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MCL coexpression mm9:409: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002113!1.18e-33!14;UBERON:0003918!1.18e-33!14;UBERON:0011143!1.18e-33!14;UBERON:0005095!1.18e-33!14;UBERON:0007687!1.18e-33!14;UBERON:0006554!7.21e-26!18;UBERON:0001008!1.97e-24!19;UBERON:0000489!5.70e-22!21;UBERON:0003103!5.73e-10!43;UBERON:0005172!1.47e-08!49;UBERON:0005173!1.47e-08!49;UBERON:0002417!1.47e-08!49;UBERON:0000916!1.47e-08!49
|ontology_enrichment_uberon=UBERON:0002113!1.18e-33!14;UBERON:0003918!1.18e-33!14;UBERON:0011143!1.18e-33!14;UBERON:0005095!1.18e-33!14;UBERON:0007687!1.18e-33!14;UBERON:0006554!7.21e-26!18;UBERON:0001008!1.97e-24!19;UBERON:0000489!5.70e-22!21;UBERON:0003103!5.73e-10!43;UBERON:0005172!1.47e-08!49;UBERON:0005173!1.47e-08!49;UBERON:0002417!1.47e-08!49;UBERON:0000916!1.47e-08!49
|tfbs_overrepresentation_for_novel_motifs=0.162057,0.239198,0.144778,0.191238,0.572598,1.10473,0.270195,0.614792,0.15797,0.115943,0.236307,0.260789,0.340991,0.766078,0.615754,0,0.44163,0.552297,0.130179,0.278706,0.385752,0.519892,0.279154,1.43683,0.149704,0.301898,0.849653,0.216938,0.691298,0.393858,0.206597,0.531719,0.0739139,0.249044,0.0880674,0.115941,0.0693463,0.257981,0.468707,0.0468666,0.56228,0.210373,0.46646,0.620985,0.0747075,0.183361,0.372907,0.228683,0.800575,0.343195,0.426383,0.323798,0.372474,0.661847,0.67813,0.28555,0.722962,0.25091,0.111806,0.283926,0.513661,0.331566,0.172226,0.4166,0.294453,0.451957,0.806865,1.14503,0.509463,1.00145,0.414221,0.353861,0.0896041,0.709559,0.0246496,0.234413,0.468707,0.363297,0.498264,0.124234,0.3566,0.456892,0.330377,0.139579,0.602212,0.00517576,0.0258882,0.394307,0.377064,1.30447,0.873554,0.606796,0.543309,0.280055,0.209139,0.732474,0.606117,0.545856,0.373124,0.0619917,0.894464,0.531465,0.645628,0.4269,0.425983,0.21005,0.478524,0.225669,0.400135,0.122746,0.157325,0.647285,0.124928,0.67478,0.880323,0.263255,0.0347519,0.565346,0.442771,0.51371,0.714636,0.398522,0.303371,0.362534,0.932468,0.501574,0.758659,0.53717,0.805419,0.284377,0.629874,1.0432,0.777296,0.296474,0.9011,0.00454122,0.167758,0.211406,0.853868,1.66928,1.27308,0.811357,0.313144,0.541193,0.420352,0.605406,0.375553,1.62988,0.169369,0.0799646,0.208241,0.00366709,0.66331,0.754242,0.802114,0.739975,0.324625,0.0943424,0.483688,0.167568,0.862985,0.601424,0.501973,0.15582,1.07177,0.289792,0.0688048,0.259556,0.00651025
