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MCL coexpression mm9:981: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0005409!1.24e-12!47;UBERON:0004119!5.40e-12!118;UBERON:0000925!5.40e-12!118;UBERON:0006595!5.40e-12!118;UBERON:0000160!1.03e-11!31;UBERON:0001007!1.43e-11!116;UBERON:0001555!1.43e-11!116;UBERON:0007026!1.43e-11!116;UBERON:0004921!9.29e-11!114;UBERON:0002365!1.20e-10!25;UBERON:0002330!1.20e-10!25;UBERON:0002100!1.92e-10!90;UBERON:0009854!4.44e-10!23;UBERON:0009856!4.44e-10!23;UBERON:0002107!1.48e-09!22;UBERON:0007499!1.48e-09!22;UBERON:0006925!1.48e-09!22;UBERON:0009497!1.48e-09!22;UBERON:0000015!1.48e-09!22;UBERON:0002423!1.48e-09!22;UBERON:0006235!1.48e-09!22;UBERON:0008835!1.48e-09!22;UBERON:0003894!1.48e-09!22;UBERON:0004161!1.48e-09!22;UBERON:0008836!1.48e-09!22;UBERON:0005177!1.97e-09!79;UBERON:0004923!3.11e-09!24;UBERON:0005256!7.51e-09!45;UBERON:0005172!1.77e-08!49;UBERON:0005173!1.77e-08!49;UBERON:0002417!1.77e-08!49;UBERON:0000916!1.77e-08!49;UBERON:0003104!2.29e-08!61;UBERON:0009142!2.29e-08!61;UBERON:0000344!3.17e-08!15;UBERON:0001242!2.92e-07!13;UBERON:0000060!2.92e-07!13;UBERON:0001262!2.92e-07!13;UBERON:0004786!2.92e-07!13;UBERON:0009569!8.62e-07!66
|ontology_enrichment_uberon=UBERON:0005409!1.24e-12!47;UBERON:0004119!5.40e-12!118;UBERON:0000925!5.40e-12!118;UBERON:0006595!5.40e-12!118;UBERON:0000160!1.03e-11!31;UBERON:0001007!1.43e-11!116;UBERON:0001555!1.43e-11!116;UBERON:0007026!1.43e-11!116;UBERON:0004921!9.29e-11!114;UBERON:0002365!1.20e-10!25;UBERON:0002330!1.20e-10!25;UBERON:0002100!1.92e-10!90;UBERON:0009854!4.44e-10!23;UBERON:0009856!4.44e-10!23;UBERON:0002107!1.48e-09!22;UBERON:0007499!1.48e-09!22;UBERON:0006925!1.48e-09!22;UBERON:0009497!1.48e-09!22;UBERON:0000015!1.48e-09!22;UBERON:0002423!1.48e-09!22;UBERON:0006235!1.48e-09!22;UBERON:0008835!1.48e-09!22;UBERON:0003894!1.48e-09!22;UBERON:0004161!1.48e-09!22;UBERON:0008836!1.48e-09!22;UBERON:0005177!1.97e-09!79;UBERON:0004923!3.11e-09!24;UBERON:0005256!7.51e-09!45;UBERON:0005172!1.77e-08!49;UBERON:0005173!1.77e-08!49;UBERON:0002417!1.77e-08!49;UBERON:0000916!1.77e-08!49;UBERON:0003104!2.29e-08!61;UBERON:0009142!2.29e-08!61;UBERON:0000344!3.17e-08!15;UBERON:0001242!2.92e-07!13;UBERON:0000060!2.92e-07!13;UBERON:0001262!2.92e-07!13;UBERON:0004786!2.92e-07!13;UBERON:0009569!8.62e-07!66
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.84953,0.367606,0.434198,0.720982,0.448401,0.538088,0.173246,1.02512,2.55967,0.494602,0.526159,0.515774,0.550255,0.275867,0,0.742571,0.252772,0.160384,0.29826,0.332107,0.485665,0.549359,0.258745,0.374936,0.577606,0.466037,0.469052,0.818708,0.118137,0.455168,0.843667,0.699026,0.136998,2.13031,0.363049,4.51625,0.522578,0.221921,0.570041,0.256422,0.460258,0.450632,0.27776,0.983404,0.423266,0.662995,0.484612,0.170971,0.305876,0.725127,0.604356,0.112729,0.985264,1.00271,0.557354,0.314394,0.513517,0.145699,1.367,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.922232,1.0125,0.50864,1.03623,0.853709,0.131016,0.136938,0.651651,0.806481,0.336166,1.01677,0.759925,0.612313,0.167672,0.920903,0.491838,0.123242,0.376919,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.62322,0.585369,0.1711,0.859272,0.663249,0.332938,0.242106,0.843387,0.967837,0.725721,0.724668,1.16334,0.784351,0.480639,0.340849,0.333829,1.00333,0.96962,0.337254,2.16002,1.21576,0.254749,0.603195,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.220515,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.724779,0.120154,1.19035,0.986833,2.49691,0.569994,1.06851,0.605358,0.287226,0.39061,1.03572,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.240994,0.524587,1.56615
