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MCL coexpression mm9:744: Difference between revisions

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|ontology_enrichment_uberon=
|ontology_enrichment_uberon=
|tfbs_overrepresentation_for_novel_motifs=0.321524,2.07281,0.807108,0.360062,0.200163,0.373426,0.458558,0.785038,0.816027,0.771958,0.417132,1.13606,0.124608,1.18563,0.214197,0,0.656089,0.19356,0.364803,0.451901,0.26524,0.60924,0.469335,0.577226,0.304728,1.24179,2.32939,0.392919,0.238759,0.967915,0.379806,0.754912,2.38223,0.31333,0.614653,16.3483,1.03506,0.443753,1.53464,13.3247,0.196807,0.999982,0.56316,0.215898,0.673106,0.349801,1.41649,0.407653,0.479635,0.677281,0.639101,0.522137,0.259389,0.894161,0.911367,0.47699,0.249055,0.435119,0.68053,0.47505,0.735292,0.531188,0.433822,0.628155,0.487593,0.667546,1.04613,1.3932,0.730718,1.24673,0.76885,0.404236,0.03967,0.944464,0.659328,0.623453,0.0942164,0.567793,0.718494,0.268962,0.80832,0.673009,0.529804,0.764135,0.830765,0.318393,0.0697823,0.271714,0.583509,1.55487,1.11522,0.835661,0.767462,0.205117,0.490417,0.149272,0.122617,0.770215,0.57902,0.234357,0.541671,0.754637,0.87698,0.639679,0.638654,0.999084,0.696857,0.403887,0.273261,0.266818,0.315128,0.878738,0.26996,0.421988,1.12221,0.195318,0.212667,0.953611,0.657356,0.181004,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,0.466292,0.760818,1.04463,0.207624,0.86025,0.931072,1.01535,0.48999,1.14365,0.142597,0.329172,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,0.385031,0.581788,1.88287,0.882109,0.201635,0.0806411,0.0316649,0.895708,1.46114,0.489108,0.976367,0.523103,0.224422,0.319291,0.328917,1.1043,0.829923,0.722546,0.313083,1.52228,1.21106,0.18312,0.445669,0.19482
|tfbs_overrepresentation_for_novel_motifs=0.321524,2.07281,0.807108,0.360062,0.200163,0.373426,0.458558,0.785038,0.816027,0.771958,0.417132,1.13606,0.124608,1.18563,0.214197,0,0.656089,0.19356,0.364803,0.451901,0.26524,0.60924,0.469335,0.577226,0.304728,1.24179,2.32939,0.392919,0.238759,0.967915,0.379806,0.754912,2.38223,0.31333,0.614653,16.3483,1.03506,0.443753,1.53464,13.3247,0.196807,0.999982,0.56316,0.215898,0.673106,0.349801,1.41649,0.407653,0.479635,0.677281,0.639101,0.522137,0.259389,0.894161,0.911367,0.47699,0.249055,0.435119,0.68053,0.47505,0.735292,0.531188,0.433822,0.628155,0.487593,0.667546,1.04613,1.3932,0.730718,1.24673,0.76885,0.404236,0.03967,0.944464,0.659328,0.623453,0.0942164,0.567793,0.718494,0.268962,0.80