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MCL coexpression mm9:966: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0006695;cholesterol biosynthetic process;0.00195623805134542;108099,68603!GO:0016126;sterol biosynthetic process;0.00195623805134542;108099,68603!GO:0008203;cholesterol metabolic process;0.00476738807664171;108099,68603!GO:0006694;steroid biosynthetic process;0.00476738807664171;108099,68603!GO:0016125;sterol metabolic process;0.00476738807664171;108099,68603!GO:0004631;phosphomevalonate kinase activity;0.00735038989024635;68603!GO:0050932;regulation of pigment cell differentiation;0.0102920334871923;14682!GO:0045634;regulation of melanocyte differentiation;0.0102920334871923;14682!GO:0008202;steroid metabolic process;0.0102920334871923;108099,68603!GO:0016322;neuron remodeling;0.0160319429526234;14682!GO:0060158;dopamine receptor, phospholipase C activating pathway;0.0160319429526234;14682!GO:0021884;forebrain neuron development;0.0176312726477465;14682!GO:0016791;phosphoric monoester hydrolase activity;0.0176312726477465;19259,57028!GO:0008610;lipid biosynthetic process;0.0176312726477465;108099,68603!GO:0004679;AMP-activated protein kinase activity;0.0176312726477465;108099!GO:0006066;alcohol metabolic process;0.018147850684892;108099,68603!GO:0021879;forebrain neuron differentiation;0.018147850684892;14682!GO:0021872;generation of neurons in the forebrain;0.0195860098829364;14682!GO:0042578;phosphoric ester hydrolase activity;0.0198286620026463;19259,57028!GO:0042551;neuron maturation;0.0198286620026463;14682!GO:0007215;glutamate signaling pathway;0.0209804118909944;14682!GO:0042733;embryonic digit morphogenesis;0.0260262263429269;14682!GO:0006471;protein amino acid ADP-ribosylation;0.0299370552228139;14682!GO:0030318;melanocyte differentiation;0.0299370552228139;14682!GO:0050931;pigment cell differentiation;0.0299370552228139;14682!GO:0007212;dopamine receptor signaling pathway;0.0304755625900123;14682!GO:0021954;central nervous system neuron development;0.0342267238762276;14682!GO:0021953;central nervous system neuron differentiation;0.0377068485994009;14682!GO:0044255;cellular lipid metabolic process;0.0402783680354601;108099,68603!GO:0016776;phosphotransferase activity, phosphate group as acceptor;0.0410405751465139;68603!GO:0048066;pigmentation during development;0.0411306312227698;14682!GO:0007200;G-protein signaling, coupled to IP3 second messenger (phospholipase C activating);0.0412147581446118;14682!GO:0009791;post-embryonic development;0.0412934949740724;14682!GO:0005834;heterotrimeric G-protein complex;0.042655371467583;14682!GO:0006629;lipid metabolic process;0.042717818550928;108099,68603!GO:0007189;G-protein signaling, adenylate cyclase activating pathway;0.042717818550928;14682!GO:0001508;regulation of action potential;0.0429220077924235;14682!GO:0016788;hydrolase activity, acting on ester bonds;0.0429220077924235;19259,57028!GO:0016787;hydrolase activity;0.0478159390112852;19259,57028,14682!GO:0048015;phosphoinositide-mediated signaling;0.0482845165637295;14682!}}
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biosynthetic process;0.00195623805134542;108099,68603!GO:0016126;sterol biosynthetic process;0.00195623805134542;108099,68603!GO:0008203;cholesterol metabolic process;0.00476738807664171;108099,68603!GO:0006694;steroid biosynthetic process;0.00476738807664171;108099,68603!GO:0016125;sterol metabolic process;0.00476738807664171;108099,68603!GO:0004631;phosphomevalonate kinase activity;0.00735038989024635;68603!GO:0050932;regulation of pigment cell differentiation;0.0102920334871923;14682!GO:0045634;regulation of melanocyte differentiation;0.0102920334871923;14682!GO:0008202;steroid metabolic process;0.0102920334871923;108099,68603!GO:0016322;neuron remodeling;0.0160319429526234;14682!GO:0060158;dopamine receptor, phospholipase C activating pathway;0.0160319429526234;14682!GO:0021884;forebrain neuron