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MCL coexpression mm9:334: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000369!1.03e-13!5;UBERON:0002435!1.03e-13!5;UBERON:0000204!1.03e-13!5;UBERON:0010082!1.03e-13!5;UBERON:0002420!1.29e-08!8;UBERON:0007245!1.29e-08!8;UBERON:0010009!1.29e-08!8;UBERON:0010011!1.29e-08!8;UBERON:0000454!1.29e-08!8;UBERON:0002780!1.74e-07!39;UBERON:0001890!1.74e-07!39;UBERON:0006240!1.74e-07!39;UBERON:0003080!2.91e-07!40;UBERON:0002020!6.76e-07!34
|ontology_enrichment_uberon=UBERON:0000369!1.03e-13!5;UBERON:0002435!1.03e-13!5;UBERON:0000204!1.03e-13!5;UBERON:0010082!1.03e-13!5;UBERON:0002420!1.29e-08!8;UBERON:0007245!1.29e-08!8;UBERON:0010009!1.29e-08!8;UBERON:0010011!1.29e-08!8;UBERON:0000454!1.29e-08!8;UBERON:0002780!1.74e-07!39;UBERON:0001890!1.74e-07!39;UBERON:0006240!1.74e-07!39;UBERON:0003080!2.91e-07!40;UBERON:0002020!6.76e-07!34
|tfbs_overrepresentation_for_novel_motifs=0.687857,0.513209,0.0894988,0.397943,1.02352,0.419638,0.192737,0.0727967,0.204405,0.0133444,0.163789,0.184641,0.61373,0.20111,0.404084,0,0.915598,0.152896,0.165057,0.0551341,1.37259,0.0269888,0.200489,0.653803,0.64228,1.17751,0.307294,0.147544,0.810037,0.205066,0.430073,0.430274,0.150515,0.692923,0.0478417,0.504078,0.140835,0.182233,1.21697,0.0932741,0.360254,0.142092,0.720796,0.182247,0.0171699,0.765318,0.77462,0.476169,1.28355,0.217247,0.332337,0.239655,0.190262,0.553844,0.569458,0.206047,0.85061,1.00342,0.13935,0.204634,0.413329,0.689471,0.224761,0.323367,0.213815,0.355898,0.693798,1.02539,0.409398,0.883956,0.0802912,0.0773092,0.158212,0.599674,0.268165,0.656441,0.692559,0.274952,0.398928,0.25704,0.0782417,0.360462,0.245495,0.0680726,0.496926,0.0669719,2.02515,1.88801,0.287376,1.18318,0.758722,0.501285,0.44118,0.3811,0.277879,0.74792,0.362313,0.44358,0.283814,1.65179,0.140916,0.430036,0.538321,0.332812,0.33197,0.437288,0.991028,0.469886,0.263369,0.253898,0.0992584,0.539906,0.549141,0.167109,0.765328,0.155153,0.114081,0.803238,0.347417,1.32042,0.604565,0.306855,0.22163,0.274265,0.816304,1.03808,0.575824,0.4354,0.692394,0.387426,0.523273,0.387123,0.665113,0.616957,0.785621,0.0672984,0.348707,0.142948,0.739526,1.5459,1.15207,0.698162,0.651432,0.439187,0.326804,0.142367,0.286009,1.50665,0.108773,0.372343,0.098209,0.0210472,0.555246,0.104696,0.615417,0.629009,0.240389,0.430204,0.101676,1.16738,0.748413,1.24129,0.402392,0.323614,0.324177,0.603124,0.139687,0.183582,0.217063
