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Coexpression cluster:C490: Difference between revisions

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{{Coexpression_clusters
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35315,0.0909894,0.735819,0.101613,0.480054,5.31664e-06,0.0100058,0.341641,0.155721,0.001053,0.394885,0.0584527,0.519127,0.248521,0.355249,0.00325215,0.211091,0.0659004,2.11558e-05,0.00783034,0.00646224,2.40876e-21,0.00319188,0.305491,0.55838,0.413017,1.25758e-06,0.893989,0.0402622,0.037236,3.81308e-07,0.57887,0.00228715,1.28236e-12,2.28704e-05,0.000641179,0.630922,0.8189,0.0414001,0.541399,0.7894,0.47661,0.182512,0.746817,0.0120973,6.81341e-05,0.878628,0.0379892,0.00115607,4.71795e-05,3.21246e-07,0.00118416,0.08166,0.771273,0.0270705,0.111809,0.000895701,5.87027e-08,0.665645,0.143643,0.373236,0.0525096,0.490576,1.8835e-10,0.00843022,0.661664,0.455078,0.550605,5.92553e-10,0.0026736|tfbs_overrepresentation_for_novel_motifs=0.121383,0.946977,0.117015,0.212191,0.311264,0.606129,2.08609,0.154541,0.15167,0.441359,1.05757,0.301621,1.55205,0.717931,0.0927703,0.343795,0.450873,0.0660543,1.21435,1.48579,1.23153,0.0442178,0.592949,0.30387,0.14499,0.3198,4.60794,0.203923,2.18675,1.68314,0.5188,1.21322,0.0517705,0.0255973,0.0757346,0.355124,0.257826,0.6081,1.78132,0.897971,0.0750527,0.952768,0.128236,0.635814,0.0224227,0.135566,0.74012,0.182187,0.0472843,0.0952386,0.331306,0.27764,0.450364,0.551494,0.691633,0.261104,0.0975434,0.236404,0.0157984,0.664112,0.519357,0.270343,0.152232,0.426924,0.776161,0.397545,0.774525,1.12911,0.473932,0.971498,0.916943,0.161173,0.0433928,0.689771,0.101827,0.0900341,0.0784103,0.412445,3.06086,0.435465,2.17528,0.426001,0.284019,0.647925,0.642096,0.000343944,0.0920104,0.0691846,0.352635,1.2264,0.863265,0.617268,0.497892,0.201541,0.0939013,0.823441,0.281646,0.535841,0.356444,0.0569935,0.850238,0.492893,0.530844,0.45406,0.387815,0.186536,1.12127,0.711872,0.14483,0.602594,0.123668,0.528368,0.113792,0.570939,0.817503,1.38743,0.0177319,0.51682,1.80939,2.81255,0.682065,1.65361,0.209033,0.292875,0.923346,0.413094,0.726998,1.25439,1.71531,0.478363,1.49873,0.176632,0.73532,0.290252,0.875585,0.0134295,0.170663,0.204325,0.83506,1.67608,1.2779,0.799588,0.264127,0.532681,0.389296,0.23014,0.375295,1.51807,0.161595,0.197398,1.58509,0.0491612,0.618251,0.332338,0.269969,1.0011,0.339339,0.0861459,0.145027,0.127