development;0.0176312726477465;14682!GO:0016791;phosphoric monoester hydrolase activity;0.0176312726477465;19259,57028!GO:0008610;lipid biosynthetic process;0.0176312726477465;108099,68603!GO:0004679;AMP-activated protein kinase activity;0.0176312726477465;108099!GO:0006066;alcohol metabolic process;0.018147850684892;108099,68603!GO:0021879;forebrain neuron differentiation;0.018147850684892;14682!GO:0021872;generation of neurons in the forebrain;0.0195860098829364;14682!GO:0042578;phosphoric ester hydrolase activity;0.0198286620026463;19259,57028!GO:0042551;neuron maturation;0.0198286620026463;14682!GO:0007215;glutamate signaling pathway;0.0209804118909944;14682!GO:0042733;embryonic digit morphogenesis;0.0260262263429269;14682!GO:0006471;protein amino acid ADP-ribosylation;0.0299370552228139;14682!GO:0030318;melanocyte differentiation;0.0299370552228139;14682!GO:0050931;pigment cell differentiation;0.0299370552228139;14682!GO:0007212;dopamine receptor signaling pathway;0.0304755625900123;14682!GO:0021954;central nervous system neuron development;0.0342267238762276;14682!GO:0021953;central nervous system neuron differentiation;0.0377068485994009;14682!GO:0044255;cellular lipid metabolic process;0.0402783680354601;108099,68603!GO:0016776;phosphotransferase activity, phosphate group as acceptor;0.0410405751465139;68603!GO:0048066;pigmentation during development;0.0411306312227698;14682!GO:0007200;G-protein signaling, coupled to IP3 second messenger (phospholipase C activating);0.0412147581446118;14682!GO:0009791;post-embryonic development;0.0412934949740724;14682!GO:0005834;heterotrimeric G-protein complex;0.042655371467583;14682!GO:0006629;lipid metabolic process;0.042717818550928;108099,68603!GO:0007189;G-protein signaling, adenylate cyclase activating pathway;0.042717818550928;14682!GO:0001508;regulation of action potential;0.0429220077924235;14682!GO:0016788;hydrolase activity, acting on ester bonds;0.0429220077924235;19259,57028!GO:0016787;hydrolase activity;0.0478159390112852;19259,57028,14682!GO:0048015;phosphoinositide-mediated signaling;0.0482845165637295;14682!|ontology_enrichment_celltype=CL:0000540!3.88e-16!33;CL:0000047!3.88e-16!33;CL:0000031!3.88e-16!33;CL:0000404!3.88e-16!33;CL:0000117!4.17e-15!23;CL:0000337!4.17e-15!23;CL:0000221!3.47e-13!44;CL:0000133!3.47e-13!44;CL:0002319!4.00e-13!43;CL:0000393!2.09e-11!39;CL:0000211!2.09e-11!39;CL:0000055!1.17e-09!49|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0001017!4.57e-28!73;UBERON:0001016!1.76e-27!75;UBERON:0002346!8.34e-25!64;UBERON:0003075!8.34e-25!64;UBERON:0007284!8.34e-25!64;UBERON:0004121!2.15e-24!95;UBERON:0000924!2.15e-24!95;UBERON:0006601!2.15e-24!95;UBERON:0000073!8.38e-24!54;UBERON:0010371!1.56e-22!73;UBERON:0001049!1.88e-22!52;UBERON:0005068!1.88e-22!52;UBERON:0006241!1.88e-22!52;UBERON:0007135!1.88e-22!52;UBERON:0003056!8.86e-20!49;UBERON:0002020!2.76e-19!34;UBERON:0000955!3.98e-19!47;UBERON:0006238!3.98e-19!47;UBERON:0010314!5.01e-19!92;UBERON:0002616!1.28e-18!46;UBERON:0003080!2.12e-18!40;UBERON:0002780!7.16e-18!39;UBERON:0001890!7.16e-18!39;UBERON:0006240!7.16e-18!39;UBERON:0003528!6.20e-16!29;UBERON:0002791!6.20e-16!29;UBERON:0001893!6.20e-16!29;UBERON:0000956!4.74e-11!21;UBERON:0001869!4.74e-11!21;UBERON:0000203!4.74e-11!21;UBERON:0002619!7.54e-09!17|tfbs_overrepresentation_for_novel_motifs=0.393008,1.2286,0.367606,0.434198,0.260188,0.448401,1.33049,0.515265,0.181564,0.687027,0.494602,0.526159,2.24725,0.550255,0.275867,0,0.742571,0.252772,0.483643,1.03863,0.332107,0.485665,0.549359,0.258745,2.61436,0.577606,0.153291,0.469052,0.303071,0.757024,0.455168,0.843667,0.699026,0.425071,1.38756,3.12971,3.59366,0.522578,0.221921,2.41256,0.256422,0.460258,0.450632,0.761266,0.209497,0.423266,0.662995,0.484612,0.386968,0.305876,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,0.513517,0.447041,0.555328,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.922232,0.178433,1.82823,1.03623,1.98853,0.409836,0.