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MCL coexpression mm9:305: Difference between revisions

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{{MCL_coexpression_mm9
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type IV;1.0264030465721e-05;12829,12828!GO:0030935;sheet-forming collagen;1.0264030465721e-05;12829,12828!GO:0005578;proteinaceous extracellular matrix;8.95137449313822e-05;12829,12828,114249!GO:0030020;extracellular matrix structural constituent conferring tensile strength;0.000138789828107562;12829,12828!GO:0005581;collagen;0.000162683411100891;12829,12828!GO:0005201;extracellular matrix structural constituent;0.000286956639296994;12829,12828!GO:0022610;biological adhesion;0.000286956639296994;12829,12828,114249!GO:0007155;cell adhesion;0.000286956639296994;12829,12828,114249!GO:0005604;basement membrane;0.000286956639296994;12829,12828!GO:0006817;phosphate transport;0.000301909306294368;12829,12828!GO:0044420;extracellular matrix part;0.000519154444492749;12829,12828!GO:0015698;inorganic anion transport;0.00110422350252929;12829,12828!GO:0006820;anion transport;0.00143327435717329;12829,12828!GO:0030511;positive regulation of transforming growth factor beta receptor signaling pathway;0.00267637042317332;114249!GO:0044421;extracellular region part;0.00757457380666912;12829,12828,114249!GO:0017015;regulation of transforming growth factor beta receptor signaling pathway;0.00780308683473769;114249!GO:0016525;negative regulation of angiogenesis;0.0117466677160677;12828!GO:0001658;ureteric bud branching;0.0124794664858897;114249!GO:0005178;integrin binding;0.0144467409969544;114249!GO:0006811;ion transport;0.0159499003420278;12829,12828!GO:0045765;regulation of angiogenesis;0.0178160868730884;12828!GO:0001657;ureteric bud development;0.0181380269799052;114249!GO:0001656;metanephros development;0.0238822905630688;114249!GO:0007179;transforming growth factor beta receptor signaling pathway;0.0238822905630688;114249!GO:0032403;protein complex binding;0.0244182206755483;114249!GO:0048754;branching morphogenesis of a tube;0.0268993818387301;114249!GO:0001763;morphogenesis of a branching structure;0.0268993818387301;114249!GO:0007160;cell-matrix adhesion;0.0268993818387301;114249!GO:0009653;anatomical structure morphogenesis;0.0268993818387301;12828,114249!GO:0009967;positive regulation of signal transduction;0.0268993818387301;114249!GO:0031589;cell-substrate adhesion;0.0268993818387301;114249!GO:0001822;kidney development;0.0283830540434883;114249!GO:0001655;urogenital system development;0.0288995747536591;114249!GO:0007178;transmembrane receptor protein serine/threonine kinase signaling pathway;0.0288995747536591;114249!GO:0048513;organ development;0.0325487920399888;12828,114249!GO:0001525;angiogenesis;0.0463573022790878;12828!GO:0048731;system development;0.0463573022790878;12828,114249!GO:0035239;tube 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|gostat_on_MCL_coexpression=GO:0005587;collagen type IV;1.0264030465721e-05;12829,12828!GO:0030935;sheet-forming collagen;1.0264030465721e-05;12829,12828!GO:0005578;proteinaceous extracellular matrix;8.95137449313822e-05;12829,12828,114249!GO:0030020;extracellular matrix structural constituent conferring tensile strength;0.000138789828107562;12829,12828!GO:0005581;collagen;0.000162683411100891;12829,12828!GO:0005201;extracellular matrix structural constituent;0.000286956639296994;12829,12828!GO:0022610;biological