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MCL coexpression mm9:691: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007100!1.05e-15!18;UBERON:0000948!1.05e-15!18;UBERON:0005498!1.05e-15!18;UBERON:0004140!1.05e-15!18;UBERON:0009881!1.05e-15!18;UBERON:0004141!1.05e-15!18;UBERON:0003084!1.05e-15!18;UBERON:0007005!1.05e-15!18;UBERON:0004139!1.05e-15!18;UBERON:0004291!1.05e-15!18;UBERON:0004535!3.29e-12!23;UBERON:0001009!3.29e-12!23;UBERON:0004872!2.03e-08!33
|ontology_enrichment_uberon=UBERON:0007100!1.05e-15!18;UBERON:0000948!1.05e-15!18;UBERON:0005498!1.05e-15!18;UBERON:0004140!1.05e-15!18;UBERON:0009881!1.05e-15!18;UBERON:0004141!1.05e-15!18;UBERON:0003084!1.05e-15!18;UBERON:0007005!1.05e-15!18;UBERON:0004139!1.05e-15!18;UBERON:0004291!1.05e-15!18;UBERON:0004535!3.29e-12!23;UBERON:0001009!3.29e-12!23;UBERON:0004872!2.03e-08!33
|tfbs_overrepresentation_for_novel_motifs=0.321524,0.352573,0.297937,0.360062,0.580303,0.373426,0.458558,1.27916,0.816027,0.255527,0.417132,0.447169,0.393382,0.470194,0.613681,0,0.656089,0.19356,0.364803,0.205418,0.26524,0.954669,0.469335,0.577226,0.822446,0.496413,0.709649,0.392919,0.238759,0.271461,0.379806,0.754912,0.191698,0.646834,0.214608,0.218093,0.184038,0.443753,0.963289,0.442131,0.196807,0.38461,0.307718,0.215898,1.29974,0.349801,0.578773,0.407653,0.255625,0.241306,0.639101,0.522137,0.550735,0.894161,0.911367,0.47699,1.28651,1.11002,0.332535,0.47505,0.735292,1.31585,0.433822,0.628155,0.487593,1.60248,1.04613,1.3932,0.730718,1.24673,0.281085,0.404236,0.03967,0.944464,0.320434,0.0893951,0.646602,0.567793,0.718494,0.268962,0.80832,0.673009,0.529804,0.119727,0.830765,0.158895,0.0149522,0.572901,0.583509,1.55487,1.11522,0.835661,0.767462,0.205117,0.163126,0.149272,1.26754,0.770215,0.57902,0.0659594,0.184103,0.754637,0.87698,0.639679,0.638654,0.3842,0.696857,0.403887,0.273261,0.266818,0.315128,0.878738,0.743427,0.421988,1.12221,0.5687,0.671121,0.363536,0.657356,0.181004,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,0.466292,0.760818,1.04463,3.30025,0.86025,0.353344,1.01535,0.48999,1.14365,0.0358067,0.877308,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,0.385031,0.581788,1.88287,0.331322,0.201635,0.275954,0.0316649,0.895708,0.153911,0.489108,0.976367,1.29867,0.224422,0.319291,0.328917,1.1043,0.829923,0.722546,0.313083,0.629147,0.482049,0.53929,0.445669,4.25185
|tfbs_overrepresentation_for_novel_motifs=0.321524,0.352573,0.297937,0.360062,0.580303,0.373426,0.458558,1.27916,0.816027,0.255527,0.417132,0.447169,0.393382,0.470194,0.613681,0,0.656089,0.19356,0.364803,0.205418,0.26524,0.954669,0.469335,0.577226,0.822446,0.496413,0.709649,0.392919,0.238759,0.271461,0.379806,0.754912,0.191698,0.646834,0.214608,0.218093,0.184038,0.443753,0.963289,0.442131,0.196807,0.38461,0.307718,0.215898,1.29974,0.349801,0.578773,0.407653,0.255625,0.241306,0.639101,0.522137,0.550735,0.894161,0.911367,0.47699,1.28651,1.11002,0.332535,0.47505,