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MCL coexpression mm9:633: Difference between revisions

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{{MCL_coexpression_mm9
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domain binding;0.0269544732372761;16825!GO:0045647;negative regulation of erythrocyte differentiation;0.0319611166067959;16825!GO:0021692;cerebellar Purkinje cell layer morphogenesis;0.0319611166067959;16825!GO:0045646;regulation of erythrocyte differentiation;0.0319611166067959;16825!GO:0021694;cerebellar Purkinje cell layer formation;0.0319611166067959;16825!GO:0021702;cerebellar Purkinje cell differentiation;0.0319611166067959;16825!GO:0021697;cerebellar cortex formation;0.0319611166067959;16825!GO:0021533;cell differentiation in hindbrain;0.0319611166067959;16825!GO:0009948;anterior/posterior axis specification;0.0319611166067959;16825!GO:0021680;cerebellar Purkinje cell layer development;0.0319611166067959;16825!GO:0021696;cerebellar cortex morphogenesis;0.0319611166067959;16825!GO:0021587;cerebellum morphogenesis;0.0319611166067959;16825!GO:0021575;hindbrain morphogenesis;0.0319611166067959;16825!GO:0009798;axis specification;0.0319611166067959;16825!GO:0021695;cerebellar cortex development;0.0319611166067959;16825!GO:0045638;negative regulation of myeloid cell differentiation;0.0319611166067959;16825!GO:0022037;metencephalon development;0.0339834501736818;16825!GO:0021549;cerebellum development;0.0339834501736818;16825!GO:0000082;G1/S transition of mitotic cell cycle;0.0339834501736818;17863!GO:0001702;gastrulation with mouth forming second;0.0416765360980862;16825!GO:0045637;regulation of myeloid cell differentiation;0.0447987456827315;16825!GO:0030218;erythrocyte differentiation;0.0451311553378454;16825!GO:0051325;interphase;0.0451311553378454;17863!GO:0051329;interphase of mitotic cell cycle;0.0451311553378454;17863!GO:0030902;hindbrain 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|gostat_on_MCL_coexpression=GO:0030274;LIM domain binding;0.0269544732372761;16825!GO:0045647;negative regulation of erythrocyte differentiation;0.0319611166067959;16825!GO:0021692;cerebellar Purkinje cell layer morphogenesis;0.0319611166067959;16825!GO:0045646;regulation of erythrocyte differentiation;0.0319611166067959;16825!GO:0021694;cerebellar Purkinje cell layer formation;0.0319611166067959;16825!GO:0021702;cerebellar Purkinje cell differentiation;0.0319611166067959;16825!GO:0021697;cerebellar cortex formation;0.0319611166067959;16825!GO:0021533;cell differentiation in hindbrain;0.0319611166067959;16825!GO:0009948;anterior/posterior axis specification;0.0319611166067959;16825!GO:0021680;cerebellar Purkinje cell layer development;0.0319611166067959;16825!GO:0021696;cerebellar cortex morphogenesis;0.0319611166067959;16825!GO:0021587;cerebellum morphogenesis;0.0319611166067959;16825!GO:0021575;hindbrain morphogenesis;0.0319611166067959;16825!GO:0009798;axis specification;0.0319611166067959;16825!GO:0021695;cerebellar cortex development;0.0319611166067959;16825!GO:0045638;negative regulation of myeloid cell differentiation;0.0319611166067959;16825!GO:0022037;metencephalon development;0.0339834501736818;16825!GO:0021549;cerebellum development;0.0339834501736818;16825!GO:0000082;G1/S transition of mitotic cell cycle;0.0339834501736818;17863!GO:0001702;gastrulation with mouth forming second;0.0416765360980862;16825!GO:0045637;regulation of myeloid cell differentiation;0.0447987456827315;16825!GO:0030218;erythrocyte differentiation;0.0451311553378454;16825!GO:0051325;interphase;0.0451311553378454;17863!GO:0051329;interphase of mitotic cell cycle;0.0451311553378454;17863!GO:0030902;hindbrain development;0.0451311553378454;16825!