adhesion;0.000286956639296994;12829,12828,114249!GO:0007155;cell adhesion;0.000286956639296994;12829,12828,114249!GO:0005604;basement membrane;0.000286956639296994;12829,12828!GO:0006817;phosphate transport;0.000301909306294368;12829,12828!GO:0044420;extracellular matrix part;0.000519154444492749;12829,12828!GO:0015698;inorganic anion transport;0.00110422350252929;12829,12828!GO:0006820;anion transport;0.00143327435717329;12829,12828!GO:0030511;positive regulation of transforming growth factor beta receptor signaling pathway;0.00267637042317332;114249!GO:0044421;extracellular region part;0.00757457380666912;12829,12828,114249!GO:0017015;regulation of transforming growth factor beta receptor signaling pathway;0.00780308683473769;114249!GO:0016525;negative regulation of angiogenesis;0.0117466677160677;12828!GO:0001658;ureteric bud branching;0.0124794664858897;114249!GO:0005178;integrin binding;0.0144467409969544;114249!GO:0006811;ion transport;0.0159499003420278;12829,12828!GO:0045765;regulation of angiogenesis;0.0178160868730884;12828!GO:0001657;ureteric bud development;0.0181380269799052;114249!GO:0001656;metanephros development;0.0238822905630688;114249!GO:0007179;transforming growth factor beta receptor signaling pathway;0.0238822905630688;114249!GO:0032403;protein complex binding;0.0244182206755483;114249!GO:0048754;branching morphogenesis of a tube;0.0268993818387301;114249!GO:0001763;morphogenesis of a branching structure;0.0268993818387301;114249!GO:0007160;cell-matrix adhesion;0.0268993818387301;114249!GO:0009653;anatomical structure morphogenesis;0.0268993818387301;12828,114249!GO:0009967;positive regulation of signal transduction;0.0268993818387301;114249!GO:0031589;cell-substrate adhesion;0.0268993818387301;114249!GO:0001822;kidney development;0.0283830540434883;114249!GO:0001655;urogenital system development;0.0288995747536591;114249!GO:0007178;transmembrane receptor protein serine/threonine kinase signaling pathway;0.0288995747536591;114249!GO:0048513;organ development;0.0325487920399888;12828,114249!GO:0001525;angiogenesis;0.0463573022790878;12828!GO:0048731;system development;0.0463573022790878;12828,114249!GO:0035239;tube morphogenesis;0.0482587627705669;114249!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005178!2.80e-13!17;UBERON:0005181!2.80e-13!17;UBERON:0002224!2.80e-13!17;UBERON:0000915!2.80e-13!17;UBERON:0008947!2.80e-13!17;UBERON:0003258!2.80e-13!17;UBERON:0002048!5.05e-13!14;UBERON:0000117!5.05e-13!14;UBERON:0000171!5.05e-13!14;UBERON:0000170!5.05e-13!14;UBERON:0005597!5.05e-13!14;UBERON:0000118!5.05e-13!14;UBERON:0005153!6.17e-10!17;UBERON:0002113!6.74e-09!14;UBERON:0003918!6.74e-09!14;UBERON:0011143!6.74e-09!14;UBERON:0005095!6.74e-09!14;UBERON:0007687!6.74e-09!14;UBERON:0000464!7.39e-09!57;UBERON:0009569!2.15e-08!66;UBERON:0005157!8.21e-08!20;UBERON:0003135!5.34e-07!15
|tfbs_overrepresentation_for_novel_motifs=0.282271,0.661951,0.0710623,0.338886,0.125245,0.111436,0.164473,0.286724,0.525465,0.00150871,1.36304,0.156977,0.140984,0.172248,0.141341,0,0.833764,0.28293,2.11393,0.461593,0.204835,0.042472,0.17167,0.123801,0.258457,0.19018,0.233256,0.389073,0.170987,0.66723,0.368848,0.390688,0.0277557,0.0294846,0.0355679,0.0134085,0.107578,0.469672,0.427954,0.0678345,1.23045,0.376228,0.964562,0.333507,0.127531,1.10422,0.249844,0.131897,0.414004,0.696619,0.296304,0.208297,0.419501,0.511069,0.526356,1.5954,0.183928,0.149174,0.0341937,0.175527,0.37428,0.214788,0.569