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MCL coexpression mm9:261: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0009569!3.94e-11!66;UBERON:0005172!1.42e-10!49;UBERON:0005173!1.42e-10!49;UBERON:0002417!1.42e-10!49;UBERON:0000916!1.42e-10!49;UBERON:0002106!1.10e-09!6;UBERON:0004457!1.10e-09!6;UBERON:0000042!1.10e-09!6;UBERON:0004854!1.10e-09!6;UBERON:0009034!1.10e-09!6;UBERON:0002095!1.10e-09!6;UBERON:0004782!1.10e-09!6;UBERON:0003281!1.10e-09!6;UBERON:0009664!1.10e-09!6;UBERON:0002296!1.10e-09!6;UBERON:0005602!1.10e-09!6;UBERON:0001179!1.10e-09!6;UBERON:0006293!1.10e-09!6;UBERON:0001041!2.86e-09!80;UBERON:0005177!6.02e-08!79;UBERON:0003887!3.58e-07!10
|ontology_enrichment_uberon=UBERON:0009569!3.94e-11!66;UBERON:0005172!1.42e-10!49;UBERON:0005173!1.42e-10!49;UBERON:0002417!1.42e-10!49;UBERON:0000916!1.42e-10!49;UBERON:0002106!1.10e-09!6;UBERON:0004457!1.10e-09!6;UBERON:0000042!1.10e-09!6;UBERON:0004854!1.10e-09!6;UBERON:0009034!1.10e-09!6;UBERON:0002095!1.10e-09!6;UBERON:0004782!1.10e-09!6;UBERON:0003281!1.10e-09!6;UBERON:0009664!1.10e-09!6;UBERON:0002296!1.10e-09!6;UBERON:0005602!1.10e-09!6;UBERON:0001179!1.10e-09!6;UBERON:0006293!1.10e-09!6;UBERON:0001041!2.86e-09!80;UBERON:0005177!6.02e-08!79;UBERON:0003887!3.58e-07!10
|tfbs_overrepresentation_for_novel_motifs=0.2121,0.386572,0.183547,0.554666,0.403653,0.279466,0.798998,1.08451,0.367856,0.148944,0.340369,0.384124,0.188374,0.828885,0.23585,0,0.259755,0.633675,0.160901,0.438025,0.613331,0.38226,0.133942,0.399688,0.74741,0.896886,0.273327,0.0916359,0.0285758,0.453591,0.0850386,0.892346,0.193804,0.565328,0.448703,0.105131,0.180085,1.24473,0.51446,0.418456,0.203128,0.294713,0.634431,0.239128,0.523916,0.0707419,0.204367,0.326867,0.644951,0.534336,0.247239,0.166621,0.0757641,0.451112,0.465864,0.428923,0.305538,0.366398,0.132001,0.42597,0.85762,0.172475,0.909778,0.239273,0.144946,0.268299,0.584509,0.907487,0.316778,0.768874,0.164033,1.4714,0.284644,0.494514,0.386747,0.529441,0.564968,0.572368,0.307225,0.347468,0.360662,0.272401,0.171576,0.513774,0.397678,0.0937398,0.000603662,0.656538,0.207637,1.06309,0.64713,0.40175,0.34595,0.685263,0.0529479,0.254122,0.331969,0.348163,0.204536,0.359394,0.354785,0.335693,0.436484,0.247661,0.246912,0.0872264,0.290513,0.0973104,0.356705,0.0375205,0.449672,0.437975,0.151582,0.106977,1.57323,0.388768,0.363399,0.0771455,0.260696,1.60812,0.499163,1.19423,0.461462,1.08366,0.702969,0.310043,0.412705,0.340627,1.42573,1.41356,1.08232,0.917571,0.556974,0.880148,0.673182,0.0173461,0.48196,0.617124,0.628575,1.42304,1.03234,0.588705,0.93157,0.910596,0.242322,0.295293,0.595289,1.38398,0.839884,0.0836696,0.670986,0.32218,0.452434,0.129483,0.447481,0.522448,0.167242,0.255755,1.69914,0.0614775,0.637161,0.396979,0.310383,0.201723,0.239991,0.141571,0.178463,0.12017,0.189934