|tfbs_overrepresentation_for_novel_motifs=0.687857,0.513209,0.0894988,0.397943,1.02352,0.419638,0.192737,0.0727967,0.204405,0.0133444,0.163789,0.184641,0.61373,0.20111,0.404084,0,0.915598,0.152896,0.165057,0.0551341,1.37259,0.0269888,0.200489,0.653803,0.64228,1.17751,0.307294,0.147544,0.810037,0.205066,0.430073,0.430274,0.150515,0.692923,0.0478417,0.504078,0.140835,0.182233,1.21697,0.0932741,0.360254,0.142092,0.720796,0.182247,0.0171699,0.765318,0.77462,0.476169,1.28355,0.217247,0.332337,0.239655,0.190262,0.553844,0.569458,0.206047,0.85061,1.00342,0.13935,0.204634,0.413329,0.689471,0.224761,0.323367,0.213815,0.355898,0.693798,1.02539,0.409398,0.883956,0.0802912,0.0773092,0.158212,0.599674,0.268165,0.656441,0.692559,0.274952,0.398928,0.25704,0.0782417,0.360462,0.245495,0.0680726,0.496926,0.0669719,2.02515,1.88801,0.287376,1.18318,0.758722,0.501285,0.44118,0.3811,0.277879,0.74792,0.362313,0.44358,0.283814,1.65179,0.140916,0.430036,0.538321,0.332812,0.33197,0.437288,0.991028,0.469886,0.263369,0.253898,0.0992584,0.539906,0.549141,0.167109,0.765328,0.155153,0.114081,0.803238,0.347417,1.32042,0.604565,0.306855,0.22163,0.274265,0.816304,1.03808,0.575824,0.4354,0.692394,0.387426,0.523273,0.387123,0.665113,0.616957,0.785621,0.0672984,0.348707,0.142948,0.739526,1.5459,1.15207,0.698162,0.651432,0.439187,0.326804,0.142367,0.286009,1.50665,0.108773,0.372343,0.098209,0.0210472,0.555246,0.104696,0.615417,0.629009,0.240389,0.430204,0.101676,1.16738,0.748413,1.24129,0.402392,0.323614,0.324177,0.603124,0.139687,0.183582,0.217063
|tfbs_overrepresentation_jaspar=MA0003.1;0.0146026,MA0004.1;0.126659,MA0006.1;0.699047,MA0007.1;0.376537,MA0009.1;1.14834,MA0014.1;0.208889,MA0017.1;1.20061,MA0019.1;0.30302,MA0024.1;0.415603,MA0025.1;0.660968,MA0027.1;2.04174,MA0028.1;0.186822,MA0029.1;0.397373,MA0030.1;0.402861,MA0031.1;0.975206,MA0038.1;0.62805,MA0040.1;0.463641,MA0041.1;0.607211,MA0042.1;0.273359,MA0043.1;0.53743,MA0046.1;0.483941,MA0048.1;0.715446,MA0050.1;0.149886,MA0051.1;0.226644,MA0052.1;0.47061,MA0055.1;0.0383365,MA0056.1;0,MA0057.1;0.14014,MA0058.1;0.264426,MA0059.1;0.588924,MA0060.1;1.06672,MA0061.1;0.0296722,MA0063.1;0,MA0066.1;0.609771,MA0067.1;0.764133,MA0068.1;0.449127,MA0069.1;1.18716,MA0070.1;1.16914,MA0071.1;1.43385,MA0072.1;1.15342,MA0073.1;9.2374,MA0074.1;0.550954,MA0076.1;0.064121,MA0077.1;1.11336,MA0078.1;0.250627,MA0081.1;0.644573,MA0083.1;0.536725,MA0084.1;1.07765,MA0087.1;0.4987,MA0088.1;0.41334,MA0089.1;0,MA0090.1;0.708683,MA0091.1;0.134352,MA0092.1;0.349135,MA0093.1;0.196448,MA0095.1;0,MA0098.1;0,MA0100.1;0.180237,MA0101.1;0.292678,MA0103.1;0.218786,MA0105.1;0.669937,MA0106.1;0.256379,MA0107.1;0.0580742,MA0108.2;0.320962,MA0109.1;0,MA0111.1;0.115252,MA0113.1;0.2357,MA0114.1;0.287365,MA0115.1;1.33437,MA0116.1;0.0459718,MA0117.1;0.511373,MA0119.1;1.0261,MA0122.1;0.528896,MA0124.1;0.714453,MA0125.1;0.646095,MA0130.1;0,MA0131.1;0.810613,MA0132.1;0,MA0133.1;0,MA0135.1;0.569948,MA0136.1;0.583392,MA0139.1;0.35839,MA0140.1;0.180161,MA0141.1;0.892059,MA0142.1;0.361451,MA0143.1;1.28115,MA0144.1;0.293322,MA0145