573,0.287721,0.541628,0.318903,0.648538,0.976882,0.968919,0.836509,0.063053,0.301094,0.000600854,0.555978,0.00566569,0.00465613,1.43908,0.241622,0.946593,0.0575393,0.0556789,0.32329,0.612722,0.467951,0.455476,0.00576928,3.6649,0.274959,0.253413,1.13385,0.712592,0.459726,0.401262,0.130852,0.0193136,0.0728776,0.137297,0.403591,0.25003,2.08061,0.0253676,0.390457,0.495886,0.29676,0.295953,0.117743,0.342607,0.129587,0.0594702,0.206909,0.97238,1.24398,0.0579851,0.434758,0.719117,0.11984,0.452141,0.105758,0.31076,1.12635,0.560777,0.271955,1.06439,0.240971,0.769516,0.363346,0.169628,0.395657,0.647155,0.133722,0.481183,0.328832,0.620289,0.185736,0.739171,0.000460993,0.0869147,0.378248,0.693638,1.49553,1.10287,0.652839,0.199449,0.399329,0.291009,0.118235,0.702352,1.45635,1.03381,0.126902,0.458746,0.0114872,1.27598,0.636231,0.185128,0.584782,0.208987,0.990277,0.586076,0.0867803,0.702412,0.454746,0.953986,0.0785906,0.288496,0.180287,0.106601,0.472773,0.000257866
|tfbs_overrepresentation_jaspar=MA0003.1;0.00216423,MA0004.1;0.104042,MA0006.1;0.137005,MA0007.1;0.0963695,MA0009.1;1.06114,MA0014.1;0.122564,MA0017.1;3.09915,MA0019.1;0.73962,MA0024.1;0.37648,MA0025.1;0.616209,MA0027.1;1.99083,MA0028.1;0.0372733,MA0029.1;0.358857,MA0030.1;0.364159,MA0031.1;0.335674,MA0038.1;0.190128,MA0040.1;1.08391,MA0041.1;0.516309,MA0042.1;0.840167,MA0043.1;0.495015,MA0046.1;0.442826,MA0048.1;0.0477447,MA0050.1;0.394575,MA0051.1;0.570537,MA0052.1;0.429851,MA0055.1;0.0074089,MA0056.1;0,MA0057.1;0.494507,MA0058.1;0.216391,MA0059.1;0.499284,MA0060.1;0.355914,MA0061.1;1.87985,MA0063.1;0,MA0066.1;0.182901,MA0067.1;0.717937,MA0068.1;0.0419267,MA0069.1;0.430137,MA0070.1;0.421986,MA0071.1;0.124599,MA0072.1;0.414891,MA0073.1;0.0518555,MA0074.1;0.160032,MA0076.1;0.0491916,MA0077.1;0.396883,MA0078.1;0.218627,MA0081.1;0.551199,MA0083.1;0.494326,MA0084.1;1.02883,MA0087.1;0.457205,MA0088.1;0.0452858,MA0089.1;0,MA0090.1;0.0869074,MA0091.1;0.357896,MA0092.1;0.29369,MA0093.1;0.0399156,MA0095.1;0,MA0098.1;0,MA0100.1;0.152909,MA0101.1;0.241986,MA0103.1;0.700634,MA0105.1;0.331176,MA0106.1;0.63693,MA0107.1;0.168906,MA0108.2;0.285422,MA0109.1;0,MA0111.1;1.58736,MA0113.1;0.20458,MA0114.1;0.22556,MA0115.1;0.497446,MA0116.1;0.136803,MA0117.1;0.469566,MA0119.1;0.0688632,MA0122.1;0.486676,MA0124.1;1.6053,MA0125.1;0.601578,MA0130.1;0,MA0131.1;0.264933,MA0132.1;0,MA0133.1;0,MA0135.1;0.526836,MA0136.1;0.988731,MA0139.1;0.0490456,MA0140.1;0.152839,MA0141.1;0.197414,MA0142.1;0.324241,MA0143.1;0.215799,MA0144.1;0.0210846,MA0145.1;0.0542189,MA0146.1;0.00651565,MA0147.1;0.102772,MA0148.1;0.112635,MA0149.1;0.0709954,MA0062.2;0.348193,MA0035.2;0.155719,MA0039.2;0.255607,MA0138.2;0.259078,MA0002.2;0.139327,MA0137.2;0.194129,MA0104.2;0.0123672,MA0047.2;0.554999,MA0112.2;0.114958,MA0065.2;0.33798,MA0150.1;0.0963127,MA0151.1;0,MA0152.1;0.55517,MA0153.1;0.541494,MA0154.1;1.04275,MA0155.1;0.256374,MA0156.1;1.57074,MA0157.1;0.299365,MA0158.1;0,MA0159.1;0.026509,MA0160.1;0.366505,MA0161.1;0,MA0162.1;0.00364499,MA0163.1;0.130749,MA0164.1;2.24234,MA0080.2;1.0582,MA0018.2;0.179043,MA0099.2;0.254459,MA0079.2;0.00572422,MA0102.2;1.07954,MA0258.1;0.393446,MA0259.1;0.021443,MA0442.1;0
}}

Latest revision as of 15:04, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr19:23066908..23066911,-p@chr19:23066908..23066911
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Mm9::chr1:82474666..82474671,-p@chr1:82474666..82474671