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.84953,0.367606,0.434198,0.720982,0.448401,0.538088,0.173246,1.02512,2.55967,0.494602,0.526159,0.515774,0.550255,0.275867,0,0.742571,0.252772,0.160384,0.29826,0.332107,0.485665,0.549359,0.258745,0.374936,0.577606,0.466037,0.469052,0.818708,0.118137,0.455168,0.843667,0.699026,0.136998,2.13031,0.363049,4.51625,0.522578,0.221921,0.570041,0.256422,0.460258,0.450632,0.27776,0.983404,0.423266,0.662995,0.484612,0.170971,0.305876,0.725127,0.604356,0.112729,0.985264,1.00271,0.557354,0.314394,0.513517,0.145699,1.367,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.922232,1.0125,0.50864,1.03623,0.853709,0.131016,0.136938,0.651651,0.806481,0.336166,1.01677,0.759925,0.612313,0.167672,0.920903,0.491838,0.123242,0.376919,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.62322,0.585369,0.1711,0.859272,0.663249,0.332938,0.242106,0.843387,0.967837,0.725721,0.724668,1.16334,0.784351,0.480639,0.340849,0.333829,1.00333,0.96962,0.337254,2.16002,1.21576,0.254749,0.603195,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.220515,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.724779,0.120154,1.19035,0.986833,2.49691,0.569994,1.06851,0.605358,0.287226,0.39061,1.03572,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.240994,0.524587,1.56615
|tfbs_overrepresentation_jaspar=MA0003.1;4.61746,MA0004.1;0.434673,MA0006.1;0.747445,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;1.97336,MA0017.1;0.296816,MA0019.1;0.688051,MA0024.1;0.826339,MA0025.1;1.10341,MA0027.1;2.51754,MA0028.1;0.769859,MA0029.1;0.804619,MA0030.1;0.811181,MA0031.1;0.775627,MA0038.1;0.577528,MA0040.1;0.882616,MA0041.1;0.360875,MA0042.1;0.348174,MA0043.1;0.966833,MA0046.1;0.906029,MA0048.1;1.13456,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;0.117901,MA0056.1;0,MA0057.1;0.643187,MA0058.1;0.90507,MA0059.1;0.353484,MA0060.1;1.08928,MA0061.1;0.638933,MA0063.1;0,MA0066.1;0.566617,MA0067.1;1.21448,MA0068.1;0.0965831,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;0.577203,MA0074.1;0.531046,MA0076.1;0.845594,MA0077.1;0.851175,MA0078.1;0.61926,MA0081.1;0.375851,MA0083.1;0.96604,MA0084.1;1.54225,MA0087.1;0.922929,MA0088.1;0.229377,MA0089.1;0,MA0090.1;0.401197,MA0091.1;0.447561,MA0092.1;0.401504,MA0093.1;0.787675,MA0095.1;0,MA0098.1;0,MA0100.1;0.519598,MA0101.1;0.362124,MA0103.1;0.307078,MA0105.1;0.823589,MA0106.1;0.626997,MA0107.1;0.301222,MA0108.2;0.710846,MA0109.1;0,MA0111.1;0.415012,MA0113.1;1.45892,MA0114.1;0.633896,MA0115.1;0.969632,MA0116.1;0.747001,MA0117.1;0.937363,MA0119.1;1.69575,MA0122.1;0.957212,MA0124.1;1.16127,MA0125.1;1.0872,MA0130.1;0,MA0131.1;1.63575,MA0132.1;0,MA0133.1;0,MA0135.1;1.00325,MA0136.1;0.550755,MA0139.1;0.169849,MA0140.1;0.519484,MA0141.1;0.325895,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;0.225588,MA0145.1;1.87609,MA0146.1;1.31232,MA0147.1;1.24068,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;1.36227,MA0035.2;0.524137,MA0039.2;3.74793,MA0138.2;0.675599,MA0002.2;0.513194,MA0137.2;0.32312,MA0104.2;1.64215,MA0047.2;0.576767,MA0112.2;0.527225,MA0065.2;0.0704227,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.100744,MA0155.1;0.275377,MA0156.1;0.314185,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.246253,MA0160.1;0.453546,MA0161.1;0,MA0162.1;0.439322,MA0163.1;1.36861,MA0164.1;0.551114,MA0080.2;0.302064,MA0018.2;1.37842,MA0099.2;0.669311,MA0079.2;1.39218,MA0102.2;1.59466,MA0258.1;0.210437,MA0259.1;0.643936,MA0442.1;0
}}
}}

Revision as of 12:37, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr1:135027844..135027860,+p2@Ppp1r15b
Mm9::chr1:135027865..135027941,+p1@Ppp1r15b
Mm9::chr1:75165234..75165257,+p1@Zfand2b
Mm9::chr3:131153142..131153199,-p@chr3:131153142..131153199