|ontology_enrichment_celltype=CL:0000988!5.59e-11!32;CL:0002032!5.59e-11!32;CL:0000037!5.59e-11!32;CL:0000566!5.59e-11!32;CL:0000837!5.59e-11!32;CL:0000838!1.71e-07!12;CL:0002031!3.09e-07!25;CL:0000084!8.85e-07!11;CL:0000827!8.85e-07!11
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!2.66e-18!45;UBERON:0003061!2.66e-18!45;UBERON:0002193!8.87e-18!48;UBERON:0002405!8.87e-18!48;UBERON:0004177!2.01e-16!29;UBERON:0005057!2.01e-16!29;UBERON:0000077!7.17e-14!35;UBERON:0000065!1.03e-13!41;UBERON:0001004!4.00e-13!42;UBERON:0002370!1.90e-12!23;UBERON:0000974!1.90e-12!23;UBERON:0004807!1.90e-12!23;UBERON:0005058!1.90e-12!23;UBERON:0003351!1.90e-12!23;UBERON:0009113!1.90e-12!23;UBERON:0003295!1.90e-12!23;UBERON:0009722!1.90e-12!23;UBERON:0005562!1.90e-12!23;UBERON:0007690!1.90e-12!23;UBERON:0006562!1.27e-11!24;UBERON:0003408!1.27e-11!24;UBERON:0001557!1.27e-11!24;UBERON:0001042!1.27e-11!24;UBERON:0008814!1.27e-11!24;UBERON:0009145!1.27e-11!24;UBERON:0001041!9.94e-11!80;UBERON:0003081!2.41e-10!87;UBERON:0000072!1.54e-09!27;UBERON:0005911!8.61e-09!69;UBERON:0000926!1.15e-07!120;UBERON:0004120!1.15e-07!120;UBERON:0006603!1.15e-07!120
|tfbs_overrepresentation_for_novel_motifs=0.795069,0.490989,0.269904,0.329881,0.52369,0.342839,0.425757,0.106126,0.362206,0.208174,0.385334,0.414631,0.106288,1.11437,0.189961,0,0.619876,0.508485,0.096222,0.688036,0.238546,0.281622,0.436294,0.175485,0.276437,0.4628,1.05365,0.361771,0.611503,0.231659,0.921513,0.717576,0.504188,0.570676,0.556756,0.00428447,0.161521,0.411296,0.144953,0.123934,0.51597,0.353696,0.104243,0.559697,0.0302553,0.319944,0.543674,0.376103,0.0181648,0.61724,0.603113,0.488021,0.220536,0.855661,0.87275,0.443782,0.223087,0.40287,0.0851299,0.441884,0.698157,0.496904,0.769309,0.592318,0.45416,1.52656,1.00675,1.3527,0.693631,1.20659,0.253722,0.720972,0.126035,0.905636,0.0810502,0.258161,0.0786324,0.532872,0.681539,0.242107,0.724739,0.636582,0.495545,0.333618,0.792744,0.256335,1.07574,0.0651072,0.548334,1.51408,1.07554,0.797601,0.730003,1.62132,0.141946,0.129056,0.104462,0.732731,0.543917,0.764487,0.486605,1.70591,0.838603,0.603683,0.602672,0.353298,0.660145,0.372438,0.246223,0.240055,0.781068,0.840348,0.243062,1.01194,1.0825,0.512539,0.0643992,0.333247,0.621127,0.479408,0.910937,0.572279,1.17341,0.532013,1.13603,0.685116,0.433317,0.723425,1.00525,0.540802,0.821997,1.55739,0.976125,0.456508,1.10385,0.514451,0.300001,0.35497,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.354106,0.546641,1.84176,0.302077,3.03539,1.8264,0.103135,0.857198,0.133365,0.455644,0.93735,1.22588,0.199652,0.290467,0.811219,1.06466,0.791909,0.685546,0.284483,0.593295,0.448733,0.160658,0.413167,1.2411
|tfbs_overrepresentation_jaspar=MA0003.1;0.156602,MA0004.1;0.330313,MA0006.1;1.04465,MA0007.1;0.316976,MA0009.1;0.743257,MA0014.1;0.0199707,MA0017.1;0.207884,MA0019.1;0.567591,MA0024.1;0.70077,MA0025.1;0.971686,MA0027.1;2.37948,MA0028.1;0.194782,MA0029.1;0.679737,MA0030.1;0.686088,MA0031.1;0.651724,MA0038.1;0.462726,MA0040.1;0.755433,MA0041.1;0.263922,MA0042.1;0.252679,MA0043.1;0.837621,MA0046.1;0.778239,MA0048.1;0.769903,MA0050.1;0.365212,MA0051.1;0.471092,MA0052.1;0.76328,MA0055.1;1.0429,MA0056.1;0,MA0057.1;0.048013,MA0058.1;0.246908,MA0059.1;0.257372,MA0060.1;0.12537,MA0061.1;0.884293,MA0063.1;0,MA0066.1;0.452472,MA0067.1;1.08124,MA0068.1;0.418079,MA0069.1;0.76361,MA0070.1;0.75417,MA0071.1;0.364454,MA0072.1;0.745922,MA0073.1;2.58254e-05,