0.735292,1.31585,0.433822,0.628155,0.487593,1.60248,1.04613,1.3932,0.730718,1.24673,0.281085,0.404236,0.03967,0.944464,0.320434,0.0893951,0.646602,0.567793,0.718494,0.268962,0.80832,0.673009,0.529804,0.119727,0.830765,0.158895,0.0149522,0.572901,0.583509,1.55487,1.11522,0.835661,0.767462,0.205117,0.163126,0.149272,1.26754,0.770215,0.57902,0.0659594,0.184103,0.754637,0.87698,0.639679,0.638654,0.3842,0.696857,0.403887,0.273261,0.266818,0.315128,0.878738,0.743427,0.421988,1.12221,0.5687,0.671121,0.363536,0.657356,0.181004,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,0.466292,0.760818,1.04463,3.30025,0.86025,0.353344,1.01535,0.48999,1.14365,0.0358067,0.877308,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,0.385031,0.581788,1.88287,0.331322,0.201635,0.275954,0.0316649,0.895708,0.153911,0.489108,0.976367,1.29867,0.224422,0.319291,0.328917,1.1043,0.829923,0.722546,0.313083,0.629147,0.482049,0.53929,0.445669,4.25185
|tfbs_overrepresentation_jaspar=MA0003.1;0.119771,MA0004.1;0.360508,MA0006.1;0.210471,MA0007.1;0.346734,MA0009.1;0.780842,MA0014.1;0.0870561,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;1.7046,MA0030.1;0.723093,MA0031.1;0.688336,MA0038.1;2.14884,MA0040.1;0.79313,MA0041.1;0.291712,MA0042.1;0.279998,MA0043.1;0.875991,MA0046.1;0.816137,MA0048.1;0.236433,MA0050.1;0.396459,MA0051.1;0.504875,MA0052.1;0.801048,MA0055.1;0.0660514,MA0056.1;0,MA0057.1;2.2848,MA0058.1;0.752621,MA0059.1;0.777514,MA0060.1;1.40918,MA0061.1;0.973999,MA0063.1;0,MA0066.1;0.485868,MA0067.1;1.12095,MA0068.1;0.0621035,MA0069.1;0.801381,MA0070.1;0.791856,MA0071.1;0.395679,MA0072.1;0.783532,MA0073.1;0.347221,MA0074.1;0.451832,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;0.34573,MA0089.1;0,MA0090.1;0.877277,MA0091.1;0.372635,MA0092.1;0.329444,MA0093.1;0.226349,MA0095.1;0,MA0098.1;0,MA0100.1;0.440912,MA0101.1;1.44787,MA0103.1;0.67982,MA0105.1;1.56265,MA0106.1;0.543967,MA0107.1;1.24141,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;0.598671,MA0132.1;0,MA0133.1;0,MA0135.1;0.911905,MA0136.1;0.470672,MA0139.1;0.121562,MA0140.1;1.12231,MA0141.1;0.259554,MA0142.1;0.674191,MA0143.1;0.53259,MA0144.1;0.169559,MA0145.1;1.46364,MA0146.1;0.412111,MA0147.1;0.179496,MA0148.1;0.375491,MA0149.1;0.2978,MA0062.2;0.0948004,MA0035.2;2.94272,MA0039.2;0.857069,MA0138.2;1.44221,MA0002.2;0.781868,MA0137.2;0.257017,MA0104.2;0.134457,MA0047.2;0.495607,MA0112.2;0.371983,MA0065.2;0.373167,MA0150.1;0.346631,MA0151.1;0,MA0152.1;1.24029,MA0153.1;0.92832,MA0154.1;0.232525,MA0155.1;1.12565,MA0156.1;0.248865,MA0157.1;0.642984,MA0158.1;0,MA0159.1;0.550545,MA0160.1;0.378276,MA0161.1;0,MA0162.1;0.0488928,MA0163.1;0.971627,MA0164.1;0.471016,MA0080.2;0.237846,MA0018.2;0.480226,MA0099.2;0.584892,MA0079.2;0.340295,MA0102.2;1.49914,MA0258.1;0.156336,MA0259.1;0.50935,MA0442.1;0
}}
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Revision as of 12:09, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:69250139..69250150,+p@chr10:69250139..69250150