152,0.798435,0.601304,0.470393,0.805591,0.402913,0.774125,0.0484397,0.266654,0.00461972|tfbs_overrepresentation_jaspar=MA0003.1;0.325763,MA0004.1;0.193314,MA0006.1;1.06559,MA0007.1;3.87625,MA0009.1;1.41914,MA0014.1;0.00883981,MA0017.1;1.77541,MA0019.1;0.824541,MA0024.1;0.485346,MA0025.1;0.70396,MA0027.1;2.15732,MA0028.1;0.101383,MA0029.1;0.50258,MA0030.1;0.492344,MA0031.1;0.435419,MA0038.1;1.36368,MA0040.1;0.507819,MA0041.1;1.12415,MA0042.1;2.32519,MA0043.1;0.580321,MA0046.1;1.39813,MA0048.1;0.00932809,MA0050.1;0.184533,MA0051.1;0.266537,MA0052.1;0.511289,MA0055.1;0.66835,MA0056.1;0,MA0057.1;0.00844127,MA0058.1;0.12994,MA0059.1;0.405044,MA0060.1;0.0387582,MA0061.1;0.290613,MA0063.1;0,MA0066.1;0.270161,MA0067.1;0.879057,MA0068.1;0.0841176,MA0069.1;0.566544,MA0070.1;0.556335,MA0071.1;0.240074,MA0072.1;0.552241,MA0073.1;0.00449326,MA0074.1;0.265952,MA0076.1;0.139892,MA0077.1;0.545231,MA0078.1;0.346453,MA0081.1;0.129245,MA0083.1;0.586921,MA0084.1;1.06048,MA0087.1;0.550016,MA0088.1;0.0166254,MA0089.1;0,MA0090.1;0.149167,MA0091.1;0.195166,MA0092.1;0.504823,MA0093.1;0.0941737,MA0095.1;0,MA0098.1;0,MA0100.1;0.768006,MA0101.1;0.317957,MA0103.1;0.295078,MA0105.1;0.611869,MA0106.1;0.302526,MA0107.1;0.214555,MA0108.2;0.432749,MA0109.1;0,MA0111.1;0.15804,MA0113.1;2.32812,MA0114.1;0.793752,MA0115.1;0.805883,MA0116.1;0.0607301,MA0117.1;0.614633,MA0119.1;1.81557,MA0122.1;0.638621,MA0124.1;0.766407,MA0125.1;0.687166,MA0130.1;0,MA0131.1;0.361613,MA0132.1;0,MA0133.1;0,MA0135.1;0.60795,MA0136.1;0.27535,MA0139.1;1.57231,MA0140.1;0.238066,MA0141.1;0.128074,MA0142.1;0.407878,MA0143.1;0.315941,MA0144.1;1.60066,MA0145.1;0.150018,MA0146.1;0.00163852,MA0147.1;0.223797,MA0148.1;0.211171,MA0149.1;0.230803,MA0062.2;0.826291,MA0035.2;0.237534,MA0039.2;0.031743,MA0138.2;0.347473,MA0002.2;0.324376,MA0137.2;0.342218,MA0104.2;0.151208,MA0047.2;0.795472,MA0112.2;0.885708,MA0065.2;0.0221473,MA0150.1;0.145358,MA0151.1;0,MA0152.1;1.26389,MA0153.1;0.67139,MA0154.1;0.0342743,MA0155.1;0.0530942,MA0156.1;0.345664,MA0157.1;0.384449,MA0158.1;0,MA0159.1;0.840681,MA0160.1;0.222325,MA0161.1;0,MA0162.1;0.00688807,MA0163.1;0.0262946,MA0164.1;0.32594,MA0080.2;0.0942207,MA0018.2;0.30364,MA0099.2;0.243305,MA0079.2;5.95052e-06,MA0102.2;1.09681,MA0258.1;0.706831,MA0259.1;0.0662172,MA0442.1;0}}
|full_id=C490_Hair_Fibroblast_Synoviocyte_Olfactory_Preadipocyte_Endothelial_Osteoblast
|id=C490
}}