MA0074.1;1.89006,MA0076.1;0.223625,MA0077.1;0.724865,MA0078.1;0.502121,MA0081.1;0.277253,MA0083.1;0.836845,MA0084.1;1.4063,MA0087.1;0.794721,MA0088.1;0.12124,MA0089.1;0,MA0090.1;0.299987,MA0091.1;0.342071,MA0092.1;0.300264,MA0093.1;0.20148,MA0095.1;0,MA0098.1;0,MA0100.1;0.408523,MA0101.1;0.265031,MA0103.1;0.619698,MA0105.1;0.0759118,MA0106.1;0.509454,MA0107.1;0.211681,MA0108.2;0.589413,MA0109.1;0,MA0111.1;0.839864,MA0113.1;0.482899,MA0114.1;0.446898,MA0115.1;0.84036,MA0116.1;0.186271,MA0117.1;0.808813,MA0119.1;0.733279,MA0122.1;0.828211,MA0124.1;1.02871,MA0125.1;0.955734,MA0130.1;0,MA0131.1;0.563262,MA0132.1;0,MA0133.1;0,MA0135.1;0.873285,MA0136.1;0.437601,MA0139.1;0.103495,MA0140.1;0.408417,MA0141.1;0.233109,MA0142.1;0.63775,MA0143.1;0.49828,MA0144.1;0.147954,MA0145.1;0.3137,MA0146.1;0.183077,MA0147.1;0.157258,MA0148.1;0.344843,MA0149.1;1.36348,MA0062.2;0.271822,MA0035.2;0.412747,MA0039.2;0.00103637,MA0138.2;0.555696,MA0002.2;1.15479,MA0137.2;0.230686,MA0104.2;0.11535,MA0047.2;0.46201,MA0112.2;0.313687,MA0065.2;0.314773,MA0150.1;0.849777,MA0151.1;0,MA0152.1;0.46211,MA0153.1;0.889592,MA0154.1;0.0529077,MA0155.1;0.154271,MA0156.1;0.634231,MA0157.1;0.606944,MA0158.1;0,MA0159.1;0.165031,MA0160.1;0.347545,MA0161.1;0,MA0162.1;0.388731,MA0163.1;0.198448,MA0164.1;1.11611,MA0080.2;0.609443,MA0018.2;0.446948,MA0099.2;0.549696,MA0079.2;0.000158926,MA0102.2;1.45844,MA0258.1;0.135621,MA0259.1;0.14914,MA0442.1;0
}}

Latest revision as of 15:38, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:126512385..126512454,+p@chr10:126512385..126512454
+
Mm9::chr10:20881239..20881254,-p5@Myb
Mm9::chr10:41788412..41788423,-p@chr10:41788412..41788423
-
Mm9::chr16:78546887..78546912,-p@chr16:78546887..78546912
-
Mm9::chr17:28144291..28144354,+p6@Anks1
Mm9::chr19:46119469..46119478,-p15@Ldb1
Mm9::chr7:134624130..134624140,+p@chr7:134624130..134624140
+
Mm9::chr7:82731249..82731262,+p@chr7:82731249..82731262
+
Mm9::chr7:82731272..82731298,+p@chr7:82731272..82731298
+
Mm9::chr7:82731305..82731334,+p@chr7:82731305..82731334
+
Mm9::chr8:75170473..75170495,+p3@Nwd1


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:0030274LIM domain binding0.0269544732372761
GO:0045647negative regulation of erythrocyte differentiation0.0319611166067959
GO:0021692cerebellar Purkinje cell layer morphogenesis0.0319611166067959
GO:0045646regulation of erythrocyte differentiation0.0319611166067959
GO:0021694cerebellar Purkinje cell layer formation0.0319611166067959
GO:0021702cerebellar Purkinje cell differentiation0.0319611166067959
GO:0021697cerebellar cortex formation0.0319611166067959
GO:0021533cell differentiation in hindbrain0.0319611166067959
GO:0009948anterior/posterior axis specification0.0319611166067959
GO:0021680cerebellar Purkinje cell layer development0.0319611166067959
GO:0021696cerebellar cortex morphogenesis0.0319611166067959
GO:0021587cerebellum morphogenesis0.0319611166067959
GO:0021575hindbrain morphogenesis0.0319611166067959
GO:0009798axis specification0.0319611166067959
GO:0021695cerebellar cortex development0.0319611166067959
GO:0045638negative regulation of myeloid cell differentiation0.0319611166067959
GO:0022037metencephalon development0.0339834501736818
GO:0021549cerebellum development0.0339834501736818
GO:0000082G1/S transition of mitotic cell cycle0.0339834501736818
GO:0001702gastrulation with mouth forming second0.0416765360980862
