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Coexpression cluster:C288: Difference between revisions

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59066e-09,0.770935,0.0190757,0.0169194,0.678034,6.36729e-14,0.740157,0.996707,0.536578,0.00527163,0.00129042,0.669282,0.052053,0.797586,0.00555874,0.78582,0.923211,0.973867,0.987365,1.58742e-07,0.99075
|tfbs_overrepresentation_for_novel_motifs=0.187734,2.92497,1.22809,0.0482979,0.127862,0.0477764,2.53978,1.80574,0.631287,1.17757,0.0387673,0.093817,0.27968,0.90421,0.00884225,0.523756,0.557188,1.68783,3.35225,4.1674,0.0679789,3.84161,0.692796,0.0434843,0.740332,1.68402,2.03416,1.50405,0.00933964,4.1103,0.572243,0.613044,2.1502,2.75662,0.568643,0.0578036,0.00544639,0.048143,0.969575,1.27968,0.0308254,1.22057,0.496642,0.987991,2.88851,1.01671,0.0756589,0.0357945,0.153161,0.466455,0.111246,0.978976,0.236885,0.265995,0.380448,0.0717921,0.734811,1.23781,2.86095,1.72382,0.241178,0.560338,0.868795,0.516202,0.0841366,0.153548,0.451923,0.777092,0.207217,0.629532,0.796113,0.00150464,0.043542,0.37887,0.00331585,0.0692471,0.609549,0.491685,4.14193,0.0213533,0.116078,0.172987,0.0839853,0.00141861,0.338961,0.0398999,1.22007,0.724704,0.124382,0.869816,1.31498,0.318564,0.224958,0.12955,0.00907508,0.0652883,0.0496878,0.70632,0.126778,1.25856,0.476151,0.221225,0.249978,0.192812,0.882901,0.0375094,0.183029,0.522762,0.0225263,0.233904,0.192854,0.248074,3.01557,0.160677,1.22775,1.10144,0.0231409,0.311454,0.152221,1.49603,0.372357,2.49633,0.177649,0.0888831,0.585292,0.953974,0.253564,0.228277,0.406216,0.0209528,0.319081,0.0336539,0.417824,0.0874218,0.541892,2.29147,0.128182,0.0448706,0.505486,1.30792,0.919291,0.473972,0.0733598,1.29526,0.148046,0.0564945,0.429776,1.15268,8.16353,0.00263474,0.0665746,1.83927e-06,0.319367,0.255637,0.076425,6.57392,0.748034,2.04624,0.241999,0.0172189,0.472954,0.305602,0.20463,0.0177723,0.157161,0.0836473,0.0456429,0.0746798,1.35651
|tfbs_overrepresentation_for_novel_motifs=0.187734,2.92497,1.22809,0.0482979,0.127862,0.0477764,2.53978,1.80574,0.631287,1.17757,0.0387673,0.093817,0.27968,0.90421,0.00884225,0.523756,0.557188,1.68783,3.35225,4.1674,0.0679789,3.84161,0.692796,0.0434843,0.740332,1.68402,2.03416,1.50405,0.00933964,4.1103,0.572243,0.613044,2.1502,2.75662,0.568643,0.0578036,0.00544639,0.048143,0.969575,1.27968,0.0308254,1.22057,0.496642,0.987991,2.88851,1.01671,0.0756589,0.0357945,0.153161,0.466455,0.111246,0.978976,0.236885,0.265995,0.380448,0.0717921,0.734811,1.23781,2.86095,1.72382,0.241178,0.560338,0.868795,0.516202,0.0841366,0.153548,0.451923,0.777092,0.207217,0.629532,0.796113,0.00150464,0.043542,0.37887,0.00331585,0.0692471,0.609549,0.491685,4.14193,0.0213533,0.116078,0.172987,0.0839853,0.00141861,0.338961,0.0398999,1.22007,0.724704,0.124382,0.869816,1.31498,0.318564,0.224958,0.12955,0.00907508,0.0652883,0.0496878