.1;0.663753,MA0146.1;0.0147284,MA0147.1;0.911853,MA0148.1;0.836385,MA0149.1;5.78394,MA0062.2;0.125873,MA0035.2;0.18328,MA0039.2;0.145091,MA0138.2;0.293335,MA0002.2;0.366396,MA0137.2;0.514948,MA0104.2;0.988517,MA0047.2;0.626771,MA0112.2;0.295523,MA0065.2;0.0863447,MA0150.1;0.11804,MA0151.1;0,MA0152.1;0.62695,MA0153.1;0.584906,MA0154.1;0.158528,MA0155.1;0.354426,MA0156.1;0.0637507,MA0157.1;0.8915,MA0158.1;0,MA0159.1;0.610644,MA0160.1;0.844124,MA0161.1;0,MA0162.1;0.159338,MA0163.1;0.2152,MA0164.1;0.201705,MA0080.2;0.464846,MA0018.2;0.208409,MA0099.2;0.288477,MA0079.2;1.99251,MA0102.2;1.12863,MA0258.1;0.107482,MA0259.1;0.124592,MA0442.1;0
}}
}}

Revision as of 11:35, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:44456621..44456634,+p@chr11:44456621..44456634
+
Mm9::chr11:44456648..44456656,+p@chr11:44456648..44456656
+
Mm9::chr12:107682982..107682991,-p@chr12:107682982..107682991
-
Mm9::chr13:98010402..98010420,+p@chr13:98010402..98010420
+
Mm9::chr13:98013895..98013931,+p@chr13:98013895..98013931
+
Mm9::chr13:98014013..98014020,+p@chr13:98014013..98014020
+
Mm9::chr17:43295228..43295255,-p1@E130008D07Rik
Mm9::chr17:85116028..85116057,-p@chr17:85116028..85116057
-
Mm9::chr18:67292732..67292740,+p@chr18:67292732..67292740
+
Mm9::chr18:67292751..67292763,+p@chr18:67292751..67292763
+
Mm9::chr1:178744297..178744320,-p3@Cep170
Mm9::chr2:116223084..116223093,-p@chr2:116223084..116223093
-
Mm9::chr2:32178964..32178975,-p@chr2:32178964..32178975
-
Mm9::chr2:69933028..69933041,+p@chr2:69933028..69933041
+
Mm9::chr3:153991607..153991627,-p2@Lhx8
Mm9::chr3:153993295..153993298,-p3@Lhx8
Mm9::chr4:131377546..131377578,-p3@Ptpru
Mm9::chr4:154597342..154597358,-p@chr4:154597342..154597358
-
Mm9::chr6:128363704..128363746,-p@chr6:128363704..128363746
-
Mm9::chr6:99154456..99154464,-p@chr6:99154456..99154464
-
Mm9::chr6:99154482..99154491,-p@chr6:99154482..99154491
-
Mm9::chr9:121905215..121905233,+p@chr9:121905215..121905233
+
Mm9::chr9:53783897..53783904,-p@chr9:53783897..53783904
-
Mm9::chr9:53783907..53783912,-p@chr9:53783907..53783912
-


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:0019198transmembrane receptor protein phosphatase activity0.0185175039719498
GO:0005001transmembrane receptor protein tyrosine phosphatase activity0.0185175039719498
GO:0021879forebrain neuron differentiation0.0475499523893807
GO:0007191dopamine receptor, adenylate cyclase activating pathway0.0475499523893807
GO:0004727prenylated protein tyrosine phosphatase activity0.0475499523893807
GO:0021872generation of neurons in the forebrain0.0475499523893807
GO:0007190adenylate cyclase activation0.0475499523893807
GO:0045762positive regulation of adenylate cyclase activity0.0475499523893807
