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MCL coexpression mm9:687: Difference between revisions

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{{MCL_coexpression_mm9
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gyrus development;0.0262970470607571;16842!GO:0008301;DNA bending activity;0.036789649505362;16842!GO:0021766;hippocampus development;0.036789649505362;16842!GO:0048341;paraxial mesoderm formation;0.036789649505362;16842!GO:0045843;negative regulation of striated muscle development;0.036789649505362;16842!GO:0048340;paraxial mesoderm morphogenesis;0.036789649505362;16842!GO:0021761;limbic system development;0.036789649505362;16842!GO:0016202;regulation of striated muscle development;0.036789649505362;16842!GO:0048339;paraxial mesoderm development;0.036789649505362;16842!GO:0021543;pallium development;0.036789649505362;16842!GO:0003705;RNA polymerase II transcription factor activity, enhancer binding;0.0373162793455809;16842!GO:0006508;proteolysis;0.0373162793455809;30843,76560!GO:0030879;mammary gland development;0.0373162793455809;16842!GO:0030111;regulation of Wnt receptor signaling pathway;0.0373162793455809;16842!GO:0021537;telencephalon development;0.0373162793455809;16842!GO:0001707;mesoderm formation;0.0373162793455809;16842!GO:0048332;mesoderm morphogenesis;0.0373162793455809;16842!GO:0001890;placenta development;0.0373162793455809;16842!GO:0001704;formation of primary germ layer;0.0373162793455809;16842!GO:0001756;somitogenesis;0.0433140977382263;16842!GO:0042475;odontogenesis of dentine-containing teeth;0.0449942592133951;16842!GO:0042476;odontogenesis;0.045330154040783;16842!GO:0000151;ubiquitin ligase 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|gostat_on_MCL_coexpression=GO:0021542;dentate gyrus development;0.0262970470607571;16842!GO:0008301;DNA bending activity;0.036789649505362;16842!GO:0021766;hippocampus development;0.036789649505362;16842!GO:0048341;paraxial mesoderm formation;0.036789649505362;16842!GO:0045843;negative regulation of striated muscle development;0.036789649505362;16842!GO:0048340;paraxial mesoderm morphogenesis;0.036789649505362;16842!GO:0021761;limbic system development;0.036789649505362;16842!GO:0016202;regulation of striated muscle development;0.036789649505362;16842!GO:0048339;paraxial mesoderm development;0.036789649505362;16842!GO:0021543;pallium development;0.036789649505362;16842!GO:0003705;RNA polymerase II transcription factor activity, enhancer binding;0.0373162793455809;16842!GO:0006508;proteolysis;0.0373162793455809;30843,76560!GO:0030879;mammary gland development;0.0373162793455809;16842!GO:0030111;regulation of Wnt receptor signaling pathway;0.0373162793455809;16842!GO:0021537;telencephalon development;0.0373162793455809;16842!GO:0001707;mesoderm formation;0.0373162793455809;16842!GO:0048332;mesoderm morphogenesis;0.0373162793455809;16842!GO:0001890;placenta development;0.0373162793455809;16842!GO:0001704;formation of primary germ layer;0.0373162793455809;16842!GO:0001756;somitogenesis;0.0433140977382263;16842!GO:0042475;odontogenesis of dentine-containing teeth;0.0449942592133951;16842!GO:0042476;odontogenesis;0.045330154040783;16842!GO:0000151;ubiquitin ligase complex;0.0456363404987191;30843!GO:0035282;segmentation;0.0459165321860133;16842!