|tfbs_overrepresentation_for_novel_motifs=0.162057,0.239198,0.144778,0.191238,0.572598,1.10473,0.270195,0.614792,0.15797,0.115943,0.236307,0.260789,0.340991,0.766078,0.615754,0,0.44163,0.552297,0.130179,0.278706,0.385752,0.519892,0.279154,1.43683,0.149704,0.301898,0.849653,0.216938,0.691298,0.393858,0.206597,0.531719,0.0739139,0.249044,0.0880674,0.115941,0.0693463,0.257981,0.468707,0.0468666,0.56228,0.210373,0.46646,0.620985,0.0747075,0.183361,0.372907,0.228683,0.800575,0.343195,0.426383,0.323798,0.372474,0.661847,0.67813,0.28555,0.722962,0.25091,0.111806,0.283926,0.513661,0.331566,0.172226,0.4166,0.294453,0.451957,0.806865,1.14503,0.509463,1.00145,0.414221,0.353861,0.0896041,0.709559,0.0246496,0.234413,0.468707,0.363297,0.498264,0.124234,0.3566,0.456892,0.330377,0.139579,0.602212,0.00517576,0.0258882,0.394307,0.377064,1.30447,0.873554,0.606796,0.543309,0.280055,0.209139,0.732474,0.606117,0.545856,0.373124,0.0619917,0.894464,0.531465,0.645628,0.4269,0.425983,0.21005,0.478524,0.225669,0.400135,0.122746,0.157325,0.647285,0.124928,0.67478,0.880323,0.263255,0.0347519,0.565346,0.442771,0.51371,0.714636,0.398522,0.303371,0.362534,0.932468,0.501574,0.758659,0.53717,0.805419,0.284377,0.629874,1.0432,0.777296,0.296474,0.9011,0.00454122,0.167758,0.211406,0.853868,1.66928,1.27308,0.811357,0.313144,0.541193,0.420352,0.605406,0.375553,1.62988,0.169369,0.0799646,0.208241,0.00366709,0.66331,0.754242,0.802114,0.739975,0.324625,0.0943424,0.483688,0.167568,0.862985,0.601424,0.501973,0.15582,1.07177,0.289792,0.0688048,0.259556,0.00651025
|tfbs_overrepresentation_jaspar=MA0003.1;5.87279e-05,MA0004.1;0.191582,MA0006.1;0.0854592,MA0007.1;0.181021,MA0009.1;0.5557,MA0014.1;0.00614145,MA0017.1;0.673859,MA0019.1;0.394308,MA0024.1;0.516087,MA0025.1;0.773017,MA0027.1;2.16618,MA0028.1;0.0910441,MA0029.1;0.496599,MA0030.1;0.502474,MA0031.1;1.18689,MA0038.1;0.815918,MA0040.1;0.567108,MA0041.1;0.140298,MA0042.1;1.32684,MA0043.1;0.644695,MA0046.1;4.81363,MA0048.1;0.0629374,MA0050.1;0.219748,MA0051.1;0.309072,MA0052.1;0.574473,MA0055.1;0.12934,MA0056.1;0,MA0057.1;0.0109462,MA0058.1;0.127732,MA0059.1;0.13543,MA0060.1;0.0476793,MA0061.1;0.824437,MA0063.1;0,MA0066.1;0.795934,MA0067.1;0.879099,MA0068.1;0.309163,MA0069.1;0.574784,MA0070.1;0.565924,MA0071.1;0.625332,MA0072.1;0.558195,MA0073.1;0.129157,MA0074.1;1.3445,MA0076.1;0.110983,MA0077.1;0.538513,MA0078.1;0.89286,MA0081.1;0.458627,MA0083.1;0.643958,MA0084.1;1.1979,MA0087.1;0.604077,MA0088.1;0.0849312,MA0089.1;0,MA0090.1;0.969034,MA0091.1;0.200988,MA0092.1;0.969912,MA0093.1;0.0955883,MA0095.1;0,MA0098.1;0,MA0100.1;0.255651,MA0101.1;0.435524,MA0103.1;0.345124,MA0105.1;0.239813,MA0106.1;0.342589,MA0107.1;0.686139,MA0108.2;0.413973,MA0109.1;0,MA0111.1;0.177475,MA0113.1;0.319332,MA0114.1;0.215695,MA0115.1;0.647296,MA0116.1;0.08535,MA0117.1;0.617392,MA0119.1;0.436476,MA0122.1;1.53613,MA0124.1;0.828115,MA0125.1;0.757653,MA0130.1;0,MA0131.1;0.390422,MA0132.1;0,MA0133.1;0,MA0135.1;0.67864,MA0136.1;0.280269,MA0139.1;0.0357525,MA0140.1;0.710317,MA0141.1;0.37559,MA0142.1;0.457961,MA0143.1