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MCL coexpression mm9:353: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0003076!7.37e-20!12;UBERON:0003057!7.37e-20!12;UBERON:0002240!1.15e-15!6;UBERON:0005174!1.15e-15!6;UBERON:0001137!1.15e-15!6;UBERON:0001948!3.10e-13!5;UBERON:0002315!3.10e-13!5;UBERON:0000073!2.49e-09!54;UBERON:0001049!1.06e-08!52;UBERON:0005068!1.06e-08!52;UBERON:0006241!1.06e-08!52;UBERON:0007135!1.06e-08!52;UBERON:0002257!1.51e-08!3;UBERON:0002346!2.88e-07!64;UBERON:0003075!2.88e-07!64;UBERON:0007284!2.88e-07!64;UBERON:0001017!7.37e-07!73;UBERON:0004733!9.41e-07!6;UBERON:0004732!9.41e-07!6;UBERON:0002028!9.41e-07!6;UBERON:0007277!9.41e-07!6
|ontology_enrichment_uberon=UBERON:0003076!7.37e-20!12;UBERON:0003057!7.37e-20!12;UBERON:0002240!1.15e-15!6;UBERON:0005174!1.15e-15!6;UBERON:0001137!1.15e-15!6;UBERON:0001948!3.10e-13!5;UBERON:0002315!3.10e-13!5;UBERON:0000073!2.49e-09!54;UBERON:0001049!1.06e-08!52;UBERON:0005068!1.06e-08!52;UBERON:0006241!1.06e-08!52;UBERON:0007135!1.06e-08!52;UBERON:0002257!1.51e-08!3;UBERON:0002346!2.88e-07!64;UBERON:0003075!2.88e-07!64;UBERON:0007284!2.88e-07!64;UBERON:0001017!7.37e-07!73;UBERON:0004733!9.41e-07!6;UBERON:0004732!9.41e-07!6;UBERON:0002028!9.41e-07!6;UBERON:0007277!9.41e-07!6
|tfbs_overrepresentation_for_novel_motifs=0.119369,0.0613587,0.104705,0.144583,0.191527,0.910673,0.615468,0.229454,0.752205,0.211146,0.184424,0.206436,2.36973,0.223743,0.211839,0,0.374352,0.182139,1.33193,0.726362,0.0854539,0.188411,0.223092,0.0508498,0.108863,0.243873,0.0728375,0.50041,0.53096,0.122724,0.477864,0.460285,0.712306,0.0585697,0.806589,0.0464706,0.168805,0.2039,0.608153,0.115421,0.416906,0.161379,0.161515,0.214332,0.113054,1.36273,0.309657,0.177618,0.211272,0.916531,0.359925,0.729809,1.2622,0.586014,2.49375,0.22892,0.559359,0.573993,1.21011,0.227439,0.442975,0.271204,0.502154,0.350689,0.237053,0.99896,0.727642,1.06142,0.438956,0.919268,0.314287,0.0971174,0.0443679,0.632466,0.325879,2.80351,0.0120781,0.300684,0.428247,0.0875778,0.45844,0.388829,0.270104,0.217876,0.5282,0.0985324,0.874699,0.122924,0.313544,1.21975,0.793151,0.532634,0.471416,0.198642,0.0351424,0.292027,0.700484,1.19351,0.309859,0.0321057,0.0440835,0.460042,0.570262,0.946715,0.944798,0.161095,0.409409,0.174935,0.301886,0.29175,0.115332,1.40194,1.03451,0.187937,0.799811,0.412914,0.2637,0.146927,0.375433,0.668337,0.637418,0.333667,0.686386,0.299972,0.851175,0.43141,0.62924,0.465518,0.726225,0.202267,0.554981,0.140083,0.698665,0.671684,1.91846,0.183848,0.124253,0.488358,0.773792,1.58317,1.18855,0.732048,0.707182,2.05917,0.35423,0.161672,0.31213,1.54387,0.125637,0.429877,0.261373,0.0788443,1.43474,3.34864,0.238221,0.662158,0.731564,0.0633954,0.756205,0.124089,0.782756,0.527439,0.431791,0.365959,0.927041,0.232792,0.677032,0.205322,0.577271