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002370!1.69e-16!23;UBERON:0000974!1.69e-16!23;UBERON:0004807!1.69e-16!23;UBERON:0005058!1.69e-16!23;UBERON:0003351!1.69e-16!23;UBERON:0009113!1.69e-16!23;UBERON:0003295!1.69e-16!23;UBERON:0009722!1.69e-16!23;UBERON:0005562!1.69e-16!23;UBERON:0007690!1.69e-16!23;UBERON:0006562!1.38e-15!24;UBERON:0003408!1.38e-15!24;UBERON:0001557!1.38e-15!24;UBERON:0001042!1.38e-15!24;UBERON:0008814!1.38e-15!24;UBERON:0009145!1.38e-15!24;UBERON:0004177!3.07e-15!29;UBERON:0005057!3.07e-15!29;UBERON:0000991!1.91e-13!18;UBERON:0005564!1.91e-13!18;UBERON:0000072!2.92e-13!27;UBERON:0004176!2.50e-12!17;UBERON:0009196!2.50e-12!17;UBERON:0009117!2.50e-12!17;UBERON:0000077!1.27e-11!35;UBERON:0000473!2.77e-11!14;UBERON:0000065!4.90e-11!41;UBERON:0007811!8.33e-11!36;UBERON:0001004!1.25e-10!42;UBERON:0003135!2.48e-10!15;UBERON:0002193!5.50e-10!48;UBERON:0002405!5.50e-10!48;UBERON:0002390!7.51e-10!45;UBERON:0003061!7.51e-10!45;UBERON:0003101!1.68e-09!16;UBERON:0000079!1.68e-09!16;UBERON:0005156!2.35e-09!26;UBERON:0000990!2.35e-09!26;UBERON:0003133!4.27e-09!24;UBERON:0000063!4.59e-09!35;UBERON:0000926!8.82e-09!120;UBERON:0004120!8.82e-09!120;UBERON:0006603!8.82e-09!120;UBERON:0000153!3.65e-08!43;UBERON:0001048!7.36e-08!134
|tfbs_overrepresentation_for_novel_motifs=0.860199,0.588611,0.297937,0.360062,1.09907,0.373426,0.458558,1.27916,0.411053,0.479476,0.417132,0.447169,0.393382,0.470194,1.80389,0,0.656089,0.19356,0.736624,0.205418,0.732601,0.145076,0.469335,0.577226,0.304728,0.496413,0.349241,0.392919,0.238759,0.271461,0.989437,0.754912,0.560002,0.31333,0.214608,0.386349,0.184038,0.443753,0.166348,0.868806,0.196807,0.38461,0.130272,0.617704,0.249283,0.349801,0.578773,1.05036,0.255625,0.677281,0.639101,0.522137,0.935589,0.894161,0.911367,1.20022,0.695271,0.435119,0.101408,0.47505,0.735292,0.531188,0.433822,0.628155,0.487593,0.667546,2.37986,1.3932,0.730718,1.24673,1.40499,0.404236,0.03967,0.944464,1.09617,0.300089,0.313198,0.567793,0.718494,0.268962,0.80832,0.673009,0.529804,0.119727,0.830765,0.0593483,0.0149522,0.271714,0.583509,1.55487,1.11522,0.835661,1.80968,0.205117,0.490417,0.455999,0.777003,0.770215,0.57902,0.234357,0.184103,0.754637,0.87698,0.639679,0.638654,0.3842,0.696857,0.403887,0.273261,0.266818,0.315128,0.878738,0.743427,0.421988,1.12221,0.195318,0.0839537,0.363536,0.657356,0.534159,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,0.466292,0.760818,1.04463,0.207624,0.86025,0.353344,1.01535,0.48999,1.14365,0.0358067,0.329172,0.385921,1.09487,1.92247,1.5231,1.0508,1.27006,0.765172,0.632358,0.385031,0.581788,1.88287,0.331322,0.201635,0.275954,0.129005,0.895708,0.911723,0.489108,0.976367,0.523103,0.224422,0.319291,0.328917,1.1043,0.829923,0.722546,1.52068,0.629147,1.21106,0.53929,1.13282,0.0896551
|tfbs_overrepresentation_jaspar=MA0003.1;0.51522,MA0004.1;0.946922,MA0006.1;0.210471,MA0007.1;5.49209,MA0009.1;0.780842,MA0014.1;0.0870561,MA0017.1;0.233089,MA0019.1;0.603066,MA0024.1;0.737933,MA0025.1;1.01089,MA0027.1;2.42079,MA0028.1;0.625707,MA0029.1;0.716673,MA0030.1;0.723093,MA0031.1;0.688336,MA0038.1;0.496338,MA0040.1;0.79313,MA0041.1;0.291712,MA0042.1;0.279998,MA0043.1;0.875991,MA0046.1;0.816137,MA0048.1;0.509074,MA0050.1;0.396459,MA0051.1;0.504875,MA0052.1;0.801048,MA0055.1;1.21025,MA0056.1;0,MA0057.1;0.216209,MA0058.1;0.752621,MA0059.1;0.777514,MA0060.1;1.40918,MA0061.1;0.504772,MA0063.1;0,MA0066.1;0.485868,MA0067.1;1.12095,MA0068.1;0.22316,MA0069.1;0.801381,MA0070.1;0.791856,MA0071.1;0.395679,MA0072.1;0.783532,MA0073.1;0.0215953,MA0074.1;0.451832,MA0076.1;1.99258,MA0077.1;0.762273,MA0078.1;0.536502,MA0081.1;1.49375,