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MCL coexpression mm9:561: Difference between revisions

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{{MCL_coexpression_mm9
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assembly or disassembly;0.00167154048853748;12412,20588,56086!GO:0006259;DNA metabolic process;0.00267532743741777;12412,53610,20588,56086!GO:0006325;establishment and/or maintenance of chromatin architecture;0.00382075892357918;12412,20588,56086!GO:0006323;DNA packaging;0.00382075892357918;12412,20588,56086!GO:0051276;chromosome organization and biogenesis;0.00782676507747672;12412,20588,56086!GO:0005634;nucleus;0.010352760363296;12412,53610,20588,16906,56086,51886!GO:0003682;chromatin binding;0.010352760363296;12412,20588!GO:0043283;biopolymer metabolic process;0.010352760363296;12412,53610,20588,109079,56086,51886!GO:0004756;selenide, water dikinase activity;0.010352760363296;109079!GO:0016781;phosphotransferase activity, paired acceptors;0.010352760363296;109079!GO:0005701;polytene chromosome chromocenter;0.0129388234465679;12412!GO:0005700;polytene chromosome;0.0129388234465679;12412!GO:0005721;centric heterochromatin;0.0137991432826624;12412!GO:0005638;lamin filament;0.0137991432826624;16906!GO:0001940;male pronucleus;0.0137991432826624;12412!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0140998553424081;12412,53610,20588,56086,51886!GO:0001939;female pronucleus;0.0152171418786361;12412!GO:0000785;chromatin;0.0155189337054456;12412,20588!GO:0010369;chromocenter;0.0155189337054456;12412!GO:0016514;SWI/SNF complex;0.0155189337054456;20588!GO:0003677;DNA binding;0.0179870528483271;53610,20588,56086,51886!GO:0005652;nuclear lamina;0.0179870528483271;16906!GO:0005637;nuclear inner membrane;0.0179870528483271;16906!GO:0043170;macromolecule metabolic process;0.018211026510159;12412,53610,20588,109079,56086,51886!GO:0044428;nuclear part;0.0242749379943623;12412,20588,16906!GO:0044427;chromosomal part;0.026787604125647;12412,20588!GO:0045120;pronucleus;0.026787604125647;12412!GO:0006996;organelle organization and biogenesis;0.0305470632527692;12412,20588,56086!GO:0044238;primary metabolic process;0.0305470632527692;12412,53610,20588,109079,56086,51886!GO:0044237;cellular metabolic process;0.0305470632527692;12412,53610,20588,109079,56086,51886!GO:0005694;chromosome;0.0305470632527692;12412,20588!GO:0016585;chromatin remodeling complex;0.0305470632527692;20588!GO:0043231;intracellular membrane-bound organelle;0.0305470632527692;12412,53610,20588,16906,56086,51886!GO:0043227;membrane-bound organelle;0.0305470632527692;12412,53610,20588,16906,56086,51886!GO:0005720;nuclear heterochromatin;0.0338990160233967;12412!GO:0003676;nucleic acid binding;0.0420275964709632;53610,20588,56086,51886!GO:0000790;nuclear chromatin;0.0420275964709632;12412!GO:0008430;selenium binding;0.0420275964709632;109079!GO:0000792;heterochromatin;0.0463176859807975;12412!GO:0043232;intracellular non-membrane-bound organelle;0.0463176859807975;12412,20588,16906!GO:0043228;non-membrane-bound