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Coexpression cluster:C352: Difference between revisions

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{{Coexpression_clusters
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67808,0.000123023,0.0435091,0.351393,0.547412,0.911679,0.0233073,8.94677e-10,0.000859961,0.990073,0.0243261,6.35023e-05,0.35058,0.0783028,0.728221,3.65431e-06,0.538955,0.121664,0.966143,0.00214329,6.59149e-16,0.260899,0.00738092,0.621098,0.275665,0.023498,0.903667,0.00871296,2.53212e-09,0.858361,7.24862e-09,1.0274e-10,2.31373e-07,0.036643,2.54061e-07,1.80119e-08,0.0582093,0.720097,7.13446e-07,6.7926e-14,0.00525918,0.00129207,2.38005e-07,0.0327993,0.416254,1.84986e-09,3.07517e-06,0.0175211,1.37341e-10,0.046682,0.232344,0.00135909,3.44394e-07,0.00304695,8.15753e-09,0.306369,0.18921,2.83807e-07,0.00211755,0.0468678,2.79197e-15,2.945e-05,0.393697,0.00078991,1.15179e-12,1.20023e-05,1.18547e-07,0.0235172,0.0472175,0.00139998,0.881194,3.98672e-12,0.238385,0.0283809,0.00152655,7.64771e-13,2.19278e-17,0.00187181,0.00074233,4.43795e-06,2.0567e-08,0.0334166,3.92469e-14,0.754369,7.23725e-10,0.297735,0.648262,0.00334444,5.776e-08,3.79057e-08,0.140422,0.247352,0.0655401,0.000270843,1.81473e-05,4.34525e-09,0.171073,0.0140137,0.11791,0.138341,0.0283435,0.0236049,0.0128236,5.35855e-16,0.00100199,0.342114,0.517823,0.435515,0.0141838,5.01148e-07,8.50846e-06,2.25524e-14,0.000552988,9.01316e-05,2.58196e-09,0.706129,0.480575,0.00146683,0.0029007,2.00113e-18,5.96641e-06,0.170076,2.97051e-07,0.35672,0.626695,4.20794e-06,0.825224,5.40964e-09,0.0175176,1.05332e-16,3.15612e-06,9.59918e-05,1.44704e-08,0.618032,6.78975e-12,0.0997612,0.0465818,3.05221e-12,0.08328,9.13603e-07,0.5892,0.378429,7.64912e-10,2.30568e-08,7.64901e-12,5.63419e-09,0.477042,1.21235e-13,1.57782e-08,5.03979e-07,2.75528e-05,0.01596,0.503577,1.47217e-06,1.21575e-12,0.662967,0.000207374,1.35728e-19,0.000302415,4.59563e-10,0.599634,0.0361424,8.93041e-17,0.0219163,0.118483,8.81534e-05,0.057443,0.0735743,0.0220574,5.73146e-10,0.0178713,4.87992e-07,0.0744411,0.00265858,0.188946,4.44475e-08,2.03208e-05,8.29208e-07,0.000588915,0.505401,0.0319373,0.000957056,0.570889,0.183655,0.708612,0.381958,0.522497,8.39584e-05,0.329234,0.0716238,0.00367222,9.82564e-16,0.030944,3.45287e-09,0.804118,0.229685,1.56572e-22,0.00318939,6.33601e-09,4.2246e-05,0.0963476,1.06142e-10,0.00116055,3.93719e-05,2.87554e-05,2.6449e-05,0.00103194,0.215045,8.4679e-21,1.42827e-17,1.06044e-07,9.87609e-06,1.35812e-14,0.507056,0.00228586,6.77478e-20,0.000568829,8.25072e-05,0.688631,0.000351951,2.66847e-10,0.138379,0.000756091,9.17713e-19,0.292358,1.14437e-25,0.000861331,0.01654,1.40103e-06,0.0011286,0.116069,0.000209389,0.00858427,0.00779797,0.678885,9.62067e-26,0.0586174,0.838816,0.479479,6.11294e-09,0.0393951,0.0549205|tfbs_overrepresentation_for_novel_motifs=0.163367,0.0184166,1.90849,0.322944,1.20717,0.659968,0.425001,0.405405,0.397494,0.0344319,0.082933,0.16234,0.00338127,0.130546,2.63802,0.920836,0.283109,0.932143,0.494272,0.0698996,0.156113,0.00903637,0.0933127,0.813155,0.203595,0.176305,0.113263,0.307965,1.2231,0.689974,0.0733939,0.310643,1.09587,0.453331,0.0203044,0.495875,0.0196487,0.0975929,0.901731,0.190499,0.695012,1.3165,0.208384,2.62443,0.951185,0.0500962,0.426563,0.078127,0.55157,0.120364,0.185267,0.443561,0.00453998,0.370484