832,0.673009,0.529804,0.764135,0.830765,0.318393,0.0697823,0.271714,0.583509,1.55487,1.11522,0.835661,0.767462,0.205117,0.490417,0.149272,0.122617,0.770215,0.57902,0.234357,0.541671,0.754637,0.87698,0.639679,0.638654,0.999084,0.696857,0.403887,0.273261,0.266818,0.315128,0.878738,0.26996,0.421988,1.12221,0.195318,0.212667,0.953611,0.657356,0.181004,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,0.466292,0.760818,1.04463,0.207624,0.86025,0.931072,1.01535,0.48999,1.14365,0.142597,0.329172,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,0.385031,0.581788,1.88287,0.882109,0.201635,0.0806411,0.0316649,0.895708,1.46114,0.489108,0.976367,0.523103,0.224422,0.319291,0.328917,1.1043,0.829923,0.722546,0.313083,1.52228,1.21106,0.18312,0.445669,0.19482
|tfbs_overrepresentation_jaspar=MA0003.1;1.86959,MA0004.1;0.360508,MA0006.1;0.604851,MA0007.1;0.346734,MA0009.1;1.83729,MA0014.1;1.80909,MA0017.1;0.658116,MA0019.1;0.603066,MA0024.1;0.737933,MA0025.1;1.01089,MA0027.1;2.42079,MA0028.1;0.219287,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;1.02593,MA0051.1;0.504875,MA0052.1;0.801048,MA0055.1;0.17385,MA0056.1;0,MA0057.1;0.471918,MA0058.1;0.273976,MA0059.1;0.28489,MA0060.1;0.145297,MA0061.1;0.16896,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;1.02422,MA0072.1;0.783532,MA0073.1;0.00409435,MA0074.1;2.97297,MA0076.1;0.249619,MA0077.1;0.762273,MA0078.1;0.536502,MA0081.1;0.305576,MA0083.1;0.875209,MA0084.1;1.44691,MA0087.1;0.832758,MA0088.1;0.0379749,MA0089.1;0,MA0090.1;0.329158,MA0091.1;0.973668,MA0092.1;0.877917,MA0093.1;0.226349,MA0095.1;0,MA0098.1;0,MA0100.1;0.440912,MA0101.1;0.292867,MA0103.1;0.67982,MA0105.1;0.304995,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;0.167085,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;0.598671,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;0.53259,MA0144.1;0.169559,MA0145.1;0.371997,MA0146.1;0.0389394,MA0147.1;1.01679,MA0148.1;0.375491,MA0149.1;0.2978,MA0062.2;0.0948004,MA0035.2;0.44524,MA0039.2;0.11913,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;0.0424448,MA0150.1;0.346631,MA0151.1;0,MA0152.1;0.495709,MA0153.1;0.92832,MA0154.1;0.862467,MA0155.1;0.732931,MA0156.1;0.248865,MA0157.1;0.642984,MA0158.1;0,MA0159.1;1.05,MA0160.1;0.378276,MA0161.1;0,MA0162.1;0.134999,MA0163.1;0.971627,MA0164.1;1.1874,MA0080.2;0.237846,MA0018.2;0.480226,MA0099.2;0.584892,MA0079.2;4.01017,MA0102.2;1.49914,MA0258.1;0.156336,MA0259.1;0.170828,MA0442.1;0
}}
}}