organelle;0.0463176859807975;12412,20588,16906!GO:0043229;intracellular 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|gostat_on_MCL_coexpression=GO:0006333;chromatin assembly or disassembly;0.00167154048853748;12412,20588,56086!GO:0006259;DNA metabolic process;0.00267532743741777;12412,53610,20588,56086!GO:0006325;establishment and/or maintenance of chromatin architecture;0.00382075892357918;12412,20588,56086!GO:0006323;DNA packaging;0.00382075892357918;12412,20588,56086!GO:0051276;chromosome organization and biogenesis;0.00782676507747672;12412,20588,56086!GO:0005634;nucleus;0.010352760363296;12412,53610,20588,16906,56086,51886!GO:0003682;chromatin binding;0.010352760363296;12412,20588!GO:0043283;biopolymer metabolic process;0.010352760363296;12412,53610,20588,109079,56086,51886!GO:0004756;selenide, water dikinase activity;0.010352760363296;109079!GO:0016781;phosphotransferase activity, paired acceptors;0.010352760363296;109079!GO:0005701;polytene chromosome chromocenter;0.0129388234465679;12412!GO:0005700;polytene chromosome;0.0129388234465679;12412!GO:0005721;centric heterochromatin;0.0137991432826624;12412!GO:0005638;lamin filament;0.0137991432826624;16906!GO:0001940;male pronucleus;0.0137991432826624;12412!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0140998553424081;12412,53610,20588,56086,51886!GO:0001939;female pronucleus;0.0152171418786361;12412!GO:0000785;chromatin;0.0155189337054456;12412,20588!GO:0010369;chromocenter;0.0155189337054456;12412!GO:0016514;SWI/SNF complex;0.0155189337054456;20588!GO:0003677;DNA binding;0.0179870528483271;53610,20588,56086,51886!GO:0005652;nuclear lamina;0.0179870528483271;16906!GO:0005637;nuclear inner membrane;0.0179870528483271;16906!GO:0043170;macromolecule metabolic process;0.018211026510159;12412,53610,20588,109079,56086,51886!GO:0044428;nuclear part;0.0242749379943623;12412,20588,16906!GO:0044427;chromosomal part;0.026787604125647;12412,20588!GO:0045120;pronucleus;0.026787604125647;12412!GO:0006996;organelle organization and biogenesis;0.0305470632527692;12412,20588,56086!GO:0044238;primary metabolic process;0.0305470632527692;12412,53610,20588,109079,56086,51886!GO:0044237;cellular metabolic process;0.0305470632527692;12412,53610,20588,109079,56086,51886!GO:0005694;chromosome;0.0305470632527692;12412,20588!GO:0016585;chromatin remodeling complex;0.0305470632527692;20588!GO:0043231;intracellular membrane-bound organelle;0.0305470632527692;12412,53610,20588,16906,56086,51886!GO:0043227;membrane-bound organelle;0.0305470632527692;12412,53610,20588,16906,56086,51886!GO:0005720;nuclear heterochromatin;0.0338990160233967;12412!GO:0003676;nucleic acid binding;0.0420275964709632;53610,20588,56086,51886!GO:0000790;nuclear chromatin;0.0420275964709632;12412!GO:0008430;selenium binding;0.0420275964709632;109079!GO:0000792;heterochromatin;0.0463176859807975;12412!GO:0043232;intracellular non-membrane-bound organelle;0.0463176859807975;12412,20588,16906!GO:0043228;non-membrane-bound organelle;0.0463176859807975;12412,20588,16906!GO:0043229;intracellular organelle;0.0480738099214408;12412,53610,20588,16906,56086,51886!GO:0043226;organelle;0.0480738099214408;12412,53610,20588,16906,56086,51886!GO:0003723;RNA binding;0.0499254134235463;53610,51886!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000153!5.61e-08!43
