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Coexpression cluster:C3530: Difference between revisions

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{{Coexpression_clusters
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131118,0.00178627,0.00310436,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.00080862,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,2.73751e-08,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.000752649,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.0119784,0.217112,0.123917,0.184317,6.2467e-05,0.0723291,0.00356871,0.261744,1.6005e-07,0.21382,0.00176424,0.000532415,0.00140109,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.00221189,0.172134,0.176789,0.000163687,0.00162178,0.310405,0.000379247,0.0257454,0.0822373,9.03667e-05,1.39005e-07,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.0240944,0.187731,0.233626,0.189559,9.53285e-05,0.0981146,0.064145,0.000332324,0.0638699,2.29864e-09,0.0663259,0.0762523,0.128736,0.000236163,0.04411,9.09158e-07,0.089609,0.0367455,0.13497,1.63213e-07,0.00553696,0.00499908,0.0687209,0.141729,0.263159,0.255956,0.200105,0.227491,0.00569858,0.253509,0.00107794,1.04453e-10,0.00384051,0.000422974,0.160658,0.206239,0.0015491,0.00501043,0.0304659,0.0597546,0.115817,0.218052,0.0271615,0.11528,0.194982,0.190993,0.00472154,0.283218,6.14904e-07,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.00380229,0.316866,0.000967725,0.000758145,0.271275,6.33046e-05,0.270604,0.101021,0.222548,0.175934,0.000734859,0.00199458,1.37498e-05,0.0017212,0.0107847|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,2.14419,0.491742,1.84557,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,1.14835,0.305559,0.69094,1.26332,4.68287,0.635379,0.743951,2.30584,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,1.96994,2.47502,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,7.6454,1.45054,0.430728,3.81826,0.396746,1.12884,1.20029,1.74644,1.16162,1.14559,0.960908,0.498519,1.39759,2.22068,2.26789,1.76229,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,1.14422,1.27663,1.05794,0.360456,0.569121,2.74478,1.27082,1.1798,1.09802,1.90788,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.553386,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,2.76728,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,2.29164,0.318511,6.63372,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,3.92523|tfbs_overrepresentation_jaspar=MA0003.1;0.708947,MA0004.1;0.826076,MA0006.1;1.5435,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.377374,MA0017.1;2.76432,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;1.06172,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;2.13518,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;1.79391,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;4.76891,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.715722,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;2.32521,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;2.4174,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;0.107247,MA0147.1;3.48176,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.195278,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;3.15214,MA0047.2;0.973066,MA0112.2;0.731309,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;1.31345,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;1.43223,MA0163.1;1.2663,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;2.28794,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;1.40979,MA0442.1;0}}
|full_id=C3530_Myoblast_ovary_extraskeletal_Fibroblast_kidney_breast_cervix
|id=C3530
}}

Latest revision as of 12:28, 17 September 2013


Full id: C3530_Myoblast_ovary_extraskeletal_Fibroblast_kidney_breast_cervix



Phase1 CAGE Peaks

Hg19::chr15:96873921..96873946,+p1@NR2F2
Hg19::chr15:96873984..96873999,+p3@NR2F2
Hg19::chr15:96874012..96874042,+p2@NR2F2