136938,0.651651,0.806481,0.336166,0.179489,0.759925,0.612313,0.167672,0.920903,4.33535,0.0299392,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,0.733735,1.16941,0.202284,0.1711,0.859272,0.663249,1.65865,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.887702,0.386136,0.96962,0.337254,0.499714,1.21576,0.254749,1.82084,1.11602,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,1.33415,0.766041,4.11974,0.986833,0.207643,0.569994,1.06851,0.605358,0.782826,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.676555,0.524587,0.842217|tfbs_overrepresentation_jaspar=MA0003.1;1.45843,MA0004.1;0.434673,MA0006.1;0.747445,MA0007.1;1.07722,MA0009.1;0.870101,MA0014.1;4.06656,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;1.66702,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;1.64072,MA0056.1;0,MA0057.1;1.07246,MA0058.1;0.341628,MA0059.1;0.353484,MA0060.1;0.574356,MA0061.1;0.638933,MA0063.1;0,MA0066.1;0.566617,MA0067.1;1.21448,MA0068.1;1.61305,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;8.09348,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;0.49616,MA0089.1;0,MA0090.1;0.401197,MA0091.1;1.13691,MA0092.1;0.401504,MA0093.1;0.289361,MA0095.1;0,MA0098.1;0,MA0100.1;1.29122,MA0101.1;0.362124,MA0103.1;0.827743,MA0105.1;1.93163,MA0106.1;0.626997,MA0107.1;0.301222,MA0108.2;0.710846,MA0109.1;0,MA0111.1;1.06639,MA0113.1;0.598933,MA0114.1;0.222763,MA0115.1;0.969632,MA0116.1;0.747001,MA0117.1;0.937363,MA0119.1;0.951747,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;0.550755,MA0139.1;2.9589,MA0140.1;0.519484,MA0141.1;0.869985,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;0.225588,MA0145.1;0.900473,MA0146.1;1.72764,MA0147.1;0.666991,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.137653,MA0035.2;0.524137,MA0039.2;2.43328,MA0138.2;0.675599,MA0002.2;0.172399,MA0137.2;0.32312,MA0104.2;1.64215,MA0047.2;0.576767,MA0112.2;0.527225,MA0065.2;0.902537,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.677425,MA0155.1;2.62015,MA0156.1;0.314185,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.688775,MA0160.1;0.453546,MA0161.1;0,MA0162.1;5.39004,MA0163.1;3.33731,MA0164.1;0.551114,MA0080.2;0.302064,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;23.6077,MA0102.2;1.59466,MA0258.1;0.210437,MA0259.1;1.2032,MA0442.1;0}}

Latest revision as of 16:10, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr15:78744346..78744357,+p2@Pdxp
Mm9::chr19:16207236..16207263,+p3@Gnaq
Mm9::chr19:5093003..5093016,-p@chr19:5093003..5093016
-
Mm9::chr1:91476758..91476777,+p@chr1:91476758..91476777
+
Mm9::chr2:153355941..153355988,-p3@8430427H17Rik
Mm9::chr3:89263219..89263243,+p4@Pmvk
Mm9::chr5:24414378..24414401,-p9@Prkag2
Mm9::chr7:54388068..54388082,-p9@Ptpn5


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:0006695cholesterol biosynthetic process0.00195623805134542
GO:0016126sterol biosynthetic process0.00195623805134542
GO:0008203cholesterol metabolic process0.00476738807664171
GO:0006694steroid biosynthetic process0.00476738807664171
GO:0016125sterol metabolic process0.00476738807664171
GO:0004631phosphomevalonate kinase activity0.00735038989024635
GO:0050932regulation of pigment cell differentiation0.0102920334871923
GO:0045634regulation of melanocyte differentiation0.0102920334871923
GO:0008202steroid metabolic process0.0102920334871923
GO:0016322neuron remodeling0.0160319429526234
GO:0060158dopamine receptor, phospholipase C activating pathway0.0160319429526234
GO:0021884forebrain neuron development0.0176312726477465
GO:0016791phosphoric monoester hydrolase activity0.0176312726477465
GO:0008610lipid biosynthetic process0.0176312726477465
GO:0004679AMP-activated protein kinase activity0.0176312726477465
GO:0006066alcohol metabolic process0.018147850684892
GO:0021879forebrain neuron differentiation0.018147850684892
GO:0021872generation of neurons in the forebrain0.0195860098829364
GO:0042578phosphoric ester hydrolase activity0.0198286620026463