Latest revision as of 11:24, 17 September 2013


Full id: C490_Hair_Fibroblast_Synoviocyte_Olfactory_Preadipocyte_Endothelial_Osteoblast



Phase1 CAGE Peaks

Hg19::chr10:17271510..17271558,-p2@uc001iot.1
Hg19::chr10:17271561..17271615,-p4@uc001iot.1
Hg19::chr10:17271691..17271750,-p3@uc001iot.1
Hg19::chr10:17271757..17271791,-p6@uc001iot.1
Hg19::chr10:17271821..17271858,-p7@uc001iot.1
Hg19::chr10:17271866..17271897,-p5@uc001iot.1
Hg19::chr10:17272666..17272724,-p@chr10:17272666..17272724
-
Hg19::chr10:17275793..17275820,-p@chr10:17275793..17275820
-
Hg19::chr10:17275853..17275926,-p@chr10:17275853..17275926
-
Hg19::chr10:17276719..17276781,-p1@ENST00000456355
Hg19::chr10:17276801..17276827,-p5@ENST00000456355
Hg19::chr10:17277201..17277219,-p4@ENST00000456355
Hg19::chr10:17277221..17277254,-p3@ENST00000456355
Hg19::chr10:17277255..17277323,-p2@ENST00000456355
Hg19::chr10:17277365..17277388,-p@chr10:17277365..17277388
-
Hg19::chr10:17278325..17278353,-p@chr10:17278325..17278353
-
Hg19::chr10:17278354..17278389,-p@chr10:17278354..17278389
-
Hg19::chr10:17279298..17279334,-p1@CU674071
Hg19::chr10:17279393..17279433,-p2@CU674071


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>

Cell Type
Ontology termp-valuen
somatic cell8.10e-29588
multi fate stem cell3.24e-21427
somatic stem cell9.81e-20433
fibroblast6.00e-1976
stem cell4.17e-18441
mesodermal cell1.16e-17121
animal cell4.11e-15679
eukaryotic cell4.11e-15679
non-terminally differentiated cell1.11e-13106
muscle precursor cell2.89e-1358
myoblast2.89e-1358
multi-potent skeletal muscle stem cell2.89e-1358
contractile cell7.64e-1359
muscle cell1.00e-1255
electrically responsive cell1.17e-1161
electrically active cell1.17e-1161
smooth muscle cell9.28e-1143
smooth muscle myoblast9.28e-1143
connective tissue cell1.32e-10361
native cell4.81e-10722
motile cell2.76e-09386
vascular associated smooth muscle cell3.04e-0932
mesenchymal cell4.34e-09354
skin fibroblast7.27e-0923
defensive cell1.95e-0748
phagocyte1.95e-0748
stuff accumulating cell4.09e-0787
macrophage dendritic cell progenitor5.33e-0761
Uber Anatomy
Ontology termp-valuen
mesoderm4.91e-27315
mesoderm-derived structure4.91e-27315
presumptive mesoderm4.91e-27315
musculoskeletal system2.40e-21167
lateral plate mesoderm1.79e-19203
cardiovascular system1.67e-17109
vasculature2.65e-1778
vascular system2.65e-1778
circulatory system2.46e-16112
epithelial vesicle2.91e-1678
dense mesenchyme tissue5.62e-1673
somite7.07e-1671
presomitic mesoderm7.07e-1671
presumptive segmental plate7.07e-1671
dermomyotome7.07e-1671
trunk paraxial mesoderm7.07e-1671
paraxial mesoderm1.97e-1572
presumptive paraxial mesoderm1.97e-1572
splanchnic layer of lateral plate mesoderm6.07e-1583
vessel7.81e-1568
epithelial tube open at both ends7.14e-1459
blood vessel7.14e-1459
blood vasculature7.14e-1459
vascular cord7.14e-1459
multilaminar epithelium2.04e-1383
artery3.32e-1342
arterial blood vessel3.32e-1342
arterial system3.32e-1342
skeletal muscle tissue5.89e-1262
striated muscle tissue5.89e-1262
myotome5.89e-1262
muscle tissue2.80e-1164
musculature2.80e-1164
musculature of body2.80e-1164
connective tissue1.12e-10371
systemic artery3.50e-1033
systemic arterial system3.50e-1033
skeletal system3.93e-09100
unilaminar epithelium5.66e-09148
epithelial tube1.34e-08117
integument3.86e-0846
integumental system3.86e-0846
multi-cellular organism4.32e-08656
anatomical group1.00e-07625
anatomical system1.24e-07624
skeletal element2.15e-0790
mesenchyme3.15e-07160
entire embryonic mesenchyme3.15e-07160
adipose tissue4.63e-0714
aorta6.76e-0721
aortic system6.76e-0721


