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MCL coexpression mm9:690: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000945!3.55e-12!16;UBERON:0010039!3.55e-12!16;UBERON:0001264!1.16e-09!12;UBERON:0002075!4.50e-07!19
|ontology_enrichment_uberon=UBERON:0000945!3.55e-12!16;UBERON:0010039!3.55e-12!16;UBERON:0001264!1.16e-09!12;UBERON:0002075!4.50e-07!19
|tfbs_overrepresentation_for_novel_motifs=0.321524,0.352573,0.297937,0.360062,0.580303,0.373426,0.458558,0.124431,0.411053,0.255527,0.417132,1.13606,0.393382,0.470194,0.214197,0,0.656089,0.19356,3.08553,0.451901,0.26524,0.60924,0.469335,0.198877,0.304728,2.14909,0.107695,0.392919,0.238759,0.271461,0.989437,0.754912,2.38223,0.0942651,0.214608,2.38803,3.08988,0.443753,0.166348,0.868806,0.196807,0.38461,0.130272,0.617704,0.434259,1.6507,0.578773,1.05036,0.104497,0.677281,1.54311,0.522137,0.0747297,0.894161,0.911367,0.47699,0.249055,1.11002,0.101408,0.47505,0.735292,1.31585,0.140453,0.628155,0.487593,0.667546,1.04613,1.3932,0.730718,1.24673,0.76885,0.128829,0.356247,0.944464,2.20686,0.300089,1.59105,0.567793,0.718494,0.268962,0.129727,2.72206,0.529804,0.380754,0.830765,7.3027,0.182066,1.44534,0.583509,1.55487,1.11522,0.835661,0.767462,0.205117,0.163126,0.892226,1.84308,0.770215,0.57902,0.234357,0.184103,0.754637,0.87698,0.639679,0.638654,0.3842,0.696857,0.403887,0.273261,2.08168,0.315128,0.878738,1.36417,0.421988,1.12221,0.5687,0.409202,0.363536,0.657356,0.181004,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,1.17725,1.79596,1.04463,0.207624,0.86025,0.353344,1.01535,0.48999,1.14365,0.0358067,0.329172,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,1.00091,0.581788,1.88287,0.882109,0.201635,0.275954,1.27437,0.895708,0.153911,0.489108,0.976367,0.523103,0.224422,0.319291,0.876739,1.1043,0.829923,0.722546,1.52068,0.629147,0.482049,0.18312,0.445669,6.03845
|tfbs_overrepresentation_for_novel_motifs=0.321524,0.352573,0.297937,0.360062,0.580303,0.373426,0.458558,0.124431,0.411053,0.255527,0.417132,1.13606,0.393382,0.470194,0.214197,0,0.656089,0.19356,3.08553,0.451901,0.26524,0.60924,0.469335,0.198877,0.304728,2.14909,0.107695,0.392919,0.238759,0.271461,0.989437,0.754912,2.38223,0.0942651,0.214608,2.38803,3.08988,0.443753,0.166348,0.868806,0.196807,0.38461,0.130272,0.617704,0.434259,1.6507,0.578773,1.05036,0.104497,0.677281,1.54311,0.522137,0.0747297,0.894161,0.911367,0.47699,0.249055,1.11002,0.101408,0.47505,0.735292,1.31585,0.140453,0.628155,0.487593,0.667546,1.04613,1.3932,0.730718,1.24673,0.76885,0.128829,0.356247,0.944464,2.20686,0.300089,1.59105,0.567793,0.718494,0.268962,0.129727,2.72206,0.529804,0.380754,0.830765,7.3027,0.182066,1.44534,0.583509,1.55487,1.11522,0.835661,0.767462,0.205117,0.163126,0.892226,1.84308,0.770215,0.57902,0.234357,0.184103,0.754637,0.87698,0.639679,0.638654,0.3842,0.696857,0.403887,0.273261,2.08168,0.315128,0.878738,1.36417,0.421988,1.12221,0.5687,0.409202,0.363536,0.657356,0.181004,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,1.17725,1.79596,1.04463,0.207624,0.86025,0.353344,1.01535,0.48999,1.14365,0.0358067,0.329172,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,1.00091,0.581788,1.88287,0.882109,0.201635,0.275954,1.27437,0.895708,0.153911,0.489108,0.976367,0.523103,0.224422,0.319291,0.876739,1.1043,0.829923,0.722546,1.52068,0.629147,0.482049,0.18312,0.445669,6.03845
|tfbs_overrepresentation_jaspar=MA0003.1;9.01048,MA0004.1;0.360508,MA0006.1;0.210471,MA0007.1;0.346734,MA0009.1;0.780842,MA0014.1;16.5977,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;0.066679,MA0050.1;0.396459,MA0051.1;0.504875,MA0052.1;0.801048,MA0055.1;0.0139872,MA0056.1;0,MA0057.1;1.2407,MA0058.1;0.273976,MA0059.1;0.28489,MA0060.1;0.8754,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;0.395679,MA0072.1;0.783532,MA0073.1;1.10611,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;3.58386,MA0089.1;0,MA0090.1;0.329158,MA0091.1;0.372635,MA0092.1;0.329444,MA0093.1;0.226349,MA0095.1;0,MA0098.1;0,MA0100.1;0.440912,MA0101.1;0.292867,MA0103.1;0.242398,MA0105.1;0.304995,MA0106.1;0.543967,MA0107.1;0.237082,MA0108.2;0.625209,MA0109.1;0,MA0111.1;0.90605,MA0113.1;0.516916,MA0114.1;0.167085,MA0115.1;0.878749,MA0116.1;0.210297,MA0117.1;0.846964,MA0119.1;0.293392,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;1.95542,MA0146.1;2.0328,MA0147.1;0.179496,MA0148.1;0.375491,MA0149.1;6.11094,MA0062.2;0.0948004,MA0035.2;0.44524,MA0039.2;9.29149,MA0138.2;0.590987,MA0002.2;0.123715,MA0137.2;0.257017,MA0104.2;0.134457,MA0047.2;0.495607,MA0112.2;4.40092,MA0065.2;1.46688,MA0150.1;0.346631,MA0151.1;0,MA0152.1;0.495709,MA0153.1;0.92832,MA0154.1;0.0653255,MA0155.1;1.12565,MA0156.1;0.248865,MA0157.1;0.642984,MA0158.1;0,MA0159.1;0.187774,MA0160.1;0.378276,MA0161.1;0,MA0162.1;2.22848,MA0163.1;4.16028,MA0164.1;0.471016,MA0080.2;0.237846,MA0018.2;0.480226,MA0099.2;0.584892,MA0079.2;10.6877,MA0102.2;1.49914,MA0258.1;0.473611,MA0259.1;0.170828,MA0442.1;0
}}
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Revision as of 12:09, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:52111412..52111416,+p1@Nepn
Mm9::chr11:96184567..96184569,+p8@Hoxb3
Mm9::chr13:48757894..48757908,+p5@Barx1
Mm9::chr13:48758072..48758117,-p@chr13:48758072..48758117
-
Mm9::chr13:48758276..48758291,+p1@Barx1
Mm9::chr13:48758328..48758335,+p4@Barx1
Mm9::chr13:48758358..48758415,+p2@Barx1
Mm9::chr13:48758431..48758443,+p3@Barx1
Mm9::chr2:62318547..62318556,-p2@Gcg
Mm9::chr3:122393672..122393673,+p@chr3:122393672..122393673
+


