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MCL coexpression mm9:1286: Difference between revisions

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{{MCL_coexpression_mm9
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isomerase activity;0.0101745724047251;14874!GO:0016853;isomerase activity;0.0101745724047251;76866,14874!GO:0042487;regulation of odontogenesis of dentine-containing teeth;0.0162606022548207;21821!GO:0045862;positive regulation of proteolysis;0.0162606022548207;21821!GO:0006572;tyrosine catabolic process;0.0162606022548207;14874!GO:0006559;L-phenylalanine catabolic process;0.0162606022548207;14874!GO:0006558;L-phenylalanine metabolic process;0.0162606022548207;14874!GO:0005932;basal body;0.0162606022548207;21821!GO:0009074;aromatic amino acid family catabolic process;0.0162606022548207;14874!GO:0006570;tyrosine metabolic process;0.0162606022548207;14874!GO:0030162;regulation of proteolysis;0.0162606022548207;21821!GO:0019439;aromatic compound catabolic process;0.0162606022548207;14874!GO:0042733;embryonic digit morphogenesis;0.0162606022548207;21821!GO:0005930;axoneme;0.0249192623318852;21821!GO:0004364;glutathione transferase activity;0.0249192623318852;14874!GO:0009072;aromatic amino acid family metabolic process;0.0253904864530803;14874!GO:0007224;smoothened signaling pathway;0.0263858473302257;21821!GO:0007368;determination of left/right symmetry;0.0263858473302257;21821!GO:0016859;cis-trans isomerase activity;0.0263858473302257;14874!GO:0009855;determination of bilateral symmetry;0.0263858473302257;21821!GO:0009799;determination of symmetry;0.0263858473302257;21821!GO:0042475;odontogenesis of dentine-containing teeth;0.0263858473302257;21821!GO:0042476;odontogenesis;0.0263858473302257;21821!GO:0019861;flagellum;0.0263858473302257;21821!GO:0009953;dorsal/ventral pattern formation;0.027922280024024;21821!GO:0009063;amino acid catabolic process;0.0287167623369693;14874!GO:0016765;transferase activity, transferring alkyl or aryl (other than methyl) groups;0.0301337658028662;14874!GO:0005815;microtubule organizing center;0.0301337658028662;21821!GO:0009310;amine catabolic process;0.0302816543141528;14874!GO:0044270;nitrogen compound catabolic 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|gostat_on_MCL_coexpression=GO:0016034;maleylacetoacetate isomerase activity;0.0101745724047251;14874!GO:0016853;isomerase activity;0.0101745724047251;76866,14874!GO:0042487;regulation of odontogenesis of dentine-containing teeth;0.0162606022548207;21821!GO:0045862;positive regulation of proteolysis;0.0162606022548207;21821!GO:0006572;tyrosine catabolic process;0.0162606022548207;14874!GO:0006559;L-phenylalanine catabolic process;0.0162606022548207;14874!GO:0006558;L-phenylalanine metabolic process;0.0162606022548207;14874!GO:0005932;basal body;0.0162606022548207;21821!GO:0009074;aromatic amino acid family catabolic process;0.0162606022548207;14874!GO:0006570;tyrosine metabolic process;0.0162606022548207;14874!GO:0030162;regulation of proteolysis;0.0162606022548207;21821!GO:0019439;aromatic compound catabolic process;0.0162606022548207;14874!GO:0042733;embryonic digit morphogenesis;0.0162606022548207;21821!GO:0005930;axoneme;0.0249192623318852;21821!GO:0004364;glutathione transferase activity;0.0249192623318852;14874!GO:0009072;aromatic amino acid family metabolic process;0.0253904864530803;14874!GO:0007224;smoothened signaling pathway;0.0263858473302257;21821!GO:0007368;determination of left/right symmetry;0.0263858473302257;21821!GO:0016859;cis-trans isomerase activity;0.0263858473302257;14874!GO:0009855;determination of bilateral symmetry;0.0263858473302257;21821!GO:0009799;determination of symmetry;0.0263858473302257;21821!GO:0042475;odontogenesis of dentine-containing teeth;0.0263858473302257;21821!GO:0042476;odontogenesis;0.0263858473302257;21821!GO:0019861;flagellum;0.0263858473302257;21821!GO:0009953;dorsal/ventral pattern formation;0.027922280024024;21821!GO:0009063;amino acid catabolic process;0.0287167623369693;14874!GO:0016765;transferase activity, transferring alkyl or aryl (other than methyl) groups;0.0301337658028662;14874!GO:0005815;microtubule organizing center;0.0301337658028662;21821!GO:0009310;amine catabolic process;0.0302816543141528;14874!GO:0044270;nitrogen compound catabolic process;0.0302816543141528;14874!GO:0030326;embryonic limb morphogenesis;0.0319254226005781;21821!GO:0035113;embryonic appendage morphogenesis;0.0319254226005781;21821!GO:0044463;cell projection part;0.0334058050564833;21821!GO:0051247;positive regulation of protein metabolic process;0.0336828146193963;21821!GO:0035107;appendage morphogenesis;0.0336828146193963;21821!GO:0035108;limb morphogenesis;0.0336828146193963;21821!GO:0048736;appendage development;0.0336828146193963;21821!GO:0060173;limb development;0.0336828146193963;21821!GO:0009952;anterior/posterior pattern formation;0.0390185070273834;21821!GO:0006725;aromatic compound metabolic process;0.0456849239475597;14874!