|tfbs_overrepresentation_for_novel_motifs=0.119369,0.0613587,0.104705,0.144583,0.191527,0.910673,0.615468,0.229454,0.752205,0.211146,0.184424,0.206436,2.36973,0.223743,0.211839,0,0.374352,0.182139,1.33193,0.726362,0.0854539,0.188411,0.223092,0.0508498,0.108863,0.243873,0.0728375,0.50041,0.53096,0.122724,0.477864,0.460285,0.712306,0.0585697,0.806589,0.0464706,0.168805,0.2039,0.608153,0.115421,0.416906,0.161379,0.161515,0.214332,0.113054,1.36273,0.309657,0.177618,0.211272,0.916531,0.359925,0.729809,1.2622,0.586014,2.49375,0.22892,0.559359,0.573993,1.21011,0.227439,0.442975,0.271204,0.502154,0.350689,0.237053,0.99896,0.727642,1.06142,0.438956,0.919268,0.314287,0.0971174,0.0443679,0.632466,0.325879,2.80351,0.0120781,0.300684,0.428247,0.0875778,0.45844,0.388829,0.270104,0.217876,0.5282,0.0985324,0.874699,0.122924,0.313544,1.21975,0.793151,0.532634,0.471416,0.198642,0.0351424,0.292027,0.700484,1.19351,0.309859,0.0321057,0.0440835,0.460042,0.570262,0.946715,0.944798,0.161095,0.409409,0.174935,0.301886,0.29175,0.115332,1.40194,1.03451,0.187937,0.799811,0.412914,0.2637,0.146927,0.375433,0.668337,0.637418,0.333667,0.686386,0.299972,0.851175,0.43141,0.62924,0.465518,0.726225,0.202267,0.554981,0.140083,0.698665,0.671684,1.91846,0.183848,0.124253,0.488358,0.773792,1.58317,1.18855,0.732048,0.707182,2.05917,0.35423,0.161672,0.31213,1.54387,0.125637,0.429877,0.261373,0.0788443,1.43474,3.34864,0.238221,0.662158,0.731564,0.0633954,0.756205,0.124089,0.782756,0.527439,0.431791,0.365959,0.927041,0.232792,0.677032,0.205322,0.577271
|tfbs_overrepresentation_jaspar=MA0003.1;1.78698,MA0004.1;0.444991,MA0006.1;1.20311,MA0007.1;0.421767,MA0009.1;0.483331,MA0014.1;0.195323,MA0017.1;0.0678809,MA0019.1;0.878507,MA0024.1;0.445298,MA0025.1;0.694475,MA0027.1;2.07936,MA0028.1;0.477663,MA0029.1;0.426655,MA0030.1;0.43227,MA0031.1;0.402033,MA0038.1;1.26683,MA0040.1;0.494317,MA0041.1;0.10094,MA0042.1;0.312557,MA0043.1;0.569356,MA0046.1;0.514989,MA0048.1;0.369099,MA0050.1;0.506524,MA0051.1;1.29176,MA0052.1;0.501416,MA0055.1;1.94453,MA0056.1;0,MA0057.1;0.767633,MA0058.1;0.303016,MA0059.1;0.320353,MA0060.1;0.0282014,MA0061.1;0.343057,MA0063.1;0,MA0066.1;0.664275,MA0067.1;1.8739,MA0068.1;0.543816,MA0069.1;0.501715,MA0070.1;1.23487,MA0071.1;0.169125,MA0072.1;0.485733,MA0073.1;0.000130259,MA0074.1;0.603526,MA0076.1;0.0767377,MA0077.1;0.466808,MA0078.1;0.275441,MA0081.1;0.109386,MA0083.1;0.568641,MA0084.1;1.11388,MA0087.1;0.530004,MA0088.1;0.732432,MA0089.1;0,MA0090.1;0.124244,MA0091.1;0.465605,MA0092.1;1.27914,MA0093.1;0.496926,MA0095.1;0,MA0098.1;0,MA0100.1;0.201797,MA0101.1;0.101635,MA0103.1;0.253989,MA0105.1;0.515449,MA0106.1;0.769607,MA0107.1;0.0699845,MA0108.2;0.919696,MA0109.1;0,MA0111.1;0.413949,MA0113.1;0.720329,MA0114.1;0.145706,MA0115.1;0.571881,MA0116.1;0.206147,MA0117.1;0.542889,MA0119.1;0.101951,MA0122.1;0.560692,MA0124.1;0.748494,MA0125.1;0.67944,MA0130.1;0,MA0131.1;0.326061,MA0132.1;0,MA0133.1;0,MA0135.1;0.602346,MA0136.1;0.224107,MA0139.1;0.222381,MA0140.1;0.584015,MA0141.1;0.588454,MA0142.1;0.389844,MA0143.1;0.27232,MA0144.1;0.149023,MA0145.1;0.371879,MA0146.1;0.0248607,MA0147.1;0.370788,MA0148.1;0.155077,MA0149.1;0.104621,MA0062.2;0.317505,MA0035.2;0.205003,MA0039.2;0.0273381,MA0138.2;0.319705,MA0002.2;0.020674,MA0137.2;0.276466,MA0104.2;0.254432,MA0047.2;0.243248,MA0112.2;1.38655,MA0065.2;0.116416,MA0150.1;0.421594,MA0151.1;0,MA0152.1;0.243327,MA0153.1;0.617506,MA0154.1;0.201776,MA0155.1;1.21447,MA0156.1;0.0763253,MA0157.1;0.363212,MA0158.1;0,MA0159.1;0.174007,MA0160.1;0.156994,MA0161.1;0,MA0162.1;0.0749828,MA0163.1;2.0793,MA0164.1;0.224368,MA0080.2;0.0703895,MA0018.2;0.231394,MA0099.2;1.5264,MA0079.2;5.47251,MA0102.2;1.16504,MA0258.1;0.895773,MA0259.1;0.626539,MA0442.1;0
