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MCL coexpression mm9:875: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0031456;glycine betaine biosynthetic process;0.0020270640442667;218865!GO:0008812;choline dehydrogenase activity;0.0020270640442667;218865!GO:0031455;glycine betaine metabolic process;0.0020270640442667;218865!GO:0019285;glycine betaine biosynthetic process from choline;0.0020270640442667;218865!GO:0006577;betaine metabolic process;0.0020270640442667;218865!GO:0006578;betaine biosynthetic process;0.0020270640442667;218865!GO:0019695;choline metabolic process;0.00347477654474607;218865!GO:0042439;ethanolamine and derivative metabolic process;0.00608019263082758;218865!GO:0042401;biogenic amine biosynthetic process;0.0309130210236443;218865!GO:0042398;amino acid derivative biosynthetic process;0.0309130210236443;218865!GO:0004869;cysteine protease inhibitor activity;0.0309130210236443;13011!
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|ontology_enrichment_uberon=UBERON:0002193!2.11e-16!48;UBERON:0002405!2.11e-16!48;UBERON:0002390!9.96e-15!45;UBERON:0003061!9.96e-15!45;UBERON:0004177!3.57e-10!29;UBERON:0005057!3.57e-10!29;UBERON:0000077!8.44e-08!35;UBERON:0001474!7.85e-07!22;UBERON:0004765!7.85e-07!22;UBERON:0001434!7.85e-07!22
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.534222,0.367606,0.434198,0.260188,0.448401,0.538088,1.5747,0.181564,0.0447303,0.494602,0.526159,1.57591,0.550255,0.756943,0,0.742571,0.703873,1.4996,0.620214,0.332107,0.223663,0.549359,0.258745,0.374936,0.577606,2.09255,0.469052,0.303071,0.376624,0.455168,0.843667,0.250677,0.425071,0.276324,0.185086,0.242032,0.522578,1.8457,0.195877,0.256422,0.460258,0.0558565,2.13761,0.0824666,0.423266,0.662995,0.484612,0.0447507,0.305876,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,0.513517,0.145699,0.555328,0.823643,0.613749,0.560836,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.527912,0.0665967,1.03623,1.37807,0.813951,0.136938,0.651651,0.806481,0.336166,0.530481,0.759925,0.612313,2.20352,0.920903,0.108172,0.0299392,0.757533,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,0.1711,0.859272,0.663249,2.26041,1.95318,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,1.20804,0.340849,0.333829,0.386136,0.96962,0.895335,0.499714,1.21576,0.254749,0.333069,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,1.35892,0.950857,0.427043,1.10792,0.570914,1.23736,0.061199,2.7384,0.461647,1.18819,2.01886,1.6187,1.14372,1.44306,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.261837,0.766041,0.0553085,0.986833,1.76809,1.39798,1.06851,0.605358,1.42739,1.01313,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.676555,0.524587,0.842217
|tfbs_overrepresentation_jaspar=MA0003.1;0.0545917,MA0004.1;0.434673,MA0006.1;0.271714,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;0.0611475,MA0017.1;0.296816,MA0019.1;0.688051,MA0024.1;0.826339,MA0025.1;1.10341,MA0027.1;2.51754,MA0028.1;0.281528,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;0.685543,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;0.523649,MA0056.1;0,MA0057.1;0.31126,MA0058.1;0.341628,MA0059.1;2.51175,MA0060.1;0.197678,MA0061.1;0.224905,MA0063.1;0,MA0066.1;0.566617,MA0067.1;1.21448,MA0068.1;0.657844,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;0.000129679,MA0074.1;0.531046,MA0076.1;0.315013,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;0.853781,MA0089.1;0,MA0090.1;0.401197,MA0091.1;0.447561,MA0092.1;0.401504,MA0093.1;0.289361,MA0095.1;0,MA0098.1;0,MA0100.1;0.519598,MA0101.1;0.950493,MA0103.1;0.307078,MA0105.1;0.41549,MA0106.1;0.626997,MA0107.1;1.47808,MA0108.2;0.710846,MA0109.1;0,MA0111.1;0.415012,MA0113.1;0.598933,MA0114.1;0.222763,MA0115.1;0.969632,MA0116.1;0.747001,MA0117.1;0.937363,MA0119.1;0.362692,MA0122.1;0.957212,MA0124.1;1.16127,MA0125.1;1.0872,MA0130.1;0,MA0131.1;0.683521,MA0132.1;0,MA0133.1;0,MA0135.1;1.00325,MA0136.1;1.35732,MA0139.1;0.977634,MA0140.1;1.29098,MA0141.1;0.325895,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;0.225588,MA0145.1;1.35361,MA0146.1;0.198184,MA0147.1;1.24068,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.137653,MA0035.2;1.30087,MA0039.2;0.402847,MA0138.2;0.675599,MA0002.2;0.988033,MA0137.2;0.32312,MA0104.2;1.03907,MA0047.2;0.576767,MA0112.2;0.0701537,MA0065.2;0.528619,MA0150.1;2.82555,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.330759,MA0155.1;2.62015,MA0156.1;0.843735,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.246253,MA0160.1;0.453546,MA0161.1;0,MA0162.1;0.0211019,MA0163.1;0.0186439,MA0164.1;0.551114,MA0080.2;2.26,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;0.0468707,MA0102.2;1.59466,MA0258.1;0.210437,MA0259.1;0.643936,MA0442.1;0
}}