GO:0042551neuron maturation0.0198286620026463
GO:0007215glutamate signaling pathway0.0209804118909944
GO:0042733embryonic digit morphogenesis0.0260262263429269
GO:0006471protein amino acid ADP-ribosylation0.0299370552228139
GO:0030318melanocyte differentiation0.0299370552228139
GO:0050931pigment cell differentiation0.0299370552228139
GO:0007212dopamine receptor signaling pathway0.0304755625900123
GO:0021954central nervous system neuron development0.0342267238762276
GO:0021953central nervous system neuron differentiation0.0377068485994009
GO:0044255cellular lipid metabolic process0.0402783680354601
GO:0016776phosphotransferase activity, phosphate group as acceptor0.0410405751465139
GO:0048066pigmentation during development0.0411306312227698
GO:0007200G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.0412147581446118
GO:0009791post-embryonic development0.0412934949740724
GO:0005834heterotrimeric G-protein complex0.042655371467583
GO:0006629lipid metabolic process0.042717818550928
GO:0007189G-protein signaling, adenylate cyclase activating pathway0.042717818550928
GO:0001508regulation of action potential0.0429220077924235
GO:0016788hydrolase activity, acting on ester bonds0.0429220077924235
GO:0016787hydrolase activity0.0478159390112852
GO:0048015phosphoinositide-mediated signaling0.0482845165637295



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
central nervous system4.57e-2873
nervous system1.76e-2775
neurectoderm8.34e-2564
neural plate8.34e-2564
presumptive neural plate8.34e-2564
ectoderm-derived structure2.15e-2495
ectoderm2.15e-2495
presumptive ectoderm2.15e-2495
regional part of nervous system8.38e-2454
ecto-epithelium1.56e-2273
neural tube1.88e-2252
neural rod1.88e-2252
future spinal cord1.88e-2252
neural keel1.88e-2252
pre-chordal neural plate8.86e-2049
gray matter2.76e-1934
brain3.98e-1947
future brain3.98e-1947
structure with developmental contribution from neural crest5.01e-1992
regional part of brain1.28e-1846
anterior neural tube2.12e-1840
regional part of forebrain7.16e-1839
forebrain7.16e-1839
future forebrain7.16e-1839
brain grey matter6.20e-1629
regional part of telencephalon6.20e-1629
telencephalon6.20e-1629
cerebral cortex4.74e-1121
cerebral hemisphere4.74e-1121
pallium4.74e-1121
regional part of cerebral cortex7.54e-0917


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)
MA0003.11.45843
MA0004.10.434673
MA0006.10.747445
MA0007.11.07722
MA0009.10.870101
MA0014.14.06656
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
MA0048.11.66702
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.11.64072
MA0056.10
MA0057.11.07246
MA0058.10.341628
MA0059.10.353484
MA0060.10.574356
MA0061.10.638933
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.11.61305
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.18.09348
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.49616
MA0089.10
MA0090.10.401197
MA0091.11.13691
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.11.29122
MA0101.10.362124
MA0103.10.827743
MA0105.11.93163
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.11.06639
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.10.747001
MA0117.10.937363
MA0119.10.951747
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.12.9589
MA0140.10.519484
MA0141.10.869985
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.900473
MA0146.11.72764
MA0147.10.666991
MA0148.10.450593
MA0149.10.367458
MA0062.20.137653
MA0035.20.524137
MA0039.22.43328
MA0138.20.675599
MA0002.20.172399
MA0137.20.32312
MA0104.21.64215
MA0047.20.576767
MA0112.20.527225
MA0065.20.902537
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.677425
MA0155.12.62015
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.688775
MA0160.10.453546
MA0161.10
MA0162.15.39004
MA0163.13.33731
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.223.6077
MA0102.21.59466
MA0258.10.210437
MA0259.11.2032
MA0442.10
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