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Coexpression cluster:C1278: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.392069,0.465735,0.384703,0.529489,1.62733,0.52784,0.604235,0.226729,1.19284,0.200685,0.497563,0.647852,0.184039,1.44576,0.905441,0.956905,0.827563,0.786991,0.19568,0.32524,0.384762,0.23059,0.520063,0.897212,0.430372,0.670692,0.164928,0.517892,0.915262,0.150685,0.475674,0.864517,2.83783,1.64836,0.309012,0.442372,0.305874,0.529001,0.282922,1.12779,0.307642,0.459366,0.254304,0.340293,0.0257952,0.415364,0.60533,1.22101,0.0670664,0.346342,0.684981,1.49721,0.752493,0.941629,1.09491,1.45196,0.350547,0.562713,0.150585,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.232216,0.115253,1.0929,0.179863,0.168304,0.473656,0.782748,0.850825,1.90717,0.200147,0.798651,0.625403,0.229431,1.04131,0.0324537,0.322252,3.49206,0.711163,1.65172,1.27705,2.315,0.881388,0.26423,0.343884,0.277058,0.194299,0.924148,0.715799,0.132387,0.776034,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,0.327379,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,0.358137,0.474472,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.26104,0.106334,0.0685123,1.0153,0.216774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,1.51278,0.24928,0.602897,0.00626991
|tfbs_overrepresentation_for_novel_motifs=0.392069,0.465735,0.384703,0.529489,1.62733,0.52784,0.604235,0.226729,1.19284,0.200685,0.497563,0.647852,0.184039,1.44576,0.905441,0.956905,0.827563,0.786991,0.19568,0.32524,0.384762,0.23059,0.520063,0.897212,0.430372,0.670692,0.164928,0.517892,0.915262,0.150685,0.475674,0.864517,2.83783,1.64836,0.309012,0.442372,0.305874,0.529001,0.282922,1.12779,0.307642,0.459366,0.254304,0.340293,0.0257952,0.415364,0.60533,1.22101,0.0670664,0.346342,0.684981,1.49721,0.752493,0.941629,1.09491,1.45196,0.350547,0.562713,0.150585,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.232216,0.115253,1.0929,0.179863,0.168304,0.473656,0.782748,0.850825,1.90717,0.200147,0.798651,0.625403,0.229431,1.04131,0.0324537,0.322252,3.49206,0.711163,1.65172,1.27705,2.315,0.881388,0.26423,0.343884,0.277058,0.194299,0.924148,0.715799,0.132387,0.776034,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,0.327379,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,0.358137,0.474472,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.26104,0.106334,0.0685123,1.0153,0.216774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,1.51278,0.24928,0.602897,0.00626991
|tfbs_overrepresentation_jaspar=MA0003.1;0.0462779,MA0004.1;0.502801,MA0006.1;0.341337,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;0.0156227,MA0017.1;0.380797,MA0019.1;0.652951,MA0024.1;0.867125,MA0025.1;1.10816,MA0027.1;2.59001,MA0028.1;0.35747,MA0029.1;0.886702,MA0030.1;0.875089,MA0031.1;0.809638,MA0038.1;0.60704,MA0040.1;0.892629,MA0041.1;0.521615,MA0042.1;0.48922,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;1.25271,MA0050.1;0.490116,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;0.0407081,MA0056.1;0,MA0057.1;0.369442,MA0058.1;0.406232,MA0059.1;0.404929,MA0060.1;0.224688,MA0061.1;0.198335,MA0063.1;0,MA0066.1;0.607474,MA0067.1;1.29359,MA0068.1;0.488375,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;0.065183,MA0074.1;0.60198,MA0076.1;0.422297,MA0077.1;0.934645,MA0078.1;0.703614,MA0081.1;0.405093,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;0.538456,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,MA0092.1;0.467172,MA0093.1;0.344385,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.347695,MA0103.1;0.332048,MA0105.1;0.104569,MA0106.1;0.648997,MA0107.1;0.274127,MA0108.2;0.806528,MA0109.1;0,MA0111.1;0.45062,MA0113.1;0.665691,MA0114.1;0.269076,MA0115.1;1.21667,MA0116.1;0.277571,MA0117.1;1.01134,MA0119.1;1.00897,MA0122.1;1.03753,MA0124.1;1.17486,MA0125.1;1.0901,MA0130.1;0,MA0131.1;0.722072,MA0132.1;0,MA0133.1;0,MA0135.1;1.00402,MA0136.1;0.614215,MA0139.1;0.186511,MA0140.1;0.564957,MA0141.1;0.403171,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;0.254954,MA0145.1;0.276317,MA0146.1;0.0127148,MA0147.1;0.281049,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;0.193221,MA0035.2;0.564239,MA0039.2;0.0553061,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;0.36398,MA0104.2;0.223944,MA0047.2;0.636643,MA0112.2;0.0758925,MA0065.2;0.0828768,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.102476,MA0155.1;0.071478,MA0156.1;0.36627,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;0.0249953,MA0163.1;0.0167306,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;0.00447823,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;0.289405,MA0442.1;0
}}
}}

Revision as of 19:49, 22 January 2013


Full id: C1278_Smooth_Endothelial_osteosarcoma_schwannoma_large_Renal_Lymphatic



Phase1 CAGE Peaks

Hg19::chr5:54274654..54274657,-p@chr5:54274654..54274657
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Hg19::chr5:54274696..54274727,-p@chr5:54274696..54274727
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Hg19::chr5:54275165..54275184,-p@chr5:54275165..54275184
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Hg19::chr5:54281153..54281165,-p1@AB590689
Hg19::chr5:54281407..54281429,-p1@ESM1
Hg19::chr5:54281512..54281517,-p4@ESM1
Hg19::chr5:54281535..54281547,-p2@ESM1