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:0007267cell-cell signaling0.0416563664909537
GO:0030878thyroid gland development0.0416563664909537
GO:0050796regulation of insulin secretion0.0416563664909537
GO:0005667transcription factor complex0.0416563664909537
GO:0043565sequence-specific DNA binding0.0416563664909537
GO:0030178negative regulation of Wnt receptor signaling pathway0.0416563664909537
GO:0046883regulation of hormone secretion0.0416563664909537
GO:0044451nucleoplasm part0.0416563664909537
GO:0030111regulation of Wnt receptor signaling pathway0.0416563664909537
GO:0030073insulin secretion0.0416563664909537
GO:0005654nucleoplasm0.0416563664909537
GO:0030072peptide hormone secretion0.0427696953751431
GO:0002790peptide secretion0.0427696953751431
GO:0031981nuclear lumen0.0427696953751431
GO:0030855epithelial cell differentiation0.0427696953751431
GO:0015833peptide transport0.0427696953751431
GO:0046879hormone secretion0.0427696953751431
GO:0031974membrane-enclosed lumen0.0427696953751431
GO:0043233organelle lumen0.0427696953751431
GO:0035270endocrine system development0.0459066551200862
GO:0003700transcription factor activity0.0459066551200862
GO:0051046regulation of secretion0.0459066551200862



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
stomach3.55e-1216
food storage organ3.55e-1216
pancreas1.16e-0912
viscus4.50e-0719


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)
MA0003.19.01048
MA0004.10.360508
MA0006.10.210471
MA0007.10.346734
MA0009.10.780842
MA0014.116.5977
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
MA0048.10.066679
MA0050.10.396459
MA0051.10.504875
MA0052.10.801048
MA0055.10.0139872
MA0056.10
MA0057.11.2407
MA0058.10.273976
MA0059.10.28489
MA0060.10.8754
MA0061.10.16896
MA0063.10
MA0066.10.485868
MA0067.11.12095
MA0068.10.22316
MA0069.10.801381
MA0070.10.791856
MA0071.10.395679
MA0072.10.783532
MA0073.11.10611
MA0074.10.451832
MA0076.10.249619
MA0077.10.762273
MA0078.10.536502
MA0081.10.305576
MA0083.10.875209
MA0084.11.44691
MA0087.10.832758
MA0088.13.58386
MA0089.10
MA0090.10.329158
MA0091.10.372635
MA0092.10.329444
MA0093.10.226349
MA0095.10
MA0098.10
MA0100.10.440912
MA0101.10.292867
MA0103.10.242398
MA0105.10.304995
MA0106.10.543967
MA0107.10.237082
MA0108.20.625209
MA0109.10
MA0111.10.90605
MA0113.10.516916
MA0114.10.167085
MA0115.10.878749
MA0116.10.210297
MA0117.10.846964
MA0119.10.293392
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
MA0145.11.95542
MA0146.12.0328
MA0147.10.179496
MA0148.10.375491
MA0149.16.11094
MA0062.20.0948004
MA0035.20.44524
MA0039.29.29149
MA0138.20.590987
MA0002.20.123715
MA0137.20.257017
MA0104.20.134457
MA0047.20.495607
MA0112.24.40092
MA0065.21.46688
MA0150.10.346631
MA0151.10
MA0152.10.495709
MA0153.10.92832
MA0154.10.0653255
MA0155.11.12565
MA0156.10.248865
MA0157.10.642984
MA0158.10
MA0159.10.187774
MA0160.10.378276
MA0161.10
MA0162.12.22848
MA0163.14.16028
MA0164.10.471016
MA0080.20.237846
MA0018.20.480226
MA0099.20.584892
MA0079.210.6877
MA0102.21.49914
MA0258.10.473611
MA0259.10.170828
MA0442.10
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