,0.497309,0.818987,1.68613,0.114516,1.22346,2.39856,0.906297,0.138926,0.399043,0.262912,0.14927,0.238513,0.574343,0.913986,0.302792,0.761456,0.221248,0.0406816,0.0169579,0.495593,0.0602122,1.09014,0.195495,0.250834,0.300348,0.43599,1.36826,0.26214,0.149063,0.23628,0.451923,0.0200528,15.6672,0.170225,0.20212,1.00897,0.65804,0.429389,2.36589,0.534591,0.0284506,0.175805,0.720844,0.356655,0.20516,0.242749,2.11844,0.319139,0.352258,0.779618,0.652132,0.0809099,0.27418,0.128645,0.0553809,0.0243978,0.0435431,0.350081,0.347873,0.0872186,2.53532,1.82178,0.001964,0.254175,0.236884,1.53747,0.488501,1.10049,0.0957026,0.155712,0.715288,0.251373,0.133408,0.327313,0.525232,0.177167,0.429962,1.93449,0.537753,0.910989,1.60706,2.12136,0.530997,0.0925536,0.631317,1.45283,1.05945,0.597865,0.134374,0.353873,0.231743,0.110137,0.220337,1.29622,1.81079,0.0116437,0.156868,0.0107589,0.430278,1.90824,0.138651,0.789951,0.559715,0.484298,2.20979,0.0454339,0.596781,0.414981,0.299757,0.0465029,0.242939,0.454322,0.137254,2.63169,0.0125879|tfbs_overrepresentation_jaspar=MA0003.1;5.47209e-05,MA0004.1;0.288849,MA0006.1;0.279119,MA0007.1;0.0768943,MA0009.1;0.395891,MA0014.1;0.000997844,MA0017.1;0.350881,MA0019.1;0.165418,MA0024.1;0.312615,MA0025.1;0.508683,MA0027.1;1.93196,MA0028.1;0.130296,MA0029.1;0.327543,MA0030.1;0.853787,MA0031.1;0.743626,MA0038.1;0.846563,MA0040.1;0.332103,MA0041.1;0.0940493,MA0042.1;0.0792314,MA0043.1;0.39615,MA0046.1;0.386991,MA0048.1;0.0519666,MA0050.1;0.0796249,MA0051.1;0.136135,MA0052.1;0.335128,MA0055.1;0.000511248,MA0056.1;0,MA0057.1;0.046597,MA0058.1;0.0469637,MA0059.1;0.0465255,MA0060.1;0.00694078,MA0061.1;0.00444477,MA0063.1;0,MA0066.1;1.36932,MA0067.1;1.61394,MA0068.1;0.109053,MA0069.1;0.383853,MA0070.1;1.73772,MA0071.1;1.79596,MA0072.1;0.371146,MA0073.1;2.65178,MA0074.1;0.135707,MA0076.1;0.0525452,MA0077.1;2.56671,MA0078.1;1.71043,MA0081.1;0.397764,MA0083.1;1.03816,MA0084.1;0.847335,MA0087.1;0.369175,MA0088.1;0.00383201,MA0089.1;0,MA0090.1;0.461949,MA0091.1;2.71083,MA0092.1;3.09058,MA0093.1;0.0285794,MA0095.1;0,MA0098.1;0,MA0100.1;0.449302,MA0101.1;0.029437,MA0103.1;0.108135,MA0105.1;0.000377448,MA0106.1;0.949623,MA0107.1;0.0137208,MA0108.2;0.738478,MA0109.1;0,MA0111.1;0.0631734,MA0113.1;0.173209,MA0114.1;0.0128943,MA0115.1;0.603788,MA0116.1;0.176555,MA0117.1;0.427006,MA0119.1;1.01768,MA0122.1;0.44876,MA0124.1;0.566745,MA0125.1;0.493194,MA0130.1;0,MA0131.1;0.2093,MA0132.1;0,MA0133.1;0,MA0135.1;0.420972,MA0136.1;0.142619,MA0139.1;0.00355142,MA0140.1;4.66309,MA0141.1;0.17465,MA0142.1;0.247045,MA0143.1;0.173319,MA0144.1;0.144799,MA0145.1;0.374132,MA0146.1;0.000148203,MA0147.1;0.0696007,MA0148.1;0.321092,MA0149.1;0.110599,MA0062.2;0.16278,MA0035.2;1.78051,MA0039.2;0.000117436,MA0138.2;0.198014,MA0002.2;0.0316769,MA0137.2;0.136268,MA0104.2;0.00686015,MA0047.2;0.919009,MA0112.2;0.0756164,MA0065.2;0.0455466,MA0150.1;0.783414,MA0151.1;0,MA0152.1;0.119196,MA0153.1;0.478697,MA0154.1;0.37603,MA0155.1;0.200872,MA0156.1;0.0345163,MA0157.1;0.645687,MA0158.1;0,MA0159.1;0.358854,MA0160.1;0.104733,MA0161.1;0,MA0162.1;8.26733e-05,MA0163.1;0.000379398,MA0164.1;0.181076,MA0080.2;0.0286016,MA0018.2;0.163878,MA0099.2;0.379875,MA0079.2;3.22092e-07,MA0102.2;0.88257,MA0258.1;1.02444,MA0259.1;0.378383,MA0442.1;0}}
|full_id=C352_heart_mesenchymal_Skeletal_Pericytes_left_skeletal_Myoblast
|id=C352
}}