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:0005520insulin-like growth factor binding0.0192020879940343
GO:0019838growth factor binding0.0192020879940343
GO:0001558regulation of cell growth0.0192020879940343
GO:0016049cell growth0.0192020879940343
GO:0040008regulation of growth0.0192020879940343
GO:0008361regulation of cell size0.0192020879940343
GO:0008083growth factor activity0.0202141259188239
GO:0000902cell morphogenesis0.0297042008451404
GO:0032989cellular structure morphogenesis0.0297042008451404
GO:0065008regulation of biological quality0.0487975391498881
GO:0005102receptor binding0.0487975391498881
GO:0009653anatomical structure morphogenesis0.0487975391498881



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
mesodermal cell2.01e-35121
endothelial cell of vascular tree7.36e-3124
endothelial cell1.90e-3036
meso-epithelial cell1.07e-2445
lining cell1.06e-2058
barrier cell1.06e-2058
blood vessel endothelial cell1.09e-2018
embryonic blood vessel endothelial progenitor cell1.09e-2018
vascular associated smooth muscle cell2.18e-1932
muscle precursor cell1.64e-1658
myoblast1.64e-1658
multi-potent skeletal muscle stem cell1.64e-1658
smooth muscle cell1.42e-1443
smooth muscle myoblast1.42e-1443
muscle cell1.31e-1355
embryonic cell3.36e-13250
aortic smooth muscle cell2.94e-1210
contractile cell2.99e-1259
lymphangioblast4.34e-126
endothelial cell of lymphatic vessel4.34e-126
vascular lymphangioblast4.34e-126
electrically responsive cell1.22e-1161
electrically active cell1.22e-1161
smooth muscle cell of the subclavian artery1.30e-115
endothelial cell of artery1.61e-119
non-terminally differentiated cell6.99e-09106
fenestrated cell4.32e-075
glomerular endothelial cell4.32e-075
capillary endothelial cell5.74e-073
endothelial cell of umbilical vein6.23e-073
Uber Anatomy
Ontology termp-valuen
vessel2.91e-4668
epithelial tube open at both ends1.69e-3959
blood vessel1.69e-3959
blood vasculature1.69e-3959
vascular cord1.69e-3959
vasculature1.43e-3878
vascular system1.43e-3878
artery3.22e-3542
arterial blood vessel3.22e-3542
arterial system3.22e-3542
splanchnic layer of lateral plate mesoderm1.78e-3483
cardiovascular system2.90e-32109
systemic artery3.66e-3133
systemic arterial system3.66e-3133
circulatory system5.28e-31112
epithelial tube7.81e-29117
blood vessel endothelium1.09e-2018
endothelium1.09e-2018
cardiovascular system endothelium1.09e-2018
simple squamous epithelium1.71e-1822
unilaminar epithelium1.98e-18148
squamous epithelium7.21e-1825
aorta3.32e-1621
aortic system3.32e-1621
anatomical conduit9.36e-16240
tube3.39e-15192
epithelial vesicle3.81e-1578
skeletal muscle tissue5.79e-1562
striated muscle tissue5.79e-1562
myotome5.79e-1562
muscle tissue2.89e-1464
musculature2.89e-1464
musculature of body2.89e-1464
blood vessel smooth muscle2.94e-1210
arterial system smooth muscle2.94e-1210
artery smooth muscle tissue2.94e-1210
aorta smooth muscle tissue2.94e-1210
somite3.80e-1271
presomitic mesoderm3.80e-1271
presumptive segmental plate3.80e-1271
dermomyotome3.80e-1271
trunk paraxial mesoderm3.80e-1271
mesoderm3.98e-12315
mesoderm-derived structure3.98e-12315
presumptive mesoderm3.98e-12315
paraxial mesoderm7.03e-1272
presumptive paraxial mesoderm7.03e-1272
dense mesenchyme tissue1.28e-1173
thoracic segment blood vessel1.30e-115
subclavian artery1.30e-115
endothelial tube1.61e-119
arterial system endothelium1.61e-119
endothelium of artery1.61e-119
cell layer2.31e-11309
trunk blood vessel2.98e-117
epithelium4.64e-11306
multilaminar epithelium2.78e-1083
lateral plate mesoderm3.17e-10203
trunk mesenchyme1.45e-09122
lymphatic vessel7.63e-098
lymph vasculature7.63e-098
lymphatic part of lymphoid system7.63e-098
anatomical cluster2.64e-08373
trunk5.89e-08199
smooth muscle tissue1.25e-0715
microcirculatory vessel5.74e-073
endothelium of capillary5.74e-073
capillary5.74e-073
lymphoid system6.70e-0710


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)
MA0003.10.0462779
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0156227
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.11.25271
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.0407081
MA0056.10
MA0057.10.369442
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.488375
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.065183
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.538456
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.11.00897
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.276317
MA0146.10.0127148
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.0553061
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.0758925
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.071478
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.10.0167306
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.20.00447823
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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
GATA2#262435.462113600094570.01328368362592780.0469805158892067
JUN#372535.362641082429860.01397261085589020.0490565604994896
MAX#414943.68717457657550.01360570643953340.048016976137547
POLR2A#543072.147453176558070.004747636447610280.0223592353423507
STAT3#677446.011122855516710.002255779156394480.0128115351196195



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1278&oldid=2569789"