|tfbs_overrepresentation_for_novel_motifs=0.684947,0.341626,1.18988,0.765013,0.430128,0.291576,0.370193,0.0778908,0.283485,1.40965,1.58702,0.35958,0.567414,0.992198,0.15081,0,0.557619,0.133477,0.069633,0.119642,0.194751,0.634211,1.75669,0.137915,0.64994,0.405649,0.0651848,0.833023,0.985516,0.169823,0.805906,0.653099,1.9209,0.779896,2.78029,3.25115,0.790102,1.6738,0.111088,2.16092,0.136186,0.815844,0.0142091,0.152251,0.577849,0.743728,1.2144,0.863451,0.0100673,0.173974,0.541299,0.429887,0.160439,0.788877,0.805733,0.387424,0.18067,0.920073,0.0605105,0.385607,0.634076,1.1172,0.090369,0.5308,1.02791,0.568642,0.938213,1.28193,0.629645,1.13654,0.600538,0.277751,3.33687,0.838198,3.4832,0.427563,0.0552358,0.473159,0.617814,0.198007,0.0819833,0.573903,0.437131,0.0742829,0.72691,3.97567,0.552224,0.0444451,0.488122,1.44275,1.0064,0.731688,0.665283,0.143149,0.713238,0.0973538,0.0764965,0.667958,0.483845,1.80811,0.125632,0.652833,0.772062,0.541854,0.54087,1.47882,2.47776,0.319507,0.584153,1.08317,0.238877,0.773781,0.19888,0.336214,1.01331,0.134943,2.93557,0.282562,0.558838,0.123076,0.843435,0.511336,0.407285,0.472327,1.06644,1.50588,0.377415,0.658832,0.936732,0.875241,0.755703,0.273302,0.907893,0.399614,1.03449,0.377676,0.251471,0.303003,0.986296,1.80931,1.41113,0.942814,0.418119,0.66306,0.53483,0.816716,0.486482,1.76978,0.253405,1.98864,1.51728,5.44212,1.85698,0.331601,0.398786,0.869538,1.10066,0.159498,0.680297,0.700333,0.995609,0.726089,0.621734,0.237049,0.531751,0.392164,0.786757,0.358185,4.01131
|tfbs_overrepresentation_jaspar=MA0003.1;6.72247,MA0004.1;1.40032,MA0006.1;0.451962,MA0007.1;0.737361,MA0009.1;0.678286,MA0014.1;4.46847,MA0017.1;0.166909,MA0019.1;0.506787,MA0024.1;0.636635,MA0025.1;0.9035,MA0027.1;2.3071,MA0028.1;2.10691,MA0029.1;0.616052,MA0030.1;0.622264,MA0031.1;0.588678,MA0038.1;0.405578,MA0040.1;0.690239,MA0041.1;0.218039,MA0042.1;0.207696,MA0043.1;0.771094,MA0046.1;0.712646,MA0048.1;0.332541,MA0050.1;0.312673,MA0051.1;0.413609,MA0052.1;0.697946,MA0055.1;0.183408,MA0056.1;0,MA0057.1;0.878515,MA0058.1;1.73925,MA0059.1;0.608499,MA0060.1;3.52264,MA0061.1;0.113212,MA0063.1;0,MA0066.1;0.395746,MA0067.1;1.01206,MA0068.1;0.0328198,MA0069.1;0.698271,MA0070.1;0.688999,MA0071.1;0.311956,MA0072.1;0.680902,MA0073.1;0.191412,MA0074.1;0.363923,MA0076.1;1.02349,MA0077.1;1.58726,MA0078.1;0.443468,MA0081.1;0.651709,MA0083.1;0.77033,MA0084.1;1.33532,MA0087.1;0.728855,MA0088.1;0.965806,MA0089.1;0,MA0090.1;0.251458,MA0091.1;0.290854,MA0092.1;0.251716,MA0093.1;1.50408,MA0095.1;0,MA0098.1;0,MA0100.1;0.931999,MA0101.1;0.625174,MA0103.1;0.174916,MA0105.1;1.16392,MA0106.1;0.450539,MA0107.1;0.508149,MA0108.2;0.527977,MA0109.1;0,MA0111.1;0.263095,MA0113.1;0.424958,MA0114.1;0.359761,MA0115.1;