;0.332773,MA0144.1;1.25437,MA0145.1;0.0329339,MA0146.1;0.0100022,MA0147.1;0.0666796,MA0148.1;0.203219,MA0149.1;0.144679,MA0062.2;0.0237736,MA0035.2;0.259203,MA0039.2;0.00331256,MA0138.2;0.383644,MA0002.2;0.338271,MA0137.2;0.371067,MA0104.2;0.0420926,MA0047.2;0.301217,MA0112.2;0.0329313,MA0065.2;0.0973139,MA0150.1;0.53401,MA0151.1;0,MA0152.1;0.301303,MA0153.1;4.04272,MA0154.1;0.0127415,MA0155.1;0.118163,MA0156.1;0.110475,MA0157.1;1.09863,MA0158.1;0,MA0159.1;0.0715631,MA0160.1;0.205397,MA0161.1;0,MA0162.1;0.0145482,MA0163.1;0.0339329,MA0164.1;0.767642,MA0080.2;0.103116,MA0018.2;0.288261,MA0099.2;0.37828,MA0079.2;0.00230365,MA0102.2;1.24942,MA0258.1;0.0535937,MA0259.1;0.0616796,MA0442.1;0
}}
}}

Revision as of 11:42, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:102491237..102491291,-p2@Alx1
Mm9::chr10:45588552..45588568,+p@chr10:45588552..45588568
+
Mm9::chr10:50622895..50622905,+p@chr10:50622895..50622905
+
Mm9::chr12:37259377..37259386,+p@chr12:37259377..37259386
+
Mm9::chr13:115892012..115892032,-p10@Itga1
Mm9::chr13:7174912..7174917,-p@chr13:7174912..7174917
-
Mm9::chr15:98639918..98639923,-p@chr15:98639918..98639923
-
Mm9::chr2:113205651..113205663,+p@chr2:113205651..113205663
+
Mm9::chr3:132528811..132528861,+p@chr3:132528811..132528861
+
Mm9::chr3:132546346..132546356,-p@chr3:132546346..132546356
-
Mm9::chr3:54490675..54490702,-p@chr3:54490675..54490702
-
Mm9::chr3:54490730..54490743,-p@chr3:54490730..54490743
-
Mm9::chr5:16903685..16903695,-p@chr5:16903685..16903695
-
Mm9::chr5:16903720..16903727,-p@chr5:16903720..16903727
-
Mm9::chr5:53400291..53400314,-p@chr5:53400291..53400314
-
Mm9::chr7:31992851..31992858,+p@chr7:31992851..31992858
+
Mm9::chr8:108119034..108119056,+p@chr8:108119034..108119056
+
Mm9::chr8:47515509..47515529,-p@chr8:47515509..47515529
-


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:0030511positive regulation of transforming growth factor beta receptor signaling pathway0.0256382161274507
GO:0017015regulation of transforming growth factor beta receptor signaling pathway0.0421083748790152
GO:0001658ureteric bud branching0.0421083748790152
GO:0005178integrin binding0.0421083748790152
GO:0001657ureteric bud development0.0421083748790152
GO:0001656metanephros development0.0421083748790152
GO:0007179transforming growth factor beta receptor signaling pathway0.0421083748790152
GO:0032403protein complex binding0.0421083748790152
GO:0048754branching morphogenesis of a tube0.0421083748790152
GO:0001763morphogenesis of a branching structure0.0421083748790152
GO:0007160cell-matrix adhesion0.0421083748790152
GO:0009967positive regulation of signal transduction0.0421083748790152
GO:0031589cell-substrate adhesion0.0421083748790152
