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MCL coexpression mm9:364: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001048!5.08e-10!134;UBERON:0004177!7.09e-09!29;UBERON:0005057!7.09e-09!29;UBERON:0000153!1.37e-08!43
|ontology_enrichment_uberon=UBERON:0001048!5.08e-10!134;UBERON:0004177!7.09e-09!29;UBERON:0005057!7.09e-09!29;UBERON:0000153!1.37e-08!43
|tfbs_overrepresentation_for_novel_motifs=0.803677,0.142888,0.735588,0.15483,0.458154,0.493109,1.20411,0.475556,0.271611,1.32858,1.08239,0.218542,0.253571,0.665571,0.0644609,0,0.38962,0.439815,0.225105,0.189639,0.310483,0.216191,1.23585,0.206855,1.2359,1.3157,0.664709,0.527289,0.566523,0.487282,0.504259,0.476579,0.434657,0.348165,0.230648,0.0587911,1.11899,0.617803,0.365025,0.304085,0.203766,0.512679,0.0387176,0.502107,0.482047,0.885707,0.323935,0.553328,0.137829,0.0792869,0.374992,0.760562,0.266413,0.603398,0.619345,0.677917,0.0837141,1.13518,0.0753109,1.94242,0.459084,0.777251,0.124057,0.958213,0.2499,0.399544,0.745869,1.08074,0.455021,0.938231,1.13692,0.792871,3.05864,0.650163,0.598389,1.16897,0.0671053,0.314806,0.444191,0.316521,0.110035,1.04303,0.774697,0.737927,1.34542,1.36368,0.0773437,0.139502,0.327889,1.23935,0.811671,0.549603,0.487824,0.216228,1.41986,0.318866,0.248387,0.490297,0.324141,0.909992,0.413671,0.476334,1.43493,0.979946,0.374608,2.2355,0.42513,0.546657,0.664746,1.07708,0.393011,0.58915,0.318143,1.09663,0.818358,0.444691,1.12275,0.475893,1.01337,0.405138,0.655146,0.348339,0.258253,0.314081,0.869916,0.447391,0.233251,0.481866,0.744444,0.0610298,0.572132,0.150169,0.716744,0.251791,0.838892,0.211231,0.133745,0.17313,0.792231,1.60311,1.2081,0.750296,0.267427,0.48577,0.369214,0.172491,0.326451,1.56378,0.135184,1.22075,0.291049,4.64774,0.60483,0.14223,0.251095,0.680035,1.39455,0.526055,0.797218,0.416368,0.801233,0.544365,0.447776,0.389566,0.366469,0.245542,0.183595,0.217399,0.355578
|tfbs_overrepresentation_for_novel_motifs=0.803677,0.142888,0.735588,0.15483,0.458154,0.493109,1.20411,0.475556,0.271611,1.32858,1.08239,0.218542,0.253571,0.665571,0.0644609,0,0.38962,0.439815,0.225105,0.189639,0.310483,0.216191,1.23585,0.206855,1.2359,1.3157,0.664709,0.527289,0.566523,0.487282,0.504259,0.476579,0.434657,0.348165,0.230648,0.0587911,1.11899,0.617803,0.365025,0.304085,0.203766,0.512679,0.0387176,0.502107,0.482047,0.885707,0.323935,0.553328,0.137829,0.0792869,0.374992,0.760562,0.266413,0.603398,0.619345,0.677917,0.0837141,1.13518,0.0753109,1.94242,0.459084,0.777251,0.124057,0.958213,0.2499,0.399544,0.745869,1.08074,0.455021,0.938231,1.13692,0.792871,3.05864,0.650163,0.598389,1.16897,0.0671053,0.314806,0.444191,0.316521,0.110035,1.04303,0.774697,0.737927,1.34542,1.36368,0.0773437,0.139502,0.327889,1.23935,0.811671,0.549603,0.487824,0.216228,1.41986,0.318866,0.248387,0.490297,0.324141,0.909992,0.413671,0.476334,1.43493,0.979946,0.374608,2.2355,0.42513,0.546657,0.664746,1.07708,0.393011,0.58915,0.318143,1.09663,0.818358,0.444691,1.12275,0.475893,1.01337,0.405138,0.655146,0.348339,0.258253,0.314081,0.869916,0.447391,0.233251,0.481866,0.744444,0.0610298,0.572132,0.150169,0.716744,0.251791,0.838892,0.211231,0.133745,0.17313,0.792231,1.60311,1.2081,0.750296,0.267427,0.48577,0.369214,0.172491,0.326451,1.56378,0.135184,1.22075,0.291049,4.64774,0.60483,0.14223,0.251095,0.680035,1.39455,0.526055,0.797218,0.416368,0.801233,0.544365,0.447776,0.389566,0.366469,0.245542,0.183595,0.217399,0.355578