,0.70632,0.126778,1.25856,0.476151,0.221225,0.249978,0.192812,0.882901,0.0375094,0.183029,0.522762,0.0225263,0.233904,0.192854,0.248074,3.01557,0.160677,1.22775,1.10144,0.0231409,0.311454,0.152221,1.49603,0.372357,2.49633,0.177649,0.0888831,0.585292,0.953974,0.253564,0.228277,0.406216,0.0209528,0.319081,0.0336539,0.417824,0.0874218,0.541892,2.29147,0.128182,0.0448706,0.505486,1.30792,0.919291,0.473972,0.0733598,1.29526,0.148046,0.0564945,0.429776,1.15268,8.16353,0.00263474,0.0665746,1.83927e-06,0.319367,0.255637,0.076425,6.57392,0.748034,2.04624,0.241999,0.0172189,0.472954,0.305602,0.20463,0.0177723,0.157161,0.0836473,0.0456429,0.0746798,1.35651
|tfbs_overrepresentation_jaspar=MA0003.1;0.0587648,MA0004.1;0.0402493,MA0006.1;0.260623,MA0007.1;0.0350407,MA0009.1;1.43212,MA0014.1;0.397377,MA0017.1;1.5989,MA0019.1;0.0961252,MA0024.1;0.215619,MA0025.1;0.390923,MA0027.1;1.78493,MA0028.1;1.07942,MA0029.1;0.228475,MA0030.1;0.220816,MA0031.1;0.179572,MA0038.1;0.0763506,MA0040.1;0.232423,MA0041.1;0.0458367,MA0042.1;0.144754,MA0043.1;0.288758,MA0046.1;0.280609,MA0048.1;0.161044,MA0050.1;0.0367154,MA0051.1;0.0746188,MA0052.1;0.235047,MA0055.1;0.528171,MA0056.1;0,MA0057.1;0.632968,MA0058.1;0.207054,MA0059.1;2.73866,MA0060.1;0.00128055,MA0061.1;0.113084,MA0063.1;0,MA0066.1;1.95915,MA0067.1;0.54503,MA0068.1;1.10381,MA0069.1;0.277823,MA0070.1;0.269786,MA0071.1;0.0612473,MA0072.1;0.266579,MA0073.1;10.2894,MA0074.1;0.932417,MA0076.1;0.712335,MA0077.1;0.261111,MA0078.1;0.120524,MA0081.1;0.653785,MA0083.1;0.294032,MA0084.1;0.71238,MA0087.1;0.26484,MA0088.1;0.63336,MA0089.1;0,MA0090.1;0.251766,MA0091.1;0.65232,MA0092.1;0.550013,MA0093.1;0.00913161,MA0095.1;0,MA0098.1;0,MA0100.1;0.0821839,MA0101.1;0.00951035,MA0103.1;4.08666,MA0105.1;0.004814,MA0106.1;0.313513,MA0107.1;0.00331032,MA0108.2;0.177698,MA0109.1;0,MA0111.1;1.17936,MA0113.1;0.102012,MA0114.1;0.63276,MA0115.1;0.479539,MA0116.1;3.30546,MA0117.1;0.316417,MA0119.1;4.27332,MA0122.1;0.336089,MA0124.1;0.444822,MA0125.1;0.376666,MA0130.1;0,MA0131.1;0.130054,MA0132.1;0,MA0133.1;0,MA0135.1;0.310984,MA0136.1;0.0792895,MA0139.1;7.83341,MA0140.1;0.0602746,MA0141.1;0.0174792,MA0142.1;0.160525,MA0143.1;0.683741,MA0144.1;0.0493315,MA0145.1;0.752587,MA0146.1;0.79201,MA0147.1;1.26855,MA0148.1;0.0478476,MA0149.1;0.207563,MA0062.2;1.75519,MA0035.2;0.060018,MA0039.2;0.251059,MA0138.2;1.83069,MA0002.2;1.04619,MA0137.2;0.0115271,MA0104.2;0.862961,MA0047.2;0.08884,MA0112.2;2.6179,MA0065.2;6.96334,MA0150.1;1.0879,MA0151.1;0,MA0152.1;0.0626927,MA0153.1;0.363372,MA0154.1;2.13193,MA0155.1;0.479771,MA0156.1;0.0575313,MA0157.1;0.144843,MA0158.1;0,MA0159.1;2.88223,MA0160.1;0.0528624,MA0161.1;0,MA0162.1;0.173278,MA0163.1;6.4759,MA0164.1;0.10802,MA0080.2;0.0464655,MA0018.2;0.094969,MA0099.2;0.0628256,MA0079.2;2.05265,MA0102.2;0.74655,MA0258.1;1.31293,MA0259.1;0.0244741,MA0442.1;0
}}
}}