Latest revision as of 11:21, 17 September 2013


Full id: C352_heart_mesenchymal_Skeletal_Pericytes_left_skeletal_Myoblast



Phase1 CAGE Peaks

Hg19::chr15:35082546..35082553,-p@chr15:35082546..35082553
-
Hg19::chr15:35082559..35082571,-p@chr15:35082559..35082571
-
Hg19::chr15:35082596..35082633,-p@chr15:35082596..35082633
-
Hg19::chr15:35082635..35082647,-p@chr15:35082635..35082647
-
Hg19::chr15:35083345..35083358,-p@chr15:35083345..35083358
-
Hg19::chr15:35083365..35083406,-p@chr15:35083365..35083406
-
Hg19::chr15:35083378..35083389,+p@chr15:35083378..35083389
+
Hg19::chr15:35083404..35083435,+p@chr15:35083404..35083435
+
Hg19::chr15:35083408..35083427,-p@chr15:35083408..35083427
-
Hg19::chr15:35083428..35083456,-p@chr15:35083428..35083456
-
Hg19::chr15:35083484..35083499,-p@chr15:35083484..35083499
-
Hg19::chr15:35084289..35084305,+p@chr15:35084289..35084305
+
Hg19::chr15:35084319..35084350,-p@chr15:35084319..35084350
-
Hg19::chr15:35084352..35084363,-p@chr15:35084352..35084363
-
Hg19::chr15:35084365..35084388,-p@chr15:35084365..35084388
-
Hg19::chr15:35084404..35084427,-p@chr15:35084404..35084427
-
Hg19::chr15:35084467..35084485,-p@chr15:35084467..35084485
-
Hg19::chr15:35084643..35084652,-p9@ACTC1
Hg19::chr15:35084709..35084723,-p3@ACTC1
Hg19::chr15:35084738..35084747,-p6@ACTC1
Hg19::chr15:35085532..35085570,+p@chr15:35085532..35085570
+
Hg19::chr15:35085564..35085575,-p@chr15:35085564..35085575
-
Hg19::chr15:35085577..35085600,-p@chr15:35085577..35085600
-
Hg19::chr15:35085699..35085713,-p@chr15:35085699..35085713
-
Hg19::chr15:35085733..35085773,-p@chr15:35085733..35085773
-
Hg19::chr15:35086926..35086948,-p4@ACTC1
Hg19::chr15:35086988..35086997,-p7@ACTC1
Hg19::chr15:35087019..35087042,-p5@ACTC1
Hg19::chr15:35087544..35087555,-p@chr15:35087544..35087555
-
Hg19::chr15:35087742..35087757,-p1@ACTC1
Hg19::chr17:46824779..46824780,+p@chr17:46824779..46824780
+
Hg19::chr1:116311404..116311413,-p5@CASQ2