|tfbs_overrepresentation_for_novel_motifs=0.2121,0.386572,0.183547,0.554666,0.403653,0.279466,0.798998,1.08451,0.367856,0.148944,0.340369,0.384124,0.188374,0.828885,0.23585,0,0.259755,0.633675,0.160901,0.438025,0.613331,0.38226,0.133942,0.399688,0.74741,0.896886,0.273327,0.0916359,0.0285758,0.453591,0.0850386,0.892346,0.193804,0.565328,0.448703,0.105131,0.180085,1.24473,0.51446,0.418456,0.203128,0.294713,0.634431,0.239128,0.523916,0.0707419,0.204367,0.326867,0.644951,0.534336,0.247239,0.166621,0.0757641,0.451112,0.465864,0.428923,0.305538,0.366398,0.132001,0.42597,0.85762,0.172475,0.909778,0.239273,0.144946,0.268299,0.584509,0.907487,0.316778,0.768874,0.164033,1.4714,0.284644,0.494514,0.386747,0.529441,0.564968,0.572368,0.307225,0.347468,0.360662,0.272401,0.171576,0.513774,0.397678,0.0937398,0.000603662,0.656538,0.207637,1.06309,0.64713,0.40175,0.34595,0.685263,0.0529479,0.254122,0.331969,0.348163,0.204536,0.359394,0.354785,0.335693,0.436484,0.247661,0.246912,0.0872264,0.290513,0.0973104,0.356705,0.0375205,0.449672,0.437975,0.151582,0.106977,1.57323,0.388768,0.363399,0.0771455,0.260696,1.60812,0.499163,1.19423,0.461462,1.08366,0.702969,0.310043,0.412705,0.340627,1.42573,1.41356,1.08232,0.917571,0.556974,0.880148,0.673182,0.0173461,0.48196,0.617124,0.628575,1.42304,1.03234,0.588705,0.93157,0.910596,0.242322,0.295293,0.595289,1.38398,0.839884,0.0836696,0.670986,0.32218,0.452434,0.129483,0.447481,0.522448,0.167242,0.255755,1.69914,0.0614775,0.637161,0.396979,0.310383,0.201723,0.239991,0.141571,0.178463,0.12017,0.189934
|tfbs_overrepresentation_jaspar=MA0003.1;0.416392,MA0004.1;0.943038,MA0006.1;0.0915448,MA0007.1;0.0693451,MA0009.1;0.356735,MA0014.1;0.00558589,MA0017.1;0.11299,MA0019.1;0.221321,MA0024.1;0.322453,MA0025.1;0.553002,MA0027.1;1.91746,MA0028.1;0.0230932,MA0029.1;0.305809,MA0030.1;0.31081,MA0031.1;0.284004,MA0038.1;0.150331,MA0040.1;0.366712,MA0041.1;0.397031,MA0042.1;1.02922,MA0043.1;0.435645,MA0046.1;0.385571,MA0048.1;0.227772,MA0050.1;0.0934518,MA0051.1;0.155655,MA0052.1;0.974861,MA0055.1;2.01431,MA0056.1;0,MA0057.1;0.0493412,MA0058.1;0.358248,MA0059.1;0.168372,MA0060.1;0.00783438,MA0061.1;0.0572065,MA0063.1;0,MA0066.1;4.27173,MA0067.1;0.652366,MA0068.1;0.0532285,MA0069.1;0.373449,MA0070.1;0.365675,MA0071.1;0.310039,MA0072.1;0.358914,MA0073.1;0.000387491,MA0074.1;0.123701,MA0076.1;0.0318933,MA0077.1;0.341791,MA0078.1;0.521853,MA0081.1;0.192641,MA0083.1;1.10972,MA0084.1;0.958921,MA0087.1;1.03221,MA0088.1;0.269089,MA0089.1;0,MA0090.1;0.221633,MA0091.1;1.46918,MA0092.1;0.482591,MA0093.1;1.13914,MA0095.1;0,MA0098.1;0,MA0100.1;0.117472,MA0101.1;0.177595,MA0103.1;0.537896,MA0105.1;0.355784,MA0106.1;0.533809,MA0107.1;0.0280799,MA0108.2;0.237143,MA0109.1;0,MA0111.1;0.512045,MA0113.1;0.490789,MA0114.1;0.150918,MA0115.1;0.437985,MA0116.1;0.708546,MA0117.1;0.411186,MA0119.1;0.178209,MA0122.1;1.09377,MA0124.1;0.604388,MA0125.1;0.538769,MA0130.1;0,MA0131.1;0.218222,MA0132.1;0,MA0133.1;0,MA0135.1;0.466327,MA0136.1;0.419326,MA0139.1;0.180641,MA0140.1;0.117411,MA0141.1;0.327475,MA0142.1;0.27329,MA0143.1;0.515613,MA0144.1;1.1282,MA0145.1;0.451873,MA0146.1;0.0233321,MA0147.1;0.172105,MA0148.1;0.59177,MA0149.1;0.723587,MA0062.2;0.117118,MA0035.2;0.119926,MA0039.2;0.000458716,MA0138.2;0.212837,MA0002.2;0.336369,MA0137.2;0.322137,MA0104.2;0.379989,MA0047.2;0.149878,MA0112.2;0.451845,MA0065.2;0.310259,MA0150.1;0.522782,MA0151.1;0,MA0152.1;0.457674,MA0153.1;0.480495,MA0154.1;0.354879,MA0155.1;0.14685,MA0156.1;0.128979,MA0157.1;0.697652,MA0158.1;0,MA0159.1;0.0719173,MA0160.1;0.598518,MA0161.1;0,MA0162.1;0.111166,MA0163.1;0.0905096,MA0164.1;0.134941,MA0080.2;0.282578,MA0018.2;0.140467,MA0099.2;0.208596,MA0079.2;5.04018e-08,MA0102.2;1.0092,MA0258.1;0.273872,MA0259.1;0.0586005,MA0442.1;0