MA0083.1;0.875209,MA0084.1;1.44691,MA0087.1;0.832758,MA0088.1;0.34573,MA0089.1;0,MA0090.1;0.329158,MA0091.1;0.372635,MA0092.1;0.329444,MA0093.1;0.642324,MA0095.1;0,MA0098.1;0,MA0100.1;0.440912,MA0101.1;0.292867,MA0103.1;0.242398,MA0105.1;0.632131,MA0106.1;0.543967,MA0107.1;0.237082,MA0108.2;0.625209,MA0109.1;0,MA0111.1;0.342068,MA0113.1;0.516916,MA0114.1;0.500166,MA0115.1;0.878749,MA0116.1;0.210297,MA0117.1;0.846964,MA0119.1;0.796817,MA0122.1;0.866511,MA0124.1;1.06819,MA0125.1;0.994853,MA0130.1;0,MA0131.1;3.6292,MA0132.1;0,MA0133.1;0,MA0135.1;0.911905,MA0136.1;0.470672,MA0139.1;0.385513,MA0140.1;0.440804,MA0141.1;0.259554,MA0142.1;0.674191,MA0143.1;1.31882,MA0144.1;0.169559,MA0145.1;0.163161,MA0146.1;0.412111,MA0147.1;0.530496,MA0148.1;0.375491,MA0149.1;0.2978,MA0062.2;2.83024,MA0035.2;0.44524,MA0039.2;0.204978,MA0138.2;0.590987,MA0002.2;0.123715,MA0137.2;0.257017,MA0104.2;0.828906,MA0047.2;0.495607,MA0112.2;0.163154,MA0065.2;0.373167,MA0150.1;0.346631,MA0151.1;0,MA0152.1;0.495709,MA0153.1;0.92832,MA0154.1;0.232525,MA0155.1;0.186607,MA0156.1;0.248865,MA0157.1;0.642984,MA0158.1;0,MA0159.1;0.550545,MA0160.1;0.378276,MA0161.1;0,MA0162.1;0.134999,MA0163.1;0.00834216,MA0164.1;0.471016,MA0080.2;0.237846,MA0018.2;0.480226,MA0099.2;0.584892,MA0079.2;0.0983396,MA0102.2;1.49914,MA0258.1;0.156336,MA0259.1;0.50935,MA0442.1;0
}}

Latest revision as of 15:43, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:21139249..21139266,+p1@uc007eor.1
Mm9::chr10:21139274..21139287,+p2@uc007eor.1
Mm9::chr13:44292827..44292838,-p@chr13:44292827..44292838
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Mm9::chr15:63302448..63302452,-p@chr15:63302448..63302452
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Mm9::chr1:125783911..125783934,-p@chr1:125783911..125783934
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Mm9::chr3:130815472..130815497,+p6@Lef1
Mm9::chr4:102786843..102786903,-p1@Wdr78
Mm9::chr4:122563323..122563339,-p7@Cap1
Mm9::chr4:147242717..147242731,-p3@Miip
Mm9::chr9:20447641..20447659,-p9@Fbxl12


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:0021542dentate gyrus development0.0262970470607571
GO:0008301DNA bending activity0.036789649505362
GO:0021766hippocampus development0.036789649505362
GO:0048341paraxial mesoderm formation0.036789649505362
GO:0045843negative regulation of striated muscle development0.036789649505362
GO:0048340paraxial mesoderm morphogenesis0.036789649505362
GO:0021761limbic system development0.036789649505362
GO:0016202regulation of striated muscle development0.036789649505362
GO:0048339paraxial mesoderm development0.036789649505362
GO:0021543pallium development0.036789649505362
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.0373162793455809
GO:0006508proteolysis0.0373162793455809
GO:0030879mammary gland development0.0373162793455809
GO:0030111regulation of Wnt receptor signaling pathway0.0373162793455809
GO:0021537telencephalon development0.0373162793455809
GO:0001707mesoderm formation0.0373162793455809
GO:0048332mesoderm morphogenesis0.0373162793455809
GO:0001890placenta development0.0373162793455809
GO:0001704formation of primary germ layer0.0373162793455809
GO:0001756somitogenesis0.0433140977382263
GO:0042475odontogenesis of dentine-containing teeth0.0449942592133951
GO:0042476odontogenesis0.045330154040783
GO:0000151ubiquitin ligase complex0.0456363404987191
GO:0035282segmentation0.0459165321860133



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