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:0003012muscle system process0.00118410366038205
GO:0006936muscle contraction0.00118410366038205
GO:0055013cardiac muscle cell development0.00148651830919581
GO:0055003cardiac myofibril assembly0.00148651830919581
GO:0030240muscle thin filament assembly0.0023783942879532
GO:0014866skeletal myofibril assembly0.00297294910149137
GO:0033018sarcoplasmic reticulum lumen0.00339760610633285
GO:0030239myofibril assembly0.003963640412321
GO:0055002striated muscle cell development0.003963640412321
GO:0055001muscle cell development0.003963640412321
GO:0048644muscle morphogenesis0.003963640412321
GO:0055008cardiac muscle morphogensis0.003963640412321
GO:0048628myoblast maturation0.00457329660360077
GO:0048627myoblast development0.0046712270532563
GO:0005790smooth endoplasmic reticulum0.0047560884407044
GO:0051146striated muscle cell differentiation0.00594467296637925
GO:0031674I band0.00594467296637925
GO:0048513organ development0.00632426293506344
GO:0031032actomyosin structure organization and biogenesis0.00657004109864965
GO:0016528sarcoplasm0.00675451458088324
GO:0016529sarcoplasmic reticulum0.00675451458088324
GO:0005884actin filament0.00675451458088324
GO:0045445myoblast differentiation0.00697750176213793
GO:0003008system process0.00792261325662865
GO:0006941striated muscle contraction0.00792261325662865
GO:0048731system development0.00792261325662865
GO:0007015actin filament organization0.00792261325662865
GO:0048741skeletal muscle fiber development0.00792261325662865
GO:0048747muscle fiber development0.00792261325662865
GO:0008016regulation of heart contraction0.00792261325662865
GO:0008307structural constituent of muscle0.00792261325662865
GO:0048469cell maturation0.00792261325662865
GO:0042692muscle cell differentiation0.00792261325662865
GO:0060047heart contraction0.00792261325662865
GO:0003015heart process0.00792261325662865
GO:0030017sarcomere0.00792261325662865
GO:0030016myofibril0.00828686013085325
GO:0021700developmental maturation0.00828686013085325
GO:0048856anatomical structure development0.00891136460950274
GO:0044449contractile fiber part0.00891136460950274
GO:0005788endoplasmic reticulum lumen0.00905228140505522
GO:0043292contractile fiber0.00905228140505522
GO:0007519skeletal muscle development0.0092558117937575
GO:0007275multicellular organismal development0.0105081979714636
GO:0014706striated muscle development0.0116129870099692
GO:0007507heart development0.0121340393807748
GO:0008015blood circulation0.0197738601654783
GO:0003013circulatory system process0.0197738601654783
GO:0032502developmental process0.0200021875907591
GO:0007517muscle development0.0204030109931313
GO:0032501multicellular organismal process0.0250604849787898
GO:0030036actin cytoskeleton organization and biogenesis0.0276371402051042
GO:0044446intracellular organelle part0.0276371402051042
GO:0044422organelle part0.0276371402051042
GO:0030029actin filament-based process0.0280015573363784
GO:0051239regulation of multicellular organismal process0.0292923472237687
GO:0015629actin cytoskeleton0.030743784251895
GO:0044444cytoplasmic part0.0318106911880442
GO:0009887organ morphogenesis0.0362888411552046