Latest revision as of 16:02, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:79251669..79251729,-p1@Prss57
Mm9::chr14:30835936..30835962,+p7@Chdh
Mm9::chr2:150396108..150396117,+p4@Cst7
Mm9::chr2:150396145..150396156,+p2@Cst7
Mm9::chr2:150396163..150396219,+p1@Cst7
Mm9::chr2:150396232..150396241,+p3@Cst7
Mm9::chr2:71176256..71176310,-p@chr2:71176256..71176310
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Mm9::chr9:114690908..114690917,-p4@Cmtm7


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:0031456glycine betaine biosynthetic process0.0020270640442667
GO:0008812choline dehydrogenase activity0.0020270640442667
GO:0031455glycine betaine metabolic process0.0020270640442667
GO:0019285glycine betaine biosynthetic process from choline0.0020270640442667
GO:0006577betaine metabolic process0.0020270640442667
GO:0006578betaine biosynthetic process0.0020270640442667
GO:0019695choline metabolic process0.00347477654474607
GO:0042439ethanolamine and derivative metabolic process0.00608019263082758
GO:0042401biogenic amine biosynthetic process0.0309130210236443
GO:0042398amino acid derivative biosynthetic process0.0309130210236443
GO:0004869cysteine protease inhibitor activity0.0309130210236443



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
hemolymphoid system2.11e-1648
immune system2.11e-1648
hematopoietic system9.96e-1545
blood island9.96e-1545
hemopoietic organ3.57e-1029
immune organ3.57e-1029
mixed endoderm/mesoderm-derived structure8.44e-0835
bone element7.85e-0722
skeletal element7.85e-0722
skeletal system7.85e-0722


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)
MA0003.10.0545917
MA0004.10.434673
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.10.0611475
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
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
MA0048.10.685543
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.523649
MA0056.10
MA0057.10.31126
MA0058.10.341628
MA0059.12.51175
MA0060.10.197678
MA0061.10.224905
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.657844
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.000129679
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.853781
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.950493
MA0103.10.307078
MA0105.10.41549
MA0106.10.626997
MA0107.11.47808
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.10.747001
MA0117.10.937363
MA0119.10.362692
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.11.35732
MA0139.10.977634
MA0140.11.29098
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.11.35361
MA0146.10.198184
MA0147.11.24068
MA0148.10.450593
MA0149.10.367458
MA0062.20.137653
MA0035.21.30087
MA0039.20.402847
MA0138.20.675599
MA0002.20.988033
MA0137.20.32312
MA0104.21.03907
MA0047.20.576767
MA0112.20.0701537
MA0065.20.528619
MA0150.12.82555
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.330759
MA0155.12.62015
MA0156.10.843735
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.10.0211019
MA0163.10.0186439
MA0164.10.551114
MA0080.22.26
MA0018.20.560731
MA0099.20.669311
MA0079.20.0468707
MA0102.21.59466
MA0258.10.210437
MA0259.10.643936
MA0442.10
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