}}
}}

Revision as of 11:27, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:102214546..102214569,-p@chr11:102214546..102214569
-
Mm9::chr11:102214630..102214658,-p@chr11:102214630..102214658
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Mm9::chr11:102218475..102218486,-p@chr11:102218475..102218486
-
Mm9::chr11:95238906..95238922,+p@chr11:95238906..95238922
+
Mm9::chr13:47201101..47201115,-p10@Dek
Mm9::chr14:69860634..69860655,-p@chr14:69860634..69860655
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Mm9::chr14:69861633..69861672,-p@chr14:69861633..69861672
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Mm9::chr14:69862027..69862070,-p@chr14:69862027..69862070
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Mm9::chr14:69867395..69867407,-p@chr14:69867395..69867407
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Mm9::chr15:103079752..103079774,-p@chr15:103079752..103079774
-
Mm9::chr16:32630179..32630192,+p@chr16:32630179..32630192
+
Mm9::chr16:32630197..32630206,+p@chr16:32630197..32630206
+
Mm9::chr17:47735613..47735657,+p@chr17:47735613..47735657
+
Mm9::chr18:64616946..64616963,-p@chr18:64616946..64616963
-
Mm9::chr1:134254052..134254079,-p@chr1:134254052..134254079
-
Mm9::chr1:134254118..134254132,-p@chr1:134254118..134254132
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Mm9::chr1:134254201..134254237,-p@chr1:134254201..134254237
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Mm9::chr1:134257248..134257260,-p@chr1:134257248..134257260
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Mm9::chr2:131014815..131014832,+p@chr2:131014815..131014832
+
Mm9::chr2:131019004..131019012,+p@chr2:131019004..131019012
+
Mm9::chr2:163453686..163453707,-p@chr2:163453686..163453707
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Mm9::chr3:100276521..100276540,-p@chr3:100276521..100276540
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Mm9::chr3:121948828..121948839,+p7@Gclm
Mm9::chr3:36466826..36466850,-p@chr3:36466826..36466850
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Mm9::chr3:84284193..84284220,+p@chr3:84284193..84284220
+
Mm9::chr4:118859919..118859942,-p@chr4:118859919..118859942
-
Mm9::chr4:135748823..135748835,+p@chr4:135748823..135748835
+
Mm9::chr4:46409733..46409745,-p@chr4:46409733..46409745
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Mm9::chr7:134362245..134362250,-p9@Sept1
Mm9::chr8:108298224..108298257,-p@chr8:108298224..108298257
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Mm9::chrX:146988548..146988561,+p3@Alas2
Mm9::chrX:147001144..147001172,+p2@Alas2


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:0005381iron ion transmembrane transporter activity0.000456819144618196
GO:0051301cell division0.000733726995788518
GO:0016538cyclin-dependent protein kinase regulator activity0.0026114002127088
GO:0006873cellular ion homeostasis0.0026114002127088
GO:0055082cellular chemical homeostasis0.0026114002127088