0.773793,MA0116.1;0.451594,MA0117.1;0.742722,MA0119.1;0.219527,MA0122.1;0.761823,MA0124.1;0.959967,MA0125.1;0.887718,MA0130.1;0,MA0131.1;0.502588,MA0132.1;0,MA0133.1;0,MA0135.1;0.806261,MA0136.1;0.38151,MA0139.1;0.5556,MA0140.1;0.353662,MA0141.1;0.18979,MA0142.1;0.575041,MA0143.1;0.439766,MA0144.1;0.1137,MA0145.1;0.223975,MA0146.1;7.29725,MA0147.1;0.386218,MA0148.1;0.293462,MA0149.1;0.223436,MA0062.2;1.19443,MA0035.2;0.357786,MA0039.2;2.57266,MA0138.2;0.495254,MA0002.2;0.0773396,MA0137.2;0.187581,MA0104.2;1.01662,MA0047.2;0.404891,MA0112.2;0.223965,MA0065.2;0.429377,MA0150.1;0.267221,MA0151.1;0,MA0152.1;0.404987,MA0153.1;0.822355,MA0154.1;0.0349712,MA0155.1;1.54988,MA0156.1;0.180505,MA0157.1;0.545026,MA0158.1;0,MA0159.1;0.403827,MA0160.1;0.296006,MA0161.1;0,MA0162.1;1.52018,MA0163.1;1.42454,MA0164.1;0.381832,MA0080.2;0.170995,MA0018.2;0.390455,MA0099.2;0.489441,MA0079.2;6.8499,MA0102.2;1.38728,MA0258.1;0.103004,MA0259.1;0.367748,MA0442.1;0
}}

Latest revision as of 15:30, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:51420342..51420359,-p1@Hnrnpab
Mm9::chr11:96650463..96650520,+p2@Cbx1
Mm9::chr11:96650527..96650538,+p3@Cbx1
Mm9::chr18:56867379..56867594,+p1@Lmnb1
Mm9::chr18:56867595..56867642,+p2@Lmnb1
Mm9::chr2:29922008..29922050,+p1@Set
Mm9::chr2:29922058..29922087,+p4@Set
Mm9::chr2:4802802..4802818,+p2@Sephs1
Mm9::chr3:151873433..151873498,+p1@Fubp1
Mm9::chr5:100407933..100407985,-p1@Hnrnpd
Mm9::chr6:18798604..18798693,+p1@Naa38
Mm9::chr9:110034519..110034606,+p1@Smarcc1
Mm9::chrX:98624993..98625047,+p1@Nono


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:0006333chromatin assembly or disassembly0.00167154048853748
GO:0006259DNA metabolic process0.00267532743741777
GO:0006325establishment and/or maintenance of chromatin architecture0.00382075892357918
GO:0006323DNA packaging0.00382075892357918
GO:0051276chromosome organization and biogenesis0.00782676507747672
GO:0005634nucleus0.010352760363296
GO:0003682chromatin binding0.010352760363296
GO:0043283biopolymer metabolic process0.010352760363296
GO:0004756selenide, water dikinase activity0.010352760363296
GO:0016781phosphotransferase activity, paired acceptors0.010352760363296
GO:0005701polytene chromosome chromocenter0.0129388234465679
GO:0005700polytene chromosome0.0129388234465679
GO:0005721centric heterochromatin0.0137991432826624
GO:0005638lamin filament0.0137991432826624
GO:0001940male pronucleus0.0137991432826624
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0140998553424081
GO:0001939female pronucleus0.0152171418786361
GO:0000785chromatin0.0155189337054456
GO:0010369chromocenter0.0155189337054456
GO:0016514SWI/SNF complex0.0155189337054456
GO:0003677DNA binding0.0179870528483271
GO:0005652nuclear lamina0.0179870528483271
GO:0005637nuclear inner membrane0.0179870528483271
GO:0043170macromolecule metabolic process0.018211026510159
GO:0044428nuclear part0.0242749379943623
GO:0044427chromosomal part0.026787604125647
GO:0045120pronucleus0.026787604125647
GO:0006996organelle organization and biogenesis0.0305470632527692