GO:0031281positive regulation of cyclase activity0.0475499523893807
GO:0051349positive regulation of lyase activity0.0475499523893807
GO:0045761regulation of adenylate cyclase activity0.0475499523893807
GO:0031279regulation of cyclase activity0.0475499523893807
GO:0007212dopamine receptor signaling pathway0.0475499523893807
GO:0051339regulation of lyase activity0.0475499523893807
GO:0007185transmembrane receptor protein tyrosine phosphatase signaling pathway0.0493029557375933



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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
hippocampal neuron6.29e-143
neuron of cerebral cortex3.55e-076


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)
MA0003.10.0146026
MA0004.10.126659
MA0006.10.699047
MA0007.10.376537
MA0009.11.14834
MA0014.10.208889
MA0017.11.20061
MA0019.10.30302
MA0024.10.415603
MA0025.10.660968
MA0027.12.04174
MA0028.10.186822
MA0029.10.397373
MA0030.10.402861
MA0031.10.975206
MA0038.10.62805
MA0040.10.463641
MA0041.10.607211
MA0042.10.273359
MA0043.10.53743
MA0046.10.483941
MA0048.10.715446
MA0050.10.149886
MA0051.10.226644
MA0052.10.47061
MA0055.10.0383365
MA0056.10
MA0057.10.14014
MA0058.10.264426
MA0059.10.588924
MA0060.11.06672
MA0061.10.0296722
MA0063.10
MA0066.10.609771
MA0067.10.764133
MA0068.10.449127
MA0069.11.18716
MA0070.11.16914
MA0071.11.43385
MA0072.11.15342
MA0073.19.2374
MA0074.10.550954
MA0076.10.064121
MA0077.11.11336
MA0078.10.250627
MA0081.10.644573
MA0083.10.536725
MA0084.11.07765
MA0087.10.4987
MA0088.10.41334
MA0089.10
MA0090.10.708683
MA0091.10.134352
MA0092.10.349135
MA0093.10.196448
MA0095.10
MA0098.10
MA0100.10.180237
MA0101.10.292678
MA0103.10.218786
MA0105.10.669937
MA0106.10.256379
MA0107.10.0580742
MA0108.20.320962
MA0109.10
MA0111.10.115252
MA0113.10.2357
MA0114.10.287365
MA0115.11.33437
MA0116.10.0459718
MA0117.10.511373
MA0119.11.0261
MA0122.10.528896
MA0124.10.714453
MA0125.10.646095
MA0130.10
MA0131.10.810613
MA0132.10
MA0133.10
MA0135.10.569948
MA0136.10.583392
MA0139.10.35839
MA0140.10.180161
MA0141.10.892059
MA0142.10.361451
MA0143.11.28115
MA0144.10.293322
MA0145.10.663753
MA0146.10.0147284
MA0147.10.911853
MA0148.10.836385
MA0149.15.78394
MA0062.20.125873
MA0035.20.18328
MA0039.20.145091
MA0138.20.293335
MA0002.20.366396
MA0137.20.514948
MA0104.20.988517
MA0047.20.626771
MA0112.20.295523
MA0065.20.0863447
MA0150.10.11804
MA0151.10
MA0152.10.62695
MA0153.10.584906
MA0154.10.158528
MA0155.10.354426
MA0156.10.0637507
MA0157.10.8915
MA0158.10
MA0159.10.610644
MA0160.10.844124
MA0161.10
MA0162.10.159338
MA0163.10.2152
MA0164.10.201705
MA0080.20.464846
MA0018.20.208409
MA0099.20.288477
MA0079.21.99251
MA0102.21.12863
MA0258.10.107482
MA0259.10.124592
MA0442.10
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