GO:0045637regulation of myeloid cell differentiation0.0447987456827315
GO:0030218erythrocyte differentiation0.0451311553378454
GO:0051325interphase0.0451311553378454
GO:0051329interphase of mitotic cell cycle0.0451311553378454
GO:0030902hindbrain development0.0451311553378454



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>

Uber Anatomy
Ontology termp-valuen
hematopoietic system2.66e-1845
blood island2.66e-1845
hemolymphoid system8.87e-1848
immune system8.87e-1848
hemopoietic organ2.01e-1629
immune organ2.01e-1629
mixed endoderm/mesoderm-derived structure7.17e-1435
respiratory tract1.03e-1341
respiratory system4.00e-1342
thymus1.90e-1223
neck1.90e-1223
respiratory system epithelium1.90e-1223
hemolymphoid system gland1.90e-1223
pharyngeal epithelium1.90e-1223
thymic region1.90e-1223
pharyngeal gland1.90e-1223
entire pharyngeal arch endoderm1.90e-1223
thymus primordium1.90e-1223
early pharyngeal endoderm1.90e-1223
pharynx1.27e-1124
gland of gut1.27e-1124
upper respiratory tract1.27e-1124
chordate pharynx1.27e-1124
pharyngeal arch system1.27e-1124
pharyngeal region of foregut1.27e-1124
foregut9.94e-1180
lateral plate mesoderm2.41e-1087
segment of respiratory tract1.54e-0927
endo-epithelium8.61e-0969
mesoderm1.15e-07120
mesoderm-derived structure1.15e-07120
presumptive mesoderm1.15e-07120


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)
MA0003.10.156602
MA0004.10.330313
MA0006.11.04465
MA0007.10.316976
MA0009.10.743257
MA0014.10.0199707
MA0017.10.207884
MA0019.10.567591
MA0024.10.70077
MA0025.10.971686
MA0027.12.37948
MA0028.10.194782
MA0029.10.679737
MA0030.10.686088
MA0031.10.651724
MA0038.10.462726
MA0040.10.755433
MA0041.10.263922
MA0042.10.252679
MA0043.10.837621
MA0046.10.778239
MA0048.10.769903
MA0050.10.365212
MA0051.10.471092
MA0052.10.76328
MA0055.11.0429
MA0056.10
MA0057.10.048013
MA0058.10.246908
MA0059.10.257372
MA0060.10.12537
MA0061.10.884293
MA0063.10
MA0066.10.452472
MA0067.11.08124
MA0068.10.418079
MA0069.10.76361
MA0070.10.75417
MA0071.10.364454
MA0072.10.745922
MA0073.12.58254e-05
MA0074.11.89006
MA0076.10.223625
MA0077.10.724865
MA0078.10.502121
MA0081.10.277253
MA0083.10.836845
MA0084.11.4063
MA0087.10.794721
MA0088.10.12124
MA0089.10
MA0090.10.299987
MA0091.10.342071
MA0092.10.300264
MA0093.10.20148
MA0095.10
MA0098.10
MA0100.10.408523
MA0101.10.265031
MA0103.10.619698
MA0105.10.0759118
MA0106.10.509454
MA0107.10.211681
MA0108.20.589413
MA0109.10
MA0111.10.839864
MA0113.10.482899
MA0114.10.446898
MA0115.10.84036
MA0116.10.186271
MA0117.10.808813
MA0119.10.733279
MA0122.10.828211
MA0124.11.02871
MA0125.10.955734
MA0130.10
MA0131.10.563262
MA0132.10
MA0133.10
MA0135.10.873285
MA0136.10.437601
MA0139.10.103495
MA0140.10.408417
MA0141.10.233109
MA0142.10.63775
MA0143.10.49828
MA0144.10.147954
MA0145.10.3137
MA0146.10.183077
MA0147.10.157258
MA0148.10.344843
MA0149.11.36348
MA0062.20.271822
MA0035.20.412747
MA0039.20.00103637
MA0138.20.555696
MA0002.21.15479
MA0137.20.230686
MA0104.20.11535
MA0047.20.46201
MA0112.20.313687
MA0065.20.314773
MA0150.10.849777
MA0151.10
MA0152.10.46211
MA0153.10.889592
MA0154.10.0529077
MA0155.10.154271
MA0156.10.634231
MA0157.10.606944
MA0158.10
MA0159.10.165031
MA0160.10.347545
MA0161.10
MA0162.10.388731
MA0163.10.198448
MA0164.11.11611
MA0080.20.609443
MA0018.20.446948
MA0099.20.549696
MA0079.20.000158926
MA0102.21.45844
MA0258.10.135621
MA0259.10.14914
MA0442.10
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