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)
MA0003.10.325763
MA0004.10.193314
MA0006.11.06559
MA0007.13.87625
MA0009.11.41914
MA0014.10.00883981
MA0017.11.77541
MA0019.10.824541
MA0024.10.485346
MA0025.10.70396
MA0027.12.15732
MA0028.10.101383
MA0029.10.50258
MA0030.10.492344
MA0031.10.435419
MA0038.11.36368
MA0040.10.507819
MA0041.11.12415
MA0042.12.32519
MA0043.10.580321
MA0046.11.39813
MA0048.10.00932809
MA0050.10.184533
MA0051.10.266537
MA0052.10.511289
MA0055.10.66835
MA0056.10
MA0057.10.00844127
MA0058.10.12994
MA0059.10.405044
MA0060.10.0387582
MA0061.10.290613
MA0063.10
MA0066.10.270161
MA0067.10.879057
MA0068.10.0841176
MA0069.10.566544
MA0070.10.556335
MA0071.10.240074
MA0072.10.552241
MA0073.10.00449326
MA0074.10.265952
MA0076.10.139892
MA0077.10.545231
MA0078.10.346453
MA0081.10.129245
MA0083.10.586921
MA0084.11.06048
MA0087.10.550016
MA0088.10.0166254
MA0089.10
MA0090.10.149167
MA0091.10.195166
MA0092.10.504823
MA0093.10.0941737
MA0095.10
MA0098.10
MA0100.10.768006
MA0101.10.317957
MA0103.10.295078
MA0105.10.611869
MA0106.10.302526
MA0107.10.214555
MA0108.20.432749
MA0109.10
MA0111.10.15804
MA0113.12.32812
MA0114.10.793752
MA0115.10.805883
MA0116.10.0607301
MA0117.10.614633
MA0119.11.81557
MA0122.10.638621
MA0124.10.766407
MA0125.10.687166
MA0130.10
MA0131.10.361613
MA0132.10
MA0133.10
MA0135.10.60795
MA0136.10.27535
MA0139.11.57231
MA0140.10.238066
MA0141.10.128074
MA0142.10.407878
MA0143.10.315941
MA0144.11.60066
MA0145.10.150018
MA0146.10.00163852
MA0147.10.223797
MA0148.10.211171
MA0149.10.230803
MA0062.20.826291
MA0035.20.237534
MA0039.20.031743
MA0138.20.347473
MA0002.20.324376
MA0137.20.342218
MA0104.20.151208
MA0047.20.795472
MA0112.20.885708
MA0065.20.0221473
MA0150.10.145358
MA0151.10
MA0152.11.26389
MA0153.10.67139
MA0154.10.0342743
MA0155.10.0530942
MA0156.10.345664
MA0157.10.384449
MA0158.10
MA0159.10.840681
MA0160.10.222325
MA0161.10
MA0162.10.00688807
MA0163.10.0262946
MA0164.10.32594
MA0080.20.0942207
MA0018.20.30364
MA0099.20.243305
MA0079.25.95052e-06
MA0102.21.09681
MA0258.10.706831
MA0259.10.0662172
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
CTCF#10664154.23178134716452.07084251553897e-081.47427894669649e-06
POLR2A#5430171.921405473762480.0001223247950698280.00164866166889893
SETDB1#986948.488426563791680.001086656417664370.0075983737014227
SP1#666792.699233284382530.002657474221002050.0146662412897502
ZBTB33#1000958.332822376310830.0002516066894176260.00271014346494301



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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