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0010371!6.77e-11!73;UBERON:0002346!7.08e-11!64;UBERON:0003075!7.08e-11!64;UBERON:0007284!7.08e-11!64;UBERON:0003056!4.91e-10!49;UBERON:0004121!9.48e-10!95;UBERON:0000924!9.48e-10!95;UBERON:0006601!9.48e-10!95;UBERON:0001049!5.85e-09!52;UBERON:0005068!5.85e-09!52;UBERON:0006241!5.85e-09!52;UBERON:0007135!5.85e-09!52;UBERON:0001017!7.08e-09!73;UBERON:0000073!1.30e-08!54;UBERON:0000955!3.61e-08!47;UBERON:0006238!3.61e-08!47;UBERON:0002616!4.02e-08!46;UBERON:0001016!4.59e-08!75;UBERON:0010314!8.87e-08!92;UBERON:0000468!1.35e-07!333;UBERON:0003080!3.08e-07!40;UBERON:0002780!4.94e-07!39;UBERON:0001890!4.94e-07!39;UBERON:0006240!4.94e-07!39;UBERON:0004111!6.60e-07!122;UBERON:0000025!8.99e-07!114
|tfbs_overrepresentation_for_novel_motifs=2.1342,1.24447,0.464605,0.535892,0.346849,0.550971,1.55624,0.247459,0.7141,0.594834,0.599767,0.632897,0.692139,0.6581,0.364314,0,0.856992,0.338549,0.656199,0.143775,0.426133,1.72037,0.657163,0.91309,1.19059,0.686615,1.85593,1.40396,0.394364,0.181062,0.558142,0.960397,0.892985,0.589948,0.956447,0.0363535,0.326478,1.52228,0.820134,0.27383,0.907317,0.56353,0.0995018,0.366415,1.9448,1.30113,0.77511,0.589246,0.0835644,0.397446,0.839084,0.714419,0.517905,1.10437,1.12205,1.59824,1.04848,0.619643,1.15584,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,0.11437,1.156,0.599223,0.19692,0.589776,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.240896,1.03903,0.198949,0.0610418,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.769162,0.685716,0.976308,1.826,1.49884,0.326561,0.960112,1.08669,0.839694,0.838613,1.38336,0.8998,1.42973,0.435642,1.92,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.247162,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.937314,1.06946,0.52828,1.2285,0.679647,1.35909,0.706252,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.920761,0.540361,0.0987301,1.10596,0.287383,0.678689,1.18867,0.71546,0.376898,0.48935,2.16235,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,0.30995
|tfbs_overrepresentation_jaspar=MA0003.1;0.476238,MA0004.1;0.536396,MA0006.1;0.359699,MA0007.1;1.29371,MA0009.1;0.987341,MA0014.1;0.12867,MA0017.1;0.387481,MA0019.1;0.800946,MA0024.1;0.942716,MA0025.1;1.22395,MA0027.1;2.64231,MA0028.1;3.55677,MA0029.1;2.12396,MA0030.1;0.927235,MA0031.1;0.890871,MA0038.1;0.686534,MA0040.1;1.00009,MA0041.1;0.457338,MA0042.1;0.443591,MA0043.1;1.08567,MA0046.1;1.02391,MA0048.1;0.161427,MA0050.1;0.57678,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;0.465302,MA0056.1;0,MA0057.1;0.149949,MA0058.1;0.436487,MA0059.1;0.449345,MA0060.1;0.757042,MA0061.1;0.307097,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;0.467569,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;0.00140584,MA0074.1;0.638014,MA0076.1;4.86596,MA0077.1;0.968053,MA0078.1;0.729877,MA0081.1;0.473489,MA0083.1;1.08487,MA0084.1;1.66561,MA0087.1;1.04109,MA0088.1;0.725434,MA0089.1;0,MA0090.1;0.500693,MA0091.1;0.55008,MA0092.1;1.25163,MA0093.1;0.379257,MA0095.1;0,MA0098.1;0,MA0100.1;1.51574,MA0101.1;0.458688,MA0103.1;0.398766,MA0105.1;0.199622,MA0106.1;0.737893,MA0107.1;0.392331,MA0108.2;0.824407,MA0109.1;0,MA0111.1;0.515457,MA0113.1;0.708789,MA0114.1;0.304661,MA0115.1;1.08851,MA0116.1;0.359483,MA0117.1;1.05576,MA0119.1;0.459301,MA0122.1;1.07591,MA0124.1;1.28237,MA0125.1;1.20757,MA0130.1;0,MA0131.1;0.796279,MA0132.1;0,MA0133.1;0,MA0135.1;1.1226,MA0136.1;0.658622,MA0139.1;0.243463,MA0140.1;0.625902,MA0141.1;0.419361,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;0.307873,MA0145.1;0.119202,MA0146.1;1.41218,MA0147.1;0.858298,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;4.14052,MA0035.2;0.630778,MA0039.2;1.05907,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;0.416331,MA0104.2;0.723439,MA0047.2;0.685741,MA0112.2;0.119197,MA0065.2;0.119561,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.159217,MA0155.1;0.132921,MA0156.1;1.84703,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.331229,MA0160.1;0.556423,MA0161.1;0,MA0162.1;0.176524,MA0163.1;0.163321,MA0164.1;0.658997,MA0080.2;1.01893,MA0018.2;1.60558,MA0099.2;0.781628,MA0079.2;0.147137,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.309517,MA0442.1;0
}}