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Mm9::chr1:82474739..82474751,-p@chr1:82474739..82474751
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Mm9::chr1:82479309..82479311,-p@chr1:82479309..82479311
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Mm9::chr1:82503103..82503129,-p@chr1:82503103..82503129
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Mm9::chr1:82583322..82583333,-p3@Col4a4
Mm9::chr1:82583335..82583354,-p2@Col4a4
Mm9::chr1:82583356..82583417,-p1@Col4a4
Mm9::chr1:82583431..82583438,-p6@Col4a4
Mm9::chr1:82583484..82583513,+p3@Col4a3
Mm9::chr1:82583517..82583563,+p2@Col4a3
Mm9::chr1:82583609..82583630,-p4@Col4a4
Mm9::chr1:82583632..82583654,-p5@Col4a4
Mm9::chr1:82583718..82583731,+p4@Col4a3
Mm9::chr1:82583748..82583767,+p1@Col4a3
Mm9::chr1:82583802..82583811,+p5@Col4a3
Mm9::chr1:82600621..82600632,+p@chr1:82600621..82600632
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Mm9::chr1:82600648..82600668,+p@chr1:82600648..82600668
+
Mm9::chr1:82672959..82672965,+p@chr1:82672959..82672965
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Mm9::chr1:82715507..82715513,+p@chr1:82715507..82715513
+
Mm9::chr3:132567778..132567830,+p@chr3:132567778..132567830
+
Mm9::chr3:132567829..132567947,-p@chr3:132567829..132567947
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Mm9::chr3:132569718..132569729,-p3@Npnt
Mm9::chr3:132611390..132611417,-p@chr3:132611390..132611417
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Mm9::chr3:132613131..132613145,-p1@Npnt
Mm9::chr5:45173720..45173732,-p@chr5:45173720..45173732
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Mm9::chr7:94429992..94429997,+p@chr7:94429992..94429997
+


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

GO IDGO nameFDR corrected p-value
GO:0005587collagen type IV1.0264030465721e-05
GO:0030935sheet-forming collagen1.0264030465721e-05
GO:0005578proteinaceous extracellular matrix8.95137449313822e-05
GO:0030020extracellular matrix structural constituent conferring tensile strength0.000138789828107562
GO:0005581collagen0.000162683411100891
GO:0005201extracellular matrix structural constituent0.000286956639296994
GO:0022610biological adhesion0.000286956639296994
GO:0007155cell adhesion0.000286956639296994
GO:0005604basement membrane0.000286956639296994
GO:0006817phosphate transport0.000301909306294368
GO:0044420extracellular matrix part0.000519154444492749
GO:0015698inorganic anion transport0.00110422350252929
GO:0006820anion transport0.00143327435717329
GO:0030511positive regulation of transforming growth factor beta receptor signaling pathway0.00267637042317332
GO:0044421extracellular region part0.00757457380666912
GO:0017015regulation of transforming growth factor beta receptor signaling pathway0.00780308683473769
GO:0016525negative regulation of angiogenesis0.0117466677160677
GO:0001658ureteric bud branching0.0124794664858897
GO:0005178integrin binding0.0144467409969544
GO:0006811ion transport0.0159499003420278
GO:0045765regulation of angiogenesis0.0178160868730884
GO:0001657ureteric bud development0.0181380269799052
GO:0001656metanephros development0.0238822905630688
GO:0007179transforming growth factor beta receptor signaling pathway0.0238822905630688
GO:0032403protein complex binding0.0244182206755483
GO:0048754branching morphogenesis of a tube0.0268993818387301
GO:0001763morphogenesis of a branching structure0.0268993818387301
GO:0007160cell-matrix adhesion0.0268993818387301
GO:0009653anatomical structure morphogenesis0.0268993818387301