+
Mm9::chr11:5797989..5798000,-p@chr11:5797989..5798000
-
Mm9::chr11:5798774..5798791,-p1@Myl7
Mm9::chr16:96422095..96422098,+p8@Sh3bgr
Mm9::chr16:96422142..96422163,+p3@Sh3bgr
Mm9::chr16:96422177..96422194,+p5@Sh3bgr
Mm9::chr1:133130237..133130256,-p@chr1:133130237..133130256
-
Mm9::chr1:174150155..174150233,-p3@Casq1
Mm9::chr3:142093138..142093152,-p@chr3:142093138..142093152
-
Mm9::chr5:23856890..23856934,-p@chr5:23856890..23856934
-


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:0033018sarcoplasmic reticulum lumen0.00854654029474607
GO:0005788endoplasmic reticulum lumen0.0284744221337796
GO:0043197dendritic spine0.0284744221337796
GO:0016529sarcoplasmic reticulum0.0402202336140673
GO:0016528sarcoplasm0.0402202336140673
GO:0005509calcium ion binding0.0402202336140673
GO:0006937regulation of muscle contraction0.0402202336140673



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>


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)
MA0003.10.119771
MA0004.10.360508
MA0006.10.210471
MA0007.10.346734
MA0009.10.780842
MA0014.10.0870561
MA0017.10.658116
MA0019.10.603066
MA0024.10.737933
MA0025.11.01089
MA0027.12.42079
MA0028.10.219287
MA0029.11.7046
MA0030.10.723093
MA0031.10.688336
MA0038.12.14884
MA0040.10.79313
MA0041.10.291712
MA0042.10.279998
MA0043.10.875991
MA0046.10.816137
MA0048.10.236433
MA0050.10.396459
MA0051.10.504875
MA0052.10.801048
MA0055.10.0660514
MA0056.10
MA0057.12.2848
MA0058.10.752621
MA0059.10.777514
MA0060.11.40918
MA0061.10.973999
MA0063.10
MA0066.10.485868
MA0067.11.12095
MA0068.10.0621035
MA0069.10.801381
MA0070.10.791856
MA0071.10.395679
MA0072.10.783532
MA0073.10.347221
MA0074.10.451832
MA0076.10.249619
MA0077.10.762273
MA0078.10.536502
MA0081.10.305576
MA0083.10.875209
MA0084.11.44691
MA0087.10.832758
MA0088.10.34573
MA0089.10
MA0090.10.877277
MA0091.10.372635
MA0092.10.329444
MA0093.10.226349
MA0095.10
MA0098.10
MA0100.10.440912
MA0101.11.44787
MA0103.10.67982
MA0105.11.56265
MA0106.10.543967
MA0107.11.24141
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
MA0131.10.598671
MA0132.10
MA0133.10
MA0135.10.911905
MA0136.10.470672
MA0139.10.121562
MA0140.11.12231
MA0141.10.259554
MA0142.10.674191
MA0143.10.53259
MA0144.10.169559
MA0145.11.46364
MA0146.10.412111
MA0147.10.179496
MA0148.10.375491
MA0149.10.2978
MA0062.20.0948004
MA0035.22.94272
MA0039.20.857069
MA0138.21.44221
MA0002.20.781868
MA0137.20.257017
MA0104.20.134457
MA0047.20.495607
MA0112.20.371983
MA0065.20.373167
MA0150.10.346631
MA0151.10
MA0152.11.24029
MA0153.10.92832
MA0154.10.232525
MA0155.11.12565
MA0156.10.248865
MA0157.10.642984
MA0158.10
MA0159.10.550545
MA0160.10.378276
MA0161.10
MA0162.10.0488928
MA0163.10.971627
MA0164.10.471016
MA0080.20.237846
MA0018.20.480226
MA0099.20.584892
MA0079.20.340295
MA0102.21.49914
MA0258.10.156336
MA0259.10.50935
MA0442.10
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