GO:0044238primary metabolic process0.0305470632527692
GO:0044237cellular metabolic process0.0305470632527692
GO:0005694chromosome0.0305470632527692
GO:0016585chromatin remodeling complex0.0305470632527692
GO:0043231intracellular membrane-bound organelle0.0305470632527692
GO:0043227membrane-bound organelle0.0305470632527692
GO:0005720nuclear heterochromatin0.0338990160233967
GO:0003676nucleic acid binding0.0420275964709632
GO:0000790nuclear chromatin0.0420275964709632
GO:0008430selenium binding0.0420275964709632
GO:0000792heterochromatin0.0463176859807975
GO:0043232intracellular non-membrane-bound organelle0.0463176859807975
GO:0043228non-membrane-bound organelle0.0463176859807975
GO:0043229intracellular organelle0.0480738099214408
GO:0043226organelle0.0480738099214408
GO:0003723RNA binding0.0499254134235463



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
anterior region of body5.61e-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)
MA0003.16.72247
MA0004.11.40032
MA0006.10.451962
MA0007.10.737361
MA0009.10.678286
MA0014.14.46847
MA0017.10.166909
MA0019.10.506787
MA0024.10.636635
MA0025.10.9035
MA0027.12.3071
MA0028.12.10691
MA0029.10.616052
MA0030.10.622264
MA0031.10.588678
MA0038.10.405578
MA0040.10.690239
MA0041.10.218039
MA0042.10.207696
MA0043.10.771094
MA0046.10.712646
MA0048.10.332541
MA0050.10.312673
MA0051.10.413609
MA0052.10.697946
MA0055.10.183408
MA0056.10
MA0057.10.878515
MA0058.11.73925
MA0059.10.608499
MA0060.13.52264
MA0061.10.113212
MA0063.10
MA0066.10.395746
MA0067.11.01206
MA0068.10.0328198
MA0069.10.698271
MA0070.10.688999
MA0071.10.311956
MA0072.10.680902
MA0073.10.191412
MA0074.10.363923
MA0076.11.02349
MA0077.11.58726
MA0078.10.443468
MA0081.10.651709
MA0083.10.77033
MA0084.11.33532
MA0087.10.728855
MA0088.10.965806
MA0089.10
MA0090.10.251458
MA0091.10.290854
MA0092.10.251716
MA0093.11.50408
MA0095.10
MA0098.10
MA0100.10.931999
MA0101.10.625174
MA0103.10.174916
MA0105.11.16392
MA0106.10.450539
MA0107.10.508149
MA0108.20.527977
MA0109.10
MA0111.10.263095
MA0113.10.424958
MA0114.10.359761
MA0115.10.773793
MA0116.10.451594
MA0117.10.742722
MA0119.10.219527
MA0122.10.761823
MA0124.10.959967
MA0125.10.887718
MA0130.10
MA0131.10.502588
MA0132.10
MA0133.10
MA0135.10.806261
MA0136.10.38151
MA0139.10.5556
MA0140.10.353662
MA0141.10.18979
MA0142.10.575041
MA0143.10.439766
MA0144.10.1137
MA0145.10.223975
MA0146.17.29725
MA0147.10.386218
MA0148.10.293462
MA0149.10.223436
MA0062.21.19443
MA0035.20.357786
MA0039.22.57266
MA0138.20.495254
MA0002.20.0773396
MA0137.20.187581
MA0104.21.01662
MA0047.20.404891
MA0112.20.223965
MA0065.20.429377
MA0150.10.267221
MA0151.10
MA0152.10.404987
MA0153.10.822355
MA0154.10.0349712
MA0155.11.54988
MA0156.10.180505
MA0157.10.545026
MA0158.10
MA0159.10.403827
MA0160.10.296006
MA0161.10
MA0162.11.52018
MA0163.11.42454
MA0164.10.381832
MA0080.20.170995
MA0018.20.390455
MA0099.20.489441
MA0079.26.8499
MA0102.21.38728
MA0258.10.103004
MA0259.10.367748
MA0442.10
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