Revision as of 18:59, 22 January 2013


Full id: C288_Chondrocyte_Renal_Pericytes_Fibroblast_aorta_Smooth_Meningeal



Phase1 CAGE Peaks

Hg19::chrX:152760428..152760447,+p1@BGN
Hg19::chrX:152770059..152770066,+p33@BGN
Hg19::chrX:152770101..152770112,+p23@BGN
Hg19::chrX:152770151..152770173,+p11@BGN
Hg19::chrX:152770174..152770191,+p27@BGN
Hg19::chrX:152770200..152770258,+p4@BGN
Hg19::chrX:152770207..152770220,-p@chrX:152770207..152770220
-
Hg19::chrX:152770262..152770308,-p@chrX:152770262..152770308
-
Hg19::chrX:152770265..152770294,+p15@BGN
Hg19::chrX:152770299..152770310,+p13@BGN
Hg19::chrX:152770690..152770747,+p@chrX:152770690..152770747
+
Hg19::chrX:152770747..152770793,-p@chrX:152770747..152770793
-
Hg19::chrX:152771310..152771324,+p22@BGN
Hg19::chrX:152771355..152771373,+p17@BGN
Hg19::chrX:152771357..152771376,-p@chrX:152771357..152771376
-
Hg19::chrX:152771377..152771404,+p14@BGN
Hg19::chrX:152771413..152771438,+p6@BGN
Hg19::chrX:152771423..152771451,-p@chrX:152771423..152771451
-
Hg19::chrX:152771450..152771463,+p19@BGN
Hg19::chrX:152771465..152771514,-p@chrX:152771465..152771514
-
Hg19::chrX:152771488..152771513,+p21@BGN
Hg19::chrX:152771988..152772002,+p@chrX:152771988..152772002
+
Hg19::chrX:152772003..152772056,+p@chrX:152772003..152772056
+
Hg19::chrX:152772015..152772028,-p@chrX:152772015..152772028
-
Hg19::chrX:152772068..152772079,+p@chrX:152772068..152772079
+
Hg19::chrX:152772312..152772340,-p@chrX:152772312..152772340
-
Hg19::chrX:152772329..152772363,+p@chrX:152772329..152772363
+
Hg19::chrX:152772356..152772373,-p@chrX:152772356..152772373
-
Hg19::chrX:152772503..152772517,+p@chrX:152772503..152772517
+
Hg19::chrX:152772540..152772564,+p@chrX:152772540..152772564
+
Hg19::chrX:152772571..152772585,+p@chrX:152772571..152772585
+
Hg19::chrX:152772597..152772622,+p@chrX:152772597..152772622
+
Hg19::chrX:152773690..152773718,+p10@BGN
Hg19::chrX:152773762..152773796,+p9@BGN
Hg19::chrX:152773830..152773842,+p25@BGN
Hg19::chrX:152773922..152773952,+p16@BGN
Hg19::chrX:152773994..152774035,+p7@BGN
Hg19::chrX:152774081..152774113,+p5@BGN
Hg19::chrX:152774119..152774158,+p12@BGN
Hg19::chrX:152774177..152774196,-p5@CU678629
Hg19::chrX:152774185..152774199,+p8@BGN
Hg19::chrX:152774275..152774309,+p3@BGN
Hg19::chrX:152774321..152774336,+p26@BGN
Hg19::chrX:152774348..152774479,+p2@BGN
Hg19::chrX:152774354..152774382,-p1@CU678629


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:0030133transport vesicle0.032585658777817
GO:0005201extracellular matrix structural constituent0.032585658777817
GO:0016023cytoplasmic membrane-bound vesicle0.032699197658576
GO:0031988membrane-bound vesicle0.032699197658576
GO:0005578proteinaceous extracellular matrix0.032699197658576
GO:0031410cytoplasmic vesicle0.032699197658576
GO:0031982vesicle0.032699197658576