GO:0001822kidney development0.0421083748790152
GO:0001655urogenital system development0.0421083748790152
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0421083748790152



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
kidney1.18e-3314
kidney mesenchyme1.18e-3314
upper urinary tract1.18e-3314
kidney rudiment1.18e-3314
kidney field1.18e-3314
urinary system structure7.21e-2618
renal system1.97e-2419
cavitated compound organ5.70e-2221
compound organ5.73e-1043
abdomen element1.47e-0849
abdominal segment element1.47e-0849
abdominal segment of trunk1.47e-0849
abdomen1.47e-0849


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)
MA0003.15.87279e-05
MA0004.10.191582
MA0006.10.0854592
MA0007.10.181021
MA0009.10.5557
MA0014.10.00614145
MA0017.10.673859
MA0019.10.394308
MA0024.10.516087
MA0025.10.773017
MA0027.12.16618
MA0028.10.0910441
MA0029.10.496599
MA0030.10.502474
MA0031.11.18689
MA0038.10.815918
MA0040.10.567108
MA0041.10.140298
MA0042.11.32684
MA0043.10.644695
MA0046.14.81363
MA0048.10.0629374
MA0050.10.219748
MA0051.10.309072
MA0052.10.574473
MA0055.10.12934
MA0056.10
MA0057.10.0109462
MA0058.10.127732
MA0059.10.13543
MA0060.10.0476793
MA0061.10.824437
MA0063.10
MA0066.10.795934
MA0067.10.879099
MA0068.10.309163
MA0069.10.574784
MA0070.10.565924
MA0071.10.625332
MA0072.10.558195
MA0073.10.129157
MA0074.11.3445
MA0076.10.110983
MA0077.10.538513
MA0078.10.89286
MA0081.10.458627
MA0083.10.643958
MA0084.11.1979
MA0087.10.604077
MA0088.10.0849312
MA0089.10
MA0090.10.969034
MA0091.10.200988
MA0092.10.969912
MA0093.10.0955883
MA0095.10
MA0098.10
MA0100.10.255651
MA0101.10.435524
MA0103.10.345124
MA0105.10.239813
MA0106.10.342589
MA0107.10.686139
MA0108.20.413973
MA0109.10
MA0111.10.177475
MA0113.10.319332
MA0114.10.215695
MA0115.10.647296
MA0116.10.08535
MA0117.10.617392
MA0119.10.436476
MA0122.11.53613
MA0124.10.828115
MA0125.10.757653
MA0130.10
MA0131.10.390422
MA0132.10
MA0133.10
MA0135.10.67864
MA0136.10.280269
MA0139.10.0357525
MA0140.10.710317
MA0141.10.37559
MA0142.10.457961
MA0143.10.332773
MA0144.11.25437
MA0145.10.0329339
MA0146.10.0100022
MA0147.10.0666796
MA0148.10.203219
MA0149.10.144679
MA0062.20.0237736
MA0035.20.259203
MA0039.20.00331256
MA0138.20.383644
MA0002.20.338271
MA0137.20.371067
MA0104.20.0420926
MA0047.20.301217
MA0112.20.0329313
MA0065.20.0973139
MA0150.10.53401
MA0151.10
MA0152.10.301303
MA0153.14.04272
MA0154.10.0127415
MA0155.10.118163
MA0156.10.110475
MA0157.11.09863
MA0158.10
MA0159.10.0715631
MA0160.10.205397
MA0161.10
MA0162.10.0145482
MA0163.10.0339329
MA0164.10.767642
MA0080.20.103116
MA0018.20.288261
MA0099.20.37828
MA0079.20.00230365
MA0102.21.24942
MA0258.10.0535937
MA0259.10.0616796
MA0442.10
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