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
trunk2.78e-23199
organism subdivision7.54e-22264
anatomical cluster3.90e-21373
mesenchyme2.84e-18160
entire embryonic mesenchyme2.84e-18160
cell layer8.84e-18309
multi-tissue structure1.71e-17342
epithelium1.23e-16306
anatomical conduit1.89e-15240
unilaminar epithelium4.07e-15148
epithelial tube1.06e-14117
trunk mesenchyme2.03e-14122
subdivision of trunk3.52e-14112
multi-cellular organism1.77e-13656
vasculature1.53e-1278
vascular system1.53e-1278
immaterial anatomical entity1.94e-12117
tube2.98e-11192
trunk region element2.92e-10101
vessel4.76e-1068
splanchnic layer of lateral plate mesoderm6.78e-1083
anatomical space9.90e-1095
abdominal segment of trunk2.21e-0960
abdomen2.21e-0960
epithelial vesicle2.83e-0978
body cavity precursor2.86e-0954
compound organ9.33e-0968
anatomical system1.80e-08624
anatomical group3.17e-08625
anatomical cavity5.91e-0861
muscle tissue9.59e-0864
musculature9.59e-0864
musculature of body9.59e-0864
simple squamous epithelium1.11e-0722
epithelial tube open at both ends1.32e-0759
blood vessel1.32e-0759
blood vasculature1.32e-0759
vascular cord1.32e-0759
skeletal muscle tissue1.58e-0762
striated muscle tissue1.58e-0762
myotome1.58e-0762
blood vessel endothelium1.80e-0718
endothelium1.80e-0718
cardiovascular system endothelium1.80e-0718
abdomen element2.20e-0754
abdominal segment element2.20e-0754
somite3.44e-0771
presomitic mesoderm3.44e-0771
presumptive segmental plate3.44e-0771
dermomyotome3.44e-0771
trunk paraxial mesoderm3.44e-0771
circulatory system3.49e-07112
duct4.45e-0719
dense mesenchyme tissue4.80e-0773
paraxial mesoderm5.11e-0772
presumptive paraxial mesoderm5.11e-0772
squamous epithelium5.19e-0725
cardiovascular system5.59e-07109


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)
MA0003.10.708947
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.12.76432
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.06172
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.12.13518
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
MA0073.11.79391
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.14.76891
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.12.32521
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.12.4174
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
MA0146.10.107247
MA0147.13.48176
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.23.15214
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.22.28794
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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
CCNT2#90536.336201576962630.003930750035764890.0189705916351779
CEBPB#105137.971147625824820.001974187055288560.0115095524096953
E2F1#186934.907389214879320.008460985347239390.0324658993563206
E2F4#1874312.66806031528440.0004917987006298980.00436500080692496
E2F6#187635.017155731697390.00791769806886330.0321494680849895
EGR1#195834.988179094810140.008056488137383440.0319964849442974
FOSL1#8061339.7135797163731.59554825631833e-050.0003707998761496
GATA3#2625327.2365163572064.94721007899563e-050.000850364834496749
GTF2B#2959331.94382993432423.06634405746243e-050.00062719527422115
GTF2F1#2962312.73966087675770.0004835525047438590.00433379730910014
HMGN3#932438.178547723350590.001827766942164210.0108565177542335
HNF4A#3172323.13229036295378.07584663437677e-050.00122681214057844
HNF4G#3174328.75342252644684.20470658818262e-050.000755956879606137
IRF1#365937.63716375356390.002244692747297240.0127861175803096
MAX#414936.452555509007120.003721913834265510.0186254412523649
MXI1#460139.96157162875930.001011470541259020.007194508741984
MYC#460935.22228187160940.007020843755740150.0293981998639141
NFYA#4800318.42558069983050.0001598135507814160.00199340349099013
NFYB#4801316.75979325353650.0002123649923296180.00245480768499314
NR2C2#7182332.61461090524092.88098172333076e-050.000604433206514547
NRF1#4899312.21027944771090.0005492172401020010.00470508566475374
RXRA#6256320.07461713913330.0001235730348432220.00165057477759193
SIN3A#2594235.408884726815140.006318961977991520.0276081856601178
SP1#666735.69838137814090.005403962701712170.0246047807395639
SREBF1#6720347.00584944048839.62099323994382e-060.00025451036296517
SRF#6722313.79717826216780.0003806615025800190.00374561020048564
TCF7L2#6934310.77017656313730.0008003181298398380.0061278904077964
YY1#752834.911170749853860.008441455341808260.0328704058179454
ZBTB7A#5134137.35190930787590.002516255860282270.0139911220674024
ZNF143#7702313.50087655222790.0004062804962997170.00388495960016903
ZNF263#1012738.221841637010680.001799043925565870.0109200481542586



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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