|tfbs_overrepresentation_jaspar=MA0003.1;1.50244,MA0004.1;0.916865,MA0006.1;1.77185,MA0007.1;0.446853,MA0009.1;0.499857,MA0014.1;1.28316,MA0017.1;0.259254,MA0019.1;0.344318,MA0024.1;2.03258,MA0025.1;0.712532,MA0027.1;2.09948,MA0028.1;2.41055,MA0029.1;0.442582,MA0030.1;0.448261,MA0031.1;0.417663,MA0038.1;0.713204,MA0040.1;0.510947,MA0041.1;0.353863,MA0042.1;0.102161,MA0043.1;0.586618,MA0046.1;0.531807,MA0048.1;1.61436,MA0050.1;1.02182,MA0051.1;0.728838,MA0052.1;0.518112,MA0055.1;0.136741,MA0056.1;0,MA0057.1;0.204512,MA0058.1;1.10711,MA0059.1;0.698078,MA0060.1;2.23398,MA0061.1;0.163238,MA0063.1;0,MA0066.1;0.248543,MA0067.1;0.817149,MA0068.1;0.214228,MA0069.1;1.2887,MA0070.1;0.509795,MA0071.1;0.180178,MA0072.1;0.502282,MA0073.1;0.0360649,MA0074.1;0.632353,MA0076.1;2.0534,MA0077.1;0.48317,MA0078.1;0.289095,MA0081.1;0.37696,MA0083.1;0.585897,MA0084.1;1.1333,MA0087.1;0.546952,MA0088.1;1.74752,MA0089.1;0,MA0090.1;0.416778,MA0091.1;0.163657,MA0092.1;0.133927,MA0093.1;1.36217,MA0095.1;0,MA0098.1;0,MA0100.1;0.612698,MA0101.1;0.720996,MA0103.1;0.273906,MA0105.1;0.848889,MA0106.1;2.22561,MA0107.1;0.952044,MA0108.2;0.363107,MA0109.1;0,MA0111.1;0.14244,MA0113.1;0.273246,MA0114.1;0.367031,MA0115.1;0.589161,MA0116.1;0.0624169,MA0117.1;0.559943,MA0119.1;0.110503,MA0122.1;0.577888,MA0124.1;0.766819,MA0125.1;1.66463,MA0130.1;0,MA0131.1;1.6184,MA0132.1;0,MA0133.1;0,MA0135.1;0.619844,MA0136.1;0.236653,MA0139.1;1.50059,MA0140.1;0.2137,MA0141.1;0.0898383,MA0142.1;0.40532,MA0143.1;0.285913,MA0144.1;0.164087,MA0145.1;0.252942,MA0146.1;1.02077,MA0147.1;2.05316,MA0148.1;0.960549,MA0149.1;0.113293,MA0062.2;1.62311,MA0035.2;0.217072,MA0039.2;0.921376,MA0138.2;0.334152,MA0002.2;0.10237,MA0137.2;0.618368,MA0104.2;3.81377,MA0047.2;0.711867,MA0112.2;0.134174,MA0065.2;0.0584336,MA0150.1;0.145553,MA0151.1;0,MA0152.1;0.256315,MA0153.1;0.635107,MA0154.1;0.227476,MA0155.1;0.301849,MA0156.1;1.00164,MA0157.1;0.378326,MA0158.1;0,MA0159.1;0.423802,MA0160.1;0.167661,MA0161.1;0,MA0162.1;2.79601,MA0163.1;0.140172,MA0164.1;0.23692,MA0080.2;0.266721,MA0018.2;0.244112,MA0099.2;0.329046,MA0079.2;0.603083,MA0102.2;1.18455,MA0258.1;0.145568,MA0259.1;1.97325,MA0442.1;0
}}
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Revision as of 11:38, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:116813978..116814010,-p2@Cpsf6
Mm9::chr10:41529426..41529460,-p1@Cep57l1
Mm9::chr10:62254991..62255038,-p1@Ccar1
Mm9::chr11:17853864..17853900,-p1@Etaa1
Mm9::chr11:23155920..23155976,+p2@Xpo1
Mm9::chr11:53520771..53520834,-p1@Rad50
Mm9::chr11:80196811..80196838,+p1@Zfp207
Mm9::chr15:55389130..55389159,+p1@Mtbp
Mm9::chr17:41071446..41071558,-p1@Cenpq
Mm9::chr18:67959755..67959801,+p1@Cep192
Mm9::chr18:89141394..89141432,+p1@Rttn
Mm9::chr1:155334769..155334792,-p1@Dhx9
Mm9::chr1:182571461..182571505,+p1@Lin9
Mm9::chr1:183074264..183074314,-p1@Nvl
Mm9::chr2:34987686..34987709,+p3@Cep110
Mm9::chr4:86257913..86257966,-p1@Haus6
Mm9::chr5:151476421..151476452,+p2@Pds5b
Mm9::chr5:34512058..34512115,-p1@Haus3
p1@Poln
Mm9::chr5:65726836..65726918,-p1@Rfc1
Mm9::chr5:66155312..66155397,+p1@N4bp2
Mm9::chr6:112646628..112646669,-p1@Rad18


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:0005634nucleus0.00512483060266638