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 mesoderm1.37e-2383
vasculature2.95e-2278
vascular system2.95e-2278
circulatory system1.12e-20112
vessel1.43e-2068
epithelial tube open at both ends3.59e-2059
blood vessel3.59e-2059
blood vasculature3.59e-2059
vascular cord3.59e-2059
cardiovascular system8.47e-20109
artery2.39e-1942
arterial blood vessel2.39e-1942
arterial system2.39e-1942
systemic artery1.07e-1533
systemic arterial system1.07e-1533
epithelial tube1.33e-15117
muscle tissue3.86e-1364
musculature3.86e-1364
musculature of body3.86e-1364
skeletal muscle tissue6.21e-1362
striated muscle tissue6.21e-1362
myotome6.21e-1362
dense mesenchyme tissue2.69e-1173
primary circulatory organ3.89e-1127
epithelial vesicle4.98e-1178
paraxial mesoderm8.24e-1172
presumptive paraxial mesoderm8.24e-1172
anatomical conduit8.88e-11240
somite1.24e-1071
presomitic mesoderm1.24e-1071
presumptive segmental plate1.24e-1071
dermomyotome1.24e-1071
trunk paraxial mesoderm1.24e-1071
heart2.41e-1024
primitive heart tube2.41e-1024
primary heart field2.41e-1024
anterior lateral plate mesoderm2.41e-1024
heart tube2.41e-1024
heart primordium2.41e-1024
cardiac mesoderm2.41e-1024
cardiogenic plate2.41e-1024
heart rudiment2.41e-1024
tube2.76e-10192
aorta1.57e-0921
aortic system1.57e-0921
multilaminar epithelium3.15e-0883
mesenchyme5.06e-08160
entire embryonic mesenchyme5.06e-08160
trunk mesenchyme6.09e-08122
cell layer9.92e-08309
unilaminar epithelium3.91e-07148
anatomical cluster4.20e-07373
epithelium5.75e-07306


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)
MA0003.10.0587648
MA0004.10.0402493
MA0006.10.260623
MA0007.10.0350407
MA0009.11.43212
MA0014.10.397377
MA0017.11.5989
MA0019.10.0961252
MA0024.10.215619
MA0025.10.390923
MA0027.11.78493
MA0028.11.07942
MA0029.10.228475
MA0030.10.220816
MA0031.10.179572
MA0038.10.0763506
MA0040.10.232423
MA0041.10.0458367
MA0042.10.144754
MA0043.10.288758
MA0046.10.280609
MA0048.10.161044
MA0050.10.0367154
MA0051.10.0746188
MA0052.10.235047
MA0055.10.528171
MA0056.10
MA0057.10.632968
MA0058.10.207054
MA0059.12.73866
MA0060.10.00128055
MA0061.10.113084
MA0063.10
MA0066.11.95915
MA0067.10.54503
MA0068.11.10381
MA0069.10.277823
MA0070.10.269786
MA0071.10.0612473
MA0072.10.266579
MA0073.110.2894
MA0074.10.932417
MA0076.10.712335
MA0077.10.261111
MA0078.10.120524
MA0081.10.653785
MA0083.10.294032
MA0084.10.71238
MA0087.10.26484
MA0088.10.63336
MA0089.10
MA0090.10.251766
MA0091.10.65232
MA0092.10.550013
MA0093.10.00913161
MA0095.10
MA0098.10
MA0100.10.0821839
MA0101.10.00951035
MA0103.14.08666
MA0105.10.004814
MA0106.10.313513
MA0107.10.00331032
MA0108.20.177698
MA0109.10
MA0111.11.17936
MA0113.10.102012
MA0114.10.63276
MA0115.10.479539
MA0116.13.30546
MA0117.10.316417
MA0119.14.27332
MA0122.10.336089
MA0124.10.444822
MA0125.10.376666
MA0130.10
MA0131.10.130054
MA0132.10
MA0133.10
MA0135.10.310984
MA0136.10.0792895
MA0139.17.83341
MA0140.10.0602746
MA0141.10.0174792
MA0142.10.160525
MA0143.10.683741
MA0144.10.0493315
MA0145.10.752587
MA0146.10.79201
MA0147.11.26855
MA0148.10.0478476
MA0149.10.207563
MA0062.21.75519
MA0035.20.060018
MA0039.20.251059
MA0138.21.83069
MA0002.21.04619
MA0137.20.0115271
MA0104.20.862961
MA0047.20.08884
MA0112.22.6179
MA0065.26.96334
MA0150.11.0879
MA0151.10
MA0152.10.0626927
MA0153.10.363372
MA0154.12.13193
MA0155.10.479771
MA0156.10.0575313
MA0157.10.144843
MA0158.10
MA0159.12.88223
MA0160.10.0528624
MA0161.10
MA0162.10.173278
MA0163.16.4759
MA0164.10.10802
MA0080.20.0464655
MA0018.20.094969
MA0099.20.0628256
MA0079.22.05265
MA0102.20.74655
MA0258.11.31293
MA0259.10.0244741
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

No analysis results for this cluster

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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C288&oldid=2568799"