}}
}}

Revision as of 11:36, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:118431001..118431046,-p4@Rbfox3
Mm9::chr11:118431276..118431314,-p3@Rbfox3
Mm9::chr11:118431626..118431637,-p16@Rbfox3
Mm9::chr13:33175964..33175973,+p2@Serpinb1b
Mm9::chr13:33175982..33176015,+p1@Serpinb1b
Mm9::chr14:33277893..33277902,-p6@Slc18a3
Mm9::chr14:33277950..33277963,-p1@Slc18a3
Mm9::chr14:68742893..68742913,-p1@Nefm
Mm9::chr17:54438043..54438057,-p1@Slc5a7
Mm9::chr2:70053872..70053879,+p@chr2:70053872..70053879
+
Mm9::chr4:137573229..137573260,+p@chr4:137573229..137573260
+
Mm9::chr4:137573261..137573269,+p@chr4:137573261..137573269
+
Mm9::chr4:150371190..150371197,+p1@Uts2
Mm9::chr7:57165440..57165441,+p13@Slc6a5
Mm9::chr7:57165453..57165473,+p3@Slc6a5
Mm9::chr7:57165482..57165497,+p2@Slc6a5
Mm9::chr7:57165576..57165593,+p5@Slc6a5
Mm9::chr7:57165602..57165612,+p6@Slc6a5
Mm9::chr7:57165629..57165651,+p4@Slc6a5
Mm9::chr7:57167425..57167443,+p@chr7:57167425..57167443
+
Mm9::chr7:57215165..57215169,+p@chr7:57215165..57215169
+
Mm9::chr7:57215305..57215314,+p@chr7:57215305..57215314
+


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:0005275amine transmembrane transporter activity1.94117445984349e-05
GO:0008504monoamine transmembrane transporter activity4.45609887683677e-05
GO:0015370solute:sodium symporter activity0.00290317603935904
GO:0022804active transmembrane transporter activity0.00290317603935904
GO:0006836neurotransmitter transport0.00290317603935904
GO:0015294solute:cation symporter activity0.00290317603935904
GO:0015837amine transport0.00290317603935904
GO:0008292acetylcholine biosynthetic process0.00602640661809018
GO:0005307choline:sodium symporter activity0.00602640661809018
GO:0008291acetylcholine metabolic process0.00903837176009507
GO:0015871choline transport0.00903837176009507
GO:0015220choline transmembrane transporter activity0.00903837176009507
GO:0015293symporter activity0.00984208619353216
GO:0031133regulation of axon diameter0.0101667754957099
GO:0045110intermediate filament bundle assembly0.0101667754957099
GO:0015844monoamine transport0.0101667754957099
GO:0042439ethanolamine and derivative metabolic process0.0123921007879047
GO:0015291secondary active transmembrane transporter activity0.0123921007879047
GO:0022857transmembrane transporter activity0.014520768102974
GO:0043195terminal button0.0154858644013815
GO:0005883neurofilament0.0154858644013815
GO:0006810transport0.0187540123604468
GO:0060053neurofilament cytoskeleton0.0187540123604468
GO:0060052neurofilament cytoskeleton organization and biogenesis0.0187540123604468
GO:0045109intermediate filament organization0.0187540123604468
GO:0033267axon part0.0187540123604468
GO:0051234establishment of localization0.0192789108118965
GO:0008088axon cargo transport0.019346727717088
GO:0042176regulation of protein catabolic process0.020112330883035
GO:0048265response to pain0.020112330883035
GO:0031594neuromuscular junction0.020112330883035
GO:0007274neuromuscular synaptic transmission0.020112330883035
GO:0009894regulation of catabolic process0.020112330883035
GO:0042136neurotransmitter biosynthetic process0.020112330883035
GO:0007271synaptic transmission, cholinergic0.020112330883035