GO:0009967positive regulation of signal transduction0.0268993818387301
GO:0031589cell-substrate adhesion0.0268993818387301
GO:0001822kidney development0.0283830540434883
GO:0001655urogenital system development0.0288995747536591
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0288995747536591
GO:0048513organ development0.0325487920399888
GO:0001525angiogenesis0.0463573022790878
GO:0048731system development0.0463573022790878
GO:0035239tube morphogenesis0.0482587627705669



Relative expression of the co-expression cluster over median <br>Analyst:




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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
thoracic cavity element2.80e-1317
thoracic segment organ2.80e-1317
thoracic cavity2.80e-1317
thoracic segment of trunk2.80e-1317
respiratory primordium2.80e-1317
endoderm of foregut2.80e-1317
lung5.05e-1314
respiratory tube5.05e-1314
respiration organ5.05e-1314
pair of lungs5.05e-1314
lung primordium5.05e-1314
lung bud5.05e-1314
epithelial bud6.17e-1017
kidney6.74e-0914
kidney mesenchyme6.74e-0914
upper urinary tract6.74e-0914
kidney rudiment6.74e-0914
kidney field6.74e-0914
anatomical space7.39e-0957
subdivision of trunk2.15e-0866
epithelial fold8.21e-0820
male reproductive organ5.34e-0715


TFBS overrepresentation<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)
MA0003.10.00216423
MA0004.10.104042
MA0006.10.137005
MA0007.10.0963695
MA0009.11.06114
MA0014.10.122564
MA0017.13.09915
MA0019.10.73962
MA0024.10.37648
MA0025.10.616209
MA0027.11.99083
MA0028.10.0372733
MA0029.10.358857
MA0030.10.364159
MA0031.10.335674
MA0038.10.190128
MA0040.11.08391
MA0041.10.516309
MA0042.10.840167
MA0043.10.495015
MA0046.10.442826
MA0048.10.0477447
MA0050.10.394575
MA0051.10.570537
MA0052.10.429851
MA0055.10.0074089
MA0056.10
MA0057.10.494507
MA0058.10.216391
MA0059.10.499284
MA0060.10.355914
MA0061.11.87985
MA0063.10
MA0066.10.182901
MA0067.10.717937
MA0068.10.0419267
MA0069.10.430137
MA0070.10.421986
MA0071.10.124599
MA0072.10.414891
MA0073.10.0518555
MA0074.10.160032
MA0076.10.0491916
MA0077.10.396883
MA0078.10.218627
MA0081.10.551199
MA0083.10.494326
MA0084.11.02883
MA0087.10.457205
MA0088.10.0452858
MA0089.10
MA0090.10.0869074
MA0091.10.357896
MA0092.10.29369
MA0093.10.0399156
MA0095.10
MA0098.10
MA0100.10.152909
MA0101.10.241986
MA0103.10.700634
MA0105.10.331176
MA0106.10.63693
MA0107.10.168906
MA0108.20.285422
MA0109.10
MA0111.11.58736
MA0113.10.20458
MA0114.10.22556
MA0115.10.497446
MA0116.10.136803
MA0117.10.469566
MA0119.10.0688632
MA0122.10.486676
MA0124.11.6053
MA0125.10.601578
MA0130.10
MA0131.10.264933
MA0132.10
MA0133.10
MA0135.10.526836
MA0136.10.988731
MA0139.10.0490456
MA0140.10.152839
MA0141.10.197414
MA0142.10.324241
MA0143.10.215799
MA0144.10.0210846
MA0145.10.0542189
MA0146.10.00651565
MA0147.10.102772
MA0148.10.112635
MA0149.10.0709954
MA0062.20.348193
MA0035.20.155719
MA0039.20.255607
MA0138.20.259078
MA0002.20.139327
MA0137.20.194129
MA0104.20.0123672
MA0047.20.554999
MA0112.20.114958
MA0065.20.33798
MA0150.10.0963127
MA0151.10
MA0152.10.55517
MA0153.10.541494
MA0154.11.04275
MA0155.10.256374
MA0156.11.57074
MA0157.10.299365
MA0158.10
MA0159.10.026509
MA0160.10.366505
MA0161.10
MA0162.10.00364499
MA0163.10.130749
MA0164.12.24234
MA0080.21.0582
MA0018.20.179043
MA0099.20.254459
MA0079.20.00572422
MA0102.21.07954
MA0258.10.393446
MA0259.10.021443
MA0442.10
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