GO:0007049cell cycle0.0171152652579545
GO:0030870Mre11 complex0.0357447406800923
GO:0022402cell cycle process0.0357447406800923
GO:0044446intracellular organelle part0.0357447406800923
GO:0044422organelle part0.0357447406800923
GO:0022403cell cycle phase0.0357447406800923
GO:0044427chromosomal part0.0402364740055755
GO:0043229intracellular organelle0.0402364740055755
GO:0043226organelle0.0402364740055755
GO:0008518reduced folate carrier activity0.0402364740055755
GO:0007089traversing start control point of mitotic cell cycle0.0402364740055755
GO:0005694chromosome0.0420588855377702
GO:0043231intracellular membrane-bound organelle0.042427193292381
GO:0043227membrane-bound organelle0.042427193292381
GO:0005635nuclear envelope0.042427193292381
GO:0044424intracellular part0.0439915766739227
GO:0000080G1 phase of mitotic cell cycle0.0465642675211963
GO:0051318G1 phase0.0465642675211963
GO:0043232intracellular non-membrane-bound organelle0.0465642675211963
GO:0043228non-membrane-bound organelle0.0465642675211963



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
primordium5.08e-10134
hemopoietic organ7.09e-0929
immune organ7.09e-0929
anterior region of body1.37e-0843


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)
MA0003.11.50244
MA0004.10.916865
MA0006.11.77185
MA0007.10.446853
MA0009.10.499857
MA0014.11.28316
MA0017.10.259254
MA0019.10.344318
MA0024.12.03258
MA0025.10.712532
MA0027.12.09948
MA0028.12.41055
MA0029.10.442582
MA0030.10.448261
MA0031.10.417663
MA0038.10.713204
MA0040.10.510947
MA0041.10.353863
MA0042.10.102161
MA0043.10.586618
MA0046.10.531807
MA0048.11.61436
MA0050.11.02182
MA0051.10.728838
MA0052.10.518112
MA0055.10.136741
MA0056.10
MA0057.10.204512
MA0058.11.10711
MA0059.10.698078
MA0060.12.23398
MA0061.10.163238
MA0063.10
MA0066.10.248543
MA0067.10.817149
MA0068.10.214228
MA0069.11.2887
MA0070.10.509795
MA0071.10.180178
MA0072.10.502282
MA0073.10.0360649
MA0074.10.632353
MA0076.12.0534
MA0077.10.48317
MA0078.10.289095
MA0081.10.37696
MA0083.10.585897
MA0084.11.1333
MA0087.10.546952
MA0088.11.74752
MA0089.10
MA0090.10.416778
MA0091.10.163657
MA0092.10.133927
MA0093.11.36217
MA0095.10
MA0098.10
MA0100.10.612698
MA0101.10.720996
MA0103.10.273906
MA0105.10.848889
MA0106.12.22561
MA0107.10.952044
MA0108.20.363107
MA0109.10
MA0111.10.14244
MA0113.10.273246
MA0114.10.367031
MA0115.10.589161
MA0116.10.0624169
MA0117.10.559943
MA0119.10.110503
MA0122.10.577888
MA0124.10.766819
MA0125.11.66463
MA0130.10
MA0131.11.6184
MA0132.10
MA0133.10
MA0135.10.619844
MA0136.10.236653
MA0139.11.50059
MA0140.10.2137
MA0141.10.0898383
MA0142.10.40532
MA0143.10.285913
MA0144.10.164087
MA0145.10.252942
MA0146.11.02077
MA0147.12.05316
MA0148.10.960549
MA0149.10.113293
MA0062.21.62311
MA0035.20.217072
MA0039.20.921376
MA0138.20.334152
MA0002.20.10237
MA0137.20.618368
MA0104.23.81377
MA0047.20.711867
MA0112.20.134174
MA0065.20.0584336
MA0150.10.145553
MA0151.10
MA0152.10.256315
MA0153.10.635107
MA0154.10.227476
MA0155.10.301849
MA0156.11.00164
MA0157.10.378326
MA0158.10
MA0159.10.423802
MA0160.10.167661
MA0161.10
MA0162.12.79601
MA0163.10.140172
MA0164.10.23692
MA0080.20.266721
MA0018.20.244112
MA0099.20.329046
MA0079.20.603083
MA0102.21.18455
MA0258.10.145568
MA0259.11.97325
MA0442.10
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