-1759
vascular cord8.64e-1759
organism subdivision1.01e-16264
artery2.88e-1642
arterial blood vessel2.88e-1642
arterial system2.88e-1642
unilaminar epithelium6.33e-16148
multi-cellular organism7.08e-16656
circulatory system7.19e-16112
trunk8.99e-16199
cardiovascular system1.18e-15109
cell layer1.63e-15309
epithelium3.96e-15306
multi-tissue structure1.40e-14342
systemic artery2.12e-1333
systemic arterial system2.12e-1333
anatomical system1.16e-12624
anatomical group1.43e-12625
anatomical cluster6.97e-12373
anatomical conduit1.77e-10240
mesoderm3.49e-10315
mesoderm-derived structure3.49e-10315
presumptive mesoderm3.49e-10315
surface structure7.77e-0999
tube6.78e-08192
compound organ1.01e-0768
developing anatomical structure1.42e-07581
aorta1.93e-0721
aortic system1.93e-0721
embryo2.20e-07592
primary circulatory organ3.42e-0727
integument3.60e-0746
integumental system3.60e-0746
heart3.81e-0724
primitive heart tube3.81e-0724
primary heart field3.81e-0724
anterior lateral plate mesoderm3.81e-0724
heart tube3.81e-0724
heart primordium3.81e-0724
cardiac mesoderm3.81e-0724
cardiogenic plate3.81e-0724
heart rudiment3.81e-0724
embryonic structure7.55e-07564


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)
MA0003.13.55314
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.14.33274
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
MA0048.10.906394
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.808182
MA0056.10
MA0057.10.450439
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.14.94062
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.12.3765
MA0084.11.5477
MA0087.11.00322
MA0088.12.86388
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.830067
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.15.28787
MA0117.11.07516
MA0119.11.12205
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.641617
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.13.7317
MA0146.12.91645
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.26.1078
MA0138.20.765223
MA0002.20.255126
MA0137.21.06611
MA0104.20.26661
MA0047.20.695777
MA0112.21.65732
MA0065.20.354331
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.11.3291
MA0155.10.318517
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.14.25353
MA0163.18.07551
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.26.53042
MA0102.21.58513
MA0258.10.788656
MA0259.10.893594
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
CTBP2#1488220.9056667797760.003653095132163690.018450798070802
CTCF#1066454.466880310895860.001144848346172360.00783479565073684
EGR1#195854.156815912341780.001617966818864440.0101300183799163
ELF1#199753.548414965672950.003446837775721690.0175243058348066
POLR2A#543062.147453176558070.01019570676818780.0380011212720019
SMC3#912637.522466422466420.005039540716828550.0234809097891973
TAF1#687252.785871904787740.01078636340290410.0397865722764674



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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