thymus1.69e-1623
neck1.69e-1623
respiratory system epithelium1.69e-1623
hemolymphoid system gland1.69e-1623
pharyngeal epithelium1.69e-1623
thymic region1.69e-1623
pharyngeal gland1.69e-1623
entire pharyngeal arch endoderm1.69e-1623
thymus primordium1.69e-1623
early pharyngeal endoderm1.69e-1623
pharynx1.38e-1524
gland of gut1.38e-1524
upper respiratory tract1.38e-1524
chordate pharynx1.38e-1524
pharyngeal arch system1.38e-1524
pharyngeal region of foregut1.38e-1524
hemopoietic organ3.07e-1529
immune organ3.07e-1529
gonad1.91e-1318
gonad primordium1.91e-1318
segment of respiratory tract2.92e-1327
external genitalia2.50e-1217
indifferent external genitalia2.50e-1217
indifferent gonad2.50e-1217
mixed endoderm/mesoderm-derived structure1.27e-1135
testis2.77e-1114
respiratory tract4.90e-1141
craniocervical region8.33e-1136
respiratory system1.25e-1042
male reproductive organ2.48e-1015
hemolymphoid system5.50e-1048
immune system5.50e-1048
hematopoietic system7.51e-1045
blood island7.51e-1045
male organism1.68e-0916
male reproductive system1.68e-0916
reproductive structure2.35e-0926
reproductive system2.35e-0926
reproductive organ4.27e-0924
organ segment4.59e-0935
mesoderm8.82e-09120
mesoderm-derived structure8.82e-09120
presumptive mesoderm8.82e-09120
anterior region of body3.65e-0843
primordium7.36e-08134


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)
MA0003.10.51522
MA0004.10.946922
MA0006.10.210471
MA0007.15.49209
MA0009.10.780842
MA0014.10.0870561
MA0017.10.233089
MA0019.10.603066
MA0024.10.737933
MA0025.11.01089
MA0027.12.42079
MA0028.10.625707
MA0029.10.716673
MA0030.10.723093
MA0031.10.688336
MA0038.10.496338
MA0040.10.79313
MA0041.10.291712
MA0042.10.279998
MA0043.10.875991
MA0046.10.816137
MA0048.10.509074
MA0050.10.396459
MA0051.10.504875
MA0052.10.801048
MA0055.11.21025
MA0056.10
MA0057.10.216209
MA0058.10.752621
MA0059.10.777514
MA0060.11.40918
MA0061.10.504772
MA0063.10
MA0066.10.485868
MA0067.11.12095
MA0068.10.22316
MA0069.10.801381
MA0070.10.791856
MA0071.10.395679
MA0072.10.783532
MA0073.10.0215953
MA0074.10.451832
MA0076.11.99258
MA0077.10.762273
MA0078.10.536502
MA0081.11.49375
MA0083.10.875209
MA0084.11.44691
MA0087.10.832758
MA0088.10.34573
MA0089.10
MA0090.10.329158
MA0091.10.372635
MA0092.10.329444
MA0093.10.642324
MA0095.10
MA0098.10
MA0100.10.440912
MA0101.10.292867
MA0103.10.242398
MA0105.10.632131
MA0106.10.543967
MA0107.10.237082
MA0108.20.625209
MA0109.10
MA0111.10.342068
MA0113.10.516916
MA0114.10.500166
MA0115.10.878749
MA0116.10.210297
MA0117.10.846964
MA0119.10.796817
MA0122.10.866511
MA0124.11.06819
MA0125.10.994853
MA0130.10
MA0131.13.6292
MA0132.10
MA0133.10
MA0135.10.911905
MA0136.10.470672
MA0139.10.385513
MA0140.10.440804
MA0141.10.259554
MA0142.10.674191
MA0143.11.31882
MA0144.10.169559
MA0145.10.163161
MA0146.10.412111
MA0147.10.530496
MA0148.10.375491
MA0149.10.2978
MA0062.22.83024
MA0035.20.44524
MA0039.20.204978
MA0138.20.590987
MA0002.20.123715
MA0137.20.257017
MA0104.20.828906
MA0047.20.495607
MA0112.20.163154
MA0065.20.373167
MA0150.10.346631
MA0151.10
MA0152.10.495709
MA0153.10.92832
MA0154.10.232525
MA0155.10.186607
MA0156.10.248865
MA0157.10.642984
MA0158.10
MA0159.10.550545
MA0160.10.378276
MA0161.10
MA0162.10.134999
MA0163.10.00834216
MA0164.10.471016
MA0080.20.237846
MA0018.20.480226
MA0099.20.584892
MA0079.20.0983396
MA0102.21.49914
MA0258.10.156336
MA0259.10.50935
MA0442.10
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