Revision as of 12:14, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr2:109533758..109533781,+p1@Bdnf
Mm9::chr5:114824999..114825005,-p@chr5:114824999..114825005
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Mm9::chr7:96658543..96658553,-p@chr7:96658543..96658553
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Mm9::chr7:96659061..96659074,-p@chr7:96659061..96659074
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Mm9::chr7:96666044..96666075,-p1@Prss23
Mm9::chr7:96666086..96666097,-p2@Prss23
Mm9::chr7:96666381..96666395,-p3@Prss23
Mm9::chr7:96666663..96666719,-p@chr7:96666663..96666719
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Mm9::chr7:96667044..96667065,-p@chr7:96667044..96667065
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Mm9::chr9:106378465..106378488,-p2@Parp3


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:0007412axon target recognition0.0238251708586333
GO:0046668regulation of retinal cell programmed cell death0.0238251708586333
GO:0014047glutamate secretion0.0238251708586333
GO:0045666positive regulation of neuron differentiation0.0238251708586333
GO:0046666retinal cell programmed cell death0.0238251708586333
GO:0007406negative regulation of neuroblast proliferation0.0238251708586333
GO:0021675nerve development0.0340284989785554
GO:0008038neuron recognition0.0357260081764982
GO:0042596fear response0.0385149342631411
GO:0050768negative regulation of neurogenesis0.0385149342631411
GO:0048167regulation of synaptic plasticity0.0385149342631411
GO:0050803regulation of synapse structure and activity0.0385149342631411
GO:0043524negative regulation of neuron apoptosis0.0385149342631411
GO:0033555multicellular organismal response to stress0.0385149342631411
GO:0007405neuroblast proliferation0.0385149342631411
GO:0045664regulation of neuron differentiation0.0385149342631411
GO:0042493response to drug0.0385149342631411
GO:0001657ureteric bud development0.0385149342631411
GO:0042490mechanoreceptor differentiation0.0385149342631411
GO:0043523regulation of neuron apoptosis0.0385149342631411
GO:0007631feeding behavior0.0385149342631411
GO:0051402neuron apoptosis0.0390556255448681
GO:0016358dendrite development0.0390556255448681
GO:0048592eye morphogenesis0.0390556255448681
GO:0008037cell recognition0.0390556255448681
GO:0050767regulation of neurogenesis0.0390556255448681
GO:0001656metanephros development0.0390556255448681
GO:0045597positive regulation of cell differentiation0.0390556255448681
GO:0007269neurotransmitter secretion0.0417962096486196
GO:0045055regulated secretory pathway0.049333415351641
GO:0007611learning and/or memory0.049333415351641
GO:0051094positive regulation of developmental process0.049333415351641
GO:0048839inner ear development0.049333415351641
GO:0001822kidney development0.049333415351641
GO:0043583ear development0.049333415351641
GO:0006916anti-apoptosis0.049333415351641
GO:0001655urogenital system development0.049333415351641
GO:0007411axon guidance0.049333415351641



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><br><br>


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)
MA0003.11.86959
MA0004.10.360508
MA0006.10.604851
MA0007.10.346734
MA0009.11.83729
MA0014.11.80909
MA0017.10.658116
MA0019.10.603066
MA0024.10.737933
MA0025.11.01089
MA0027.12.42079
MA0028.10.219287
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
MA0050.11.02593
MA0051.10.504875
MA0052.10.801048
MA0055.10.17385
MA0056.10
MA0057.10.471918
MA0058.10.273976
MA0059.10.28489
MA0060.10.145297
MA0061.10.16896
MA0063.10
MA0066.10.485868
MA0067.11.12095
MA0068.10.22316
MA0069.10.801381
MA0070.10.791856
MA0071.11.02422
MA0072.10.783532
MA0073.10.00409435
MA0074.12.97297
MA0076.10.249619
MA0077.10.762273
MA0078.10.536502
MA0081.10.305576
MA0083.10.875209
MA0084.11.44691
MA0087.10.832758
MA0088.10.0379749
MA0089.10
MA0090.10.329158
MA0091.10.973668
MA0092.10.877917
MA0093.10.226349
MA0095.10
MA0098.10
MA0100.10.440912
MA0101.10.292867
MA0103.10.67982
MA0105.10.304995
MA0106.10.543967
MA0107.10.237082
MA0108.20.625209
MA0109.10
MA0111.10.342068
MA0113.10.516916
MA0114.10.167085
MA0115.10.878749
MA0116.10.210297
MA0117.10.846964
MA0119.10.796817
MA0122.10.866511
MA0124.11.06819
MA0125.10.994853
MA0130.10
MA0131.10.598671
MA0132.10
MA0133.10
MA0135.10.911905
MA0136.10.470672
MA0139.10.385513
MA0140.10.440804
MA0141.10.259554
MA0142.10.674191
MA0143.10.53259
MA0144.10.169559
MA0145.10.371997
MA0146.10.0389394
MA0147.11.01679
MA0148.10.375491
MA0149.10.2978
MA0062.20.0948004
MA0035.20.44524
MA0039.20.11913
MA0138.20.590987
MA0002.20.123715
MA0137.20.257017
MA0104.20.828906
MA0047.20.495607
MA0112.20.163154
MA0065.20.0424448
MA0150.10.346631
MA0151.10
MA0152.10.495709
MA0153.10.92832
MA0154.10.862467
MA0155.10.732931
MA0156.10.248865
MA0157.10.642984
MA0158.10
MA0159.11.05
MA0160.10.378276
MA0161.10
MA0162.10.134999
MA0163.10.971627
MA0164.11.1874
MA0080.20.237846
MA0018.20.480226
MA0099.20.584892
MA0079.24.01017
MA0102.21.49914
MA0258.10.156336
MA0259.10.170828
MA0442.10
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