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Mm9::chr3:88259648..88259655,-p7@Sema4a
Mm9::chr3:96531690..96531717,+p2@Rnf115
Mm9::chr5:106129759..106129771,+p12@Lrrc8d
Mm9::chr5:106129777..106129854,+p2@Lrrc8d


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:0000164protein phosphatase type 1 complex0.0170930805894921
GO:0006983ER overload response0.0417110277041303
GO:0042542response to hydrogen peroxide0.0417110277041303
GO:0000302response to reactive oxygen species0.0417110277041303
GO:0033554cellular response to stress0.0417110277041303
GO:0006984ER-nuclear signaling pathway0.0417110277041303
GO:0051716cellular response to stimulus0.0417110277041303
GO:0008287protein serine/threonine phosphatase complex0.0417110277041303
GO:0006446regulation of translational initiation0.0417110277041303



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
gastrointestinal system1.24e-1247
endoderm-derived structure5.40e-12118
endoderm5.40e-12118
presumptive endoderm5.40e-12118
intestine1.03e-1131
digestive system1.43e-11116
digestive tract1.43e-11116
primitive gut1.43e-11116
subdivision of digestive tract9.29e-11114
exocrine gland1.20e-1025
exocrine system1.20e-1025
trunk1.92e-1090
digestive tract diverticulum4.44e-1023
sac4.44e-1023
liver1.48e-0922
epithelial sac1.48e-0922
digestive gland1.48e-0922
epithelium of foregut-midgut junction1.48e-0922
anatomical boundary1.48e-0922
hepatobiliary system1.48e-0922
foregut-midgut junction1.48e-0922
hepatic diverticulum1.48e-0922
liver primordium1.48e-0922
septum transversum1.48e-0922
liver bud1.48e-0922
trunk region element1.97e-0979
organ component layer3.11e-0924
trunk mesenchyme7.51e-0945
abdomen element1.77e-0849
abdominal segment element1.77e-0849
abdominal segment of trunk1.77e-0849
abdomen1.77e-0849
mesenchyme2.29e-0861
entire embryonic mesenchyme2.29e-0861
mucosa3.17e-0815
intestinal mucosa2.92e-0713
anatomical wall2.92e-0713
wall of intestine2.92e-0713
gastrointestinal system mucosa2.92e-0713
subdivision of trunk8.62e-0766


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)
MA0003.14.61746
MA0004.10.434673
MA0006.10.747445
MA0007.10.419994
MA0009.10.870101
MA0014.11.97336
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.769859
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.11.13456
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.117901
MA0056.10
MA0057.10.643187
MA0058.10.90507
MA0059.10.353484
MA0060.11.08928
MA0061.10.638933
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.0965831
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.577203
MA0074.10.531046
MA0076.10.845594
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.229377
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.787675
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.10.823589
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.11.45892
MA0114.10.633896
MA0115.10.969632
MA0116.10.747001
MA0117.10.937363
MA0119.11.69575
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.11.63575
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.169849
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.11.87609
MA0146.11.31232
MA0147.11.24068
MA0148.10.450593
MA0149.10.367458
MA0062.21.36227
MA0035.20.524137
MA0039.23.74793
MA0138.20.675599
MA0002.20.513194
MA0137.20.32312
MA0104.21.64215
MA0047.20.576767
MA0112.20.527225
MA0065.20.0704227
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.100744
MA0155.10.275377
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.10.439322
MA0163.11.36861
MA0164.10.551114
MA0080.20.302064
MA0018.21.37842
MA0099.20.669311
MA0079.21.39218
MA0102.21.59466
MA0258.10.210437
MA0259.10.643936
MA0442.10
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