Latest revision as of 16:41, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:4060221..4060234,-p2@Ccdc157
Mm9::chr11:4060235..4060285,-p1@Ccdc157
Mm9::chr11:4060289..4060308,-p3@Ccdc157
Mm9::chr12:88488099..88488151,+p2@Gstz1
Mm9::chr14:58042931..58042948,+p2@Ift88
Mm9::chr4:154460687..154460719,+p1@Morn1


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:0016034maleylacetoacetate isomerase activity0.0101745724047251
GO:0016853isomerase activity0.0101745724047251
GO:0042487regulation of odontogenesis of dentine-containing teeth0.0162606022548207
GO:0045862positive regulation of proteolysis0.0162606022548207
GO:0006572tyrosine catabolic process0.0162606022548207
GO:0006559L-phenylalanine catabolic process0.0162606022548207
GO:0006558L-phenylalanine metabolic process0.0162606022548207
GO:0005932basal body0.0162606022548207
GO:0009074aromatic amino acid family catabolic process0.0162606022548207
GO:0006570tyrosine metabolic process0.0162606022548207
GO:0030162regulation of proteolysis0.0162606022548207
GO:0019439aromatic compound catabolic process0.0162606022548207
GO:0042733embryonic digit morphogenesis0.0162606022548207
GO:0005930axoneme0.0249192623318852
GO:0004364glutathione transferase activity0.0249192623318852
GO:0009072aromatic amino acid family metabolic process0.0253904864530803
GO:0007224smoothened signaling pathway0.0263858473302257
GO:0007368determination of left/right symmetry0.0263858473302257
GO:0016859cis-trans isomerase activity0.0263858473302257
GO:0009855determination of bilateral symmetry0.0263858473302257
GO:0009799determination of symmetry0.0263858473302257
GO:0042475odontogenesis of dentine-containing teeth0.0263858473302257
GO:0042476odontogenesis0.0263858473302257
GO:0019861flagellum0.0263858473302257
GO:0009953dorsal/ventral pattern formation0.027922280024024
GO:0009063amino acid catabolic process0.0287167623369693
GO:0016765transferase activity, transferring alkyl or aryl (other than methyl) groups0.0301337658028662
GO:0005815microtubule organizing center0.0301337658028662
GO:0009310amine catabolic process0.0302816543141528
GO:0044270nitrogen compound catabolic process0.0302816543141528
GO:0030326embryonic limb morphogenesis0.0319254226005781
GO:0035113embryonic appendage morphogenesis0.0319254226005781
GO:0044463cell projection part0.0334058050564833
GO:0051247positive regulation of protein metabolic process0.0336828146193963
GO:0035107appendage morphogenesis0.0336828146193963
GO:0035108limb morphogenesis0.0336828146193963
GO:0048736appendage development0.0336828146193963
GO:0060173limb development0.0336828146193963
GO:0009952anterior/posterior pattern formation0.0390185070273834
GO:0006725aromatic compound metabolic process0.0456849239475597



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>


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)
MA0003.10.476238
MA0004.10.536396
MA0006.10.359699
MA0007.11.29371
MA0009.10.987341
MA0014.10.12867
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.13.55677
MA0029.12.12396
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.161427
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.465302
MA0056.10
MA0057.10.149949
MA0058.10.436487
MA0059.10.449345
MA0060.10.757042
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.467569
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.00140584
MA0074.10.638014
MA0076.14.86596
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.725434
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.11.25163
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.11.51574
MA0101.10.458688
MA0103.10.398766
MA0105.10.199622
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.243463
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.10.119202
MA0146.11.41218
MA0147.10.858298
MA0148.10.553294
MA0149.10.464445
MA0062.24.14052
MA0035.20.630778
MA0039.21.05907
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.723439
MA0047.20.685741
MA0112.20.119197
MA0065.20.119561
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.159217
MA0155.10.132921
MA0156.11.84703
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.10.176524
MA0163.10.163321
MA0164.10.658997
MA0080.21.01893
MA0018.21.60558
MA0099.20.781628
MA0079.20.147137
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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