GO:0051179localization0.0228123038652274
GO:0045104intermediate filament cytoskeleton organization and biogenesis0.0248654523517968
GO:0005328neurotransmitter:sodium symporter activity0.0256317698159375
GO:0045103intermediate filament-based process0.0270483470018585
GO:0005326neurotransmitter transporter activity0.0270483470018585
GO:0042401biogenic amine biosynthetic process0.0316490147677722
GO:0033555multicellular organismal response to stress0.0321783707287936
GO:0008324cation transmembrane transporter activity0.0335335216595175
GO:0042398amino acid derivative biosynthetic process0.0343874727040846
GO:0050770regulation of axonogenesis0.0360151058030516
GO:0004601peroxidase activity0.0379152230653866
GO:0016684oxidoreductase activity, acting on peroxide as acceptor0.0379152230653866
GO:0042133neurotransmitter metabolic process0.0416025674897824
GO:0050767regulation of neurogenesis0.0495108445735055



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>

Cell Type
Ontology termp-valuen
neuron of the ventral spinal cord1.51e-083
CNS neuron (sensu Vertebrata)3.15e-0723
neuroblast (sensu Vertebrata)3.15e-0723


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)
MA0003.11.78698
MA0004.10.444991
MA0006.11.20311
MA0007.10.421767
MA0009.10.483331
MA0014.10.195323
MA0017.10.0678809
MA0019.10.878507
MA0024.10.445298
MA0025.10.694475
MA0027.12.07936
MA0028.10.477663
MA0029.10.426655
MA0030.10.43227
MA0031.10.402033
MA0038.11.26683
MA0040.10.494317
MA0041.10.10094
MA0042.10.312557
MA0043.10.569356
MA0046.10.514989
MA0048.10.369099
MA0050.10.506524
MA0051.11.29176
MA0052.10.501416
MA0055.11.94453
MA0056.10
MA0057.10.767633
MA0058.10.303016
MA0059.10.320353
MA0060.10.0282014
MA0061.10.343057
MA0063.10
MA0066.10.664275
MA0067.11.8739
MA0068.10.543816
MA0069.10.501715
MA0070.11.23487
MA0071.10.169125
MA0072.10.485733
MA0073.10.000130259
MA0074.10.603526
MA0076.10.0767377
MA0077.10.466808
MA0078.10.275441
MA0081.10.109386
MA0083.10.568641
MA0084.11.11388
MA0087.10.530004
MA0088.10.732432
MA0089.10
MA0090.10.124244
MA0091.10.465605
MA0092.11.27914
MA0093.10.496926
MA0095.10
MA0098.10
MA0100.10.201797
MA0101.10.101635
MA0103.10.253989
MA0105.10.515449
MA0106.10.769607
MA0107.10.0699845
MA0108.20.919696
MA0109.10
MA0111.10.413949
MA0113.10.720329
MA0114.10.145706
MA0115.10.571881
MA0116.10.206147
MA0117.10.542889
MA0119.10.101951
MA0122.10.560692
MA0124.10.748494
MA0125.10.67944
MA0130.10
MA0131.10.326061
MA0132.10
MA0133.10
MA0135.10.602346
MA0136.10.224107
MA0139.10.222381
MA0140.10.584015
MA0141.10.588454
MA0142.10.389844
MA0143.10.27232
MA0144.10.149023
MA0145.10.371879
MA0146.10.0248607
MA0147.10.370788
MA0148.10.155077
MA0149.10.104621
MA0062.20.317505
MA0035.20.205003
MA0039.20.0273381
MA0138.20.319705
MA0002.20.020674
MA0137.20.276466
MA0104.20.254432
MA0047.20.243248
MA0112.21.38655
MA0065.20.116416
MA0150.10.421594
MA0151.10
MA0152.10.243327
MA0153.10.617506
MA0154.10.201776
MA0155.11.21447
MA0156.10.0763253
MA0157.10.363212
MA0158.10
MA0159.10.174007
MA0160.10.156994
MA0161.10
MA0162.10.0749828
MA0163.12.0793
MA0164.10.224368
MA0080.20.0703895
MA0018.20.231394
MA0099.21.5264
MA0079.25.47251
MA0102.21.16504
MA0258.10.895773
MA0259.10.626539
MA0442.10
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