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Coexpression cluster:C2779: Difference between revisions

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{{Coexpression_clusters
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31749,0.15156,0.287598,0.313858,0.223773,0.00354126,0.181895,0.253768,0.000563201,0.202977,0.0155028,0.327002,0.28543,0.222656,0.228479,0.127111,0.000269465,0.390754,0.0725176,0.279739,0.108118,0.259901,1.41893e-08,0.0708274,0.0710478,7.97431e-05,5.25768e-06,0.0539258,0.0709978,0.401939,0.00817441,0.000325197,0.242121,0.298673,0.000205581,0.106889,0.128632,0.0845989,3.27633e-05,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.00401466,0.00721029,0.0486914,0.0164443,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.000735605,0.0364266,0.291176,0.00142707,0.322827,0.229571,0.359036,0.335984,0.0156657,0.208256,0.265058,0.256405,0.362898,0.302133,0.000213981,2.65206e-05,0.279606,0.00041492,0.150674,0.251128,0.246177,0.35674,0.0737175,0.318525,0.213257,0.0458843,0.122782,0.0991993,0.289049,0.00030277,0.125746,0.112897,1.11365e-06,0.222091,0.205977,5.4669e-06,0.00453107,0.00908363,0.132374,0.285122,0.000150337,0.203996,0.276721,0.000697427,0.0386145,0.00331953|tfbs_overrepresentation_for_novel_motifs=0.590005,1.03954,0.581696,0.741427,0.534346,1.75218,0.821651,0.395818,1.01802,0.151681,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,2.28567,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.285913,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,0.0946706,0.61613,0.822818,0.694903,0.99221,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,1.34056,0.777235,0.806003,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.95118,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.934671,1.15558,0.939507,0.272395,1.17564,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,2.40834,0.717043,1.46636,1.22649,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,3.90101,0.437774,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,1.96584,0.423521,3.18664,0.0401987|tfbs_overrepresentation_jaspar=MA0003.1;0.0214529,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.0695829,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;3.85927,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.25531,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.125954,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;2.70115,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.00636811,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;1.4709,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.182167,MA0089.1;0,MA0090.1;3.80961,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;2.35545,MA0109.1;0,MA0111.1;0.655276,MA0113.1;4.8563,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;2.8366,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;0.344952,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.8309,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.0247757,MA0138.2;0.928035,MA0002.2;2.63392,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.187982,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;0.180766,MA0156.1;4.65937,MA0157.1;3.66667,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.0928415,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.000248021,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2779_Adipocyte_mature_adipose_Preadipocyte_Fibroblast_Mesenchymal_Hair
|id=C2779
}}

Latest revision as of 12:12, 17 September 2013


Full id: C2779_Adipocyte_mature_adipose_Preadipocyte_Fibroblast_Mesenchymal_Hair



Phase1 CAGE Peaks

Hg19::chr4:152148941..152148953,-p3@SH3D19
Hg19::chr4:152148984..152149004,-p4@SH3D19
Hg19::chr4:152149009..152149020,-p7@SH3D19
Hg19::chr4:152149033..152149117,-p1@SH3D19


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
splanchnic layer of lateral plate mesoderm9.88e-1983
vessel6.35e-1868
vasculature1.03e-1778
vascular system1.03e-1778
epithelial tube open at both ends1.61e-1659
blood vessel1.61e-1659
blood vasculature1.61e-1659
vascular cord1.61e-1659
circulatory system7.78e-16112
cardiovascular system3.41e-15109
multilaminar epithelium5.39e-1483
multi-cellular organism1.35e-13656
somite8.67e-1371
presomitic mesoderm8.67e-1371
presumptive segmental plate8.67e-1371
dermomyotome8.67e-1371
trunk paraxial mesoderm8.67e-1371
muscle tissue9.27e-1364
musculature9.27e-1364
musculature of body9.27e-1364
epithelial vesicle1.63e-1278
dense mesenchyme tissue2.16e-1273
paraxial mesoderm2.45e-1272
presumptive paraxial mesoderm2.45e-1272
skeletal muscle tissue3.62e-1262
striated muscle tissue3.62e-1262
myotome3.62e-1262
anatomical conduit4.95e-12240
epithelial tube9.09e-12117
anatomical system1.21e-11624
anatomical group1.74e-11625
cell layer2.43e-11309
systemic artery3.45e-1133
systemic arterial system3.45e-1133
unilaminar epithelium4.04e-11148
epithelium4.09e-11306
artery7.47e-1142
arterial blood vessel7.47e-1142
arterial system7.47e-1142
blood vessel endothelium6.57e-1018
endothelium6.57e-1018
cardiovascular system endothelium6.57e-1018
mesoderm1.64e-09315
mesoderm-derived structure1.64e-09315
presumptive mesoderm1.64e-09315
organism subdivision3.81e-09264
tube8.25e-09192
anatomical cluster9.21e-09373
aorta9.84e-0921
aortic system9.84e-0921
trunk mesenchyme1.15e-08122
embryonic structure2.85e-08564
multi-tissue structure4.98e-08342
adult organism5.87e-08114
germ layer1.40e-07560
germ layer / neural crest1.40e-07560
embryonic tissue1.40e-07560
presumptive structure1.40e-07560
germ layer / neural crest derived structure1.40e-07560
epiblast (generic)1.40e-07560
organ component layer1.73e-0766
squamous epithelium2.41e-0725
trunk2.64e-07199
surface structure3.32e-0799
endothelial tube6.83e-079
arterial system endothelium6.83e-079
endothelium of artery6.83e-079
tissue7.74e-07773
simple squamous epithelium8.39e-0722


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.13.85927
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.12.70115
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.11.4709
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.13.80961
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.22.35545
MA0109.10
MA0111.10.655276
MA0113.14.8563
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.12.8366
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.8309
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.22.63392
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.14.65937
MA0157.13.66667
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.000248021
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
FOS#235348.99795530889440.0001525147711168630.00195249940925154
FOXA1#3169411.08141974938556.62943068949433e-050.00107261210190565
JUN#3725412.51282919233634.07770316866756e-050.00074466032738673



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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