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>disease_data<br>

Cell Type
Ontology termp-valuen
cell of skeletal muscle3.98e-179
skeletal muscle myoblast3.05e-084
adipocyte of breast5.59e-072
Disease
Ontology termp-valuen
heart disease4.12e-082


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)
MA0003.15.47209e-05
MA0004.10.288849
MA0006.10.279119
MA0007.10.0768943
MA0009.10.395891
MA0014.10.000997844
MA0017.10.350881
MA0019.10.165418
MA0024.10.312615
MA0025.10.508683
MA0027.11.93196
MA0028.10.130296
MA0029.10.327543
MA0030.10.853787
MA0031.10.743626
MA0038.10.846563
MA0040.10.332103
MA0041.10.0940493
MA0042.10.0792314
MA0043.10.39615
MA0046.10.386991
MA0048.10.0519666
MA0050.10.0796249
MA0051.10.136135
MA0052.10.335128
MA0055.10.000511248
MA0056.10
MA0057.10.046597
MA0058.10.0469637
MA0059.10.0465255
MA0060.10.00694078
MA0061.10.00444477
MA0063.10
MA0066.11.36932
MA0067.11.61394
MA0068.10.109053
MA0069.10.383853
MA0070.11.73772
MA0071.11.79596
MA0072.10.371146
MA0073.12.65178
MA0074.10.135707
MA0076.10.0525452
MA0077.12.56671
MA0078.11.71043
MA0081.10.397764
MA0083.11.03816
MA0084.10.847335
MA0087.10.369175
MA0088.10.00383201
MA0089.10
MA0090.10.461949
MA0091.12.71083
MA0092.13.09058
MA0093.10.0285794
MA0095.10
MA0098.10
MA0100.10.449302
MA0101.10.029437
MA0103.10.108135
MA0105.10.000377448
MA0106.10.949623
MA0107.10.0137208
MA0108.20.738478
MA0109.10
MA0111.10.0631734
MA0113.10.173209
MA0114.10.0128943
MA0115.10.603788
MA0116.10.176555
MA0117.10.427006
MA0119.11.01768
MA0122.10.44876
MA0124.10.566745
MA0125.10.493194
MA0130.10
MA0131.10.2093
MA0132.10
MA0133.10
MA0135.10.420972
MA0136.10.142619
MA0139.10.00355142
MA0140.14.66309
MA0141.10.17465
MA0142.10.247045
MA0143.10.173319
MA0144.10.144799
MA0145.10.374132
MA0146.10.000148203
MA0147.10.0696007
MA0148.10.321092
MA0149.10.110599
MA0062.20.16278
MA0035.21.78051
MA0039.20.000117436
MA0138.20.198014
MA0002.20.0316769
MA0137.20.136268
MA0104.20.00686015
MA0047.20.919009
MA0112.20.0756164
MA0065.20.0455466
MA0150.10.783414
MA0151.10
MA0152.10.119196
MA0153.10.478697
MA0154.10.37603
MA0155.10.200872
MA0156.10.0345163
MA0157.10.645687
MA0158.10
MA0159.10.358854
MA0160.10.104733
MA0161.10
MA0162.18.26733e-05
MA0163.10.000379398
MA0164.10.181076
MA0080.20.0286016
MA0018.20.163878
MA0099.20.379875
MA0079.23.22092e-07
MA0102.20.88257
MA0258.11.02444
MA0259.10.378383
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

This analysis result is provided for C0 - C305 clusters.

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