GO:0006879cellular iron ion homeostasis0.0026114002127088
GO:0055072iron ion homeostasis0.0026114002127088
GO:0046915transition metal ion transmembrane transporter activity0.0026114002127088
GO:0050801ion homeostasis0.00265023647613552
GO:0015082di-, tri-valent inorganic cation transmembrane transporter activity0.00374559201860592
GO:0048878chemical homeostasis0.00404491782573569
GO:0019725cellular homeostasis0.00404491782573569
GO:0007049cell cycle0.00798705738009567
GO:0019887protein kinase regulator activity0.0081313237622078
GO:0048250mitochondrial iron ion transport0.0081313237622078
GO:0035229positive regulation of glutamate-cysteine ligase activity0.0081313237622078
GO:0035226glutamate-cysteine ligase catalytic subunit binding0.0081313237622078
GO:0035227regulation of glutamate-cysteine ligase activity0.0081313237622078
GO:0051351positive regulation of ligase activity0.0081313237622078
GO:0042592homeostatic process0.00854684043983682
GO:0019207kinase regulator activity0.00959426906029585
GO:0051882mitochondrial depolarization0.0106522111007838
GO:0016749N-succinyltransferase activity0.0106522111007838
GO:0004357glutamate-cysteine ligase activity0.0106522111007838
GO:0004998transferrin receptor activity0.0106522111007838
GO:0051340regulation of ligase activity0.0106522111007838
GO:0051900regulation of mitochondrial depolarization0.0106522111007838
GO:0017109glutamate-cysteine ligase complex0.0106522111007838
GO:00038705-aminolevulinate synthase activity0.0106522111007838
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.010902254789028
GO:0051188cofactor biosynthetic process0.010902254789028
GO:0055066di-, tri-valent inorganic cation homeostasis0.0110021371492729
GO:0030003cellular cation homeostasis0.0120011801332138
GO:0055080cation homeostasis0.0123224510919724
GO:0007144female meiosis I0.012520457965269
GO:0016748succinyltransferase activity0.012520457965269
GO:0051881regulation of mitochondrial membrane potential0.012520457965269
GO:0042541hemoglobin biosynthetic process0.0156168431581143
GO:0001940male pronucleus0.0156168431581143
GO:0022890inorganic cation transmembrane transporter activity0.0156168431581143
GO:0043085positive regulation of catalytic activity0.0159305284196433
GO:0001556oocyte maturation0.0171492062413345
GO:0020027hemoglobin metabolic process0.0171492062413345
GO:0001939female pronucleus0.0171492062413345
GO:0006534cysteine metabolic process0.0171492062413345
GO:0022402cell cycle process0.0172638545631914
GO:0006750glutathione biosynthetic process0.0196984864028533
GO:0007067mitosis0.0210190108072703
GO:0000087M phase of mitotic cell cycle0.0210190108072703
GO:0065008regulation of biological quality0.0210850417664668
GO:0048599oocyte development0.0232427130231152
GO:0009994oocyte differentiation0.0232427130231152
GO:0007143female meiosis0.0232427130231152
GO:0051186cofactor metabolic process0.0232427130231152
GO:0006783heme biosynthetic process0.0308229493562097
GO:0000278mitotic cell cycle0.0318412966535553
GO:0000279M phase0.0332048536694561
GO:0006779porphyrin biosynthetic process0.0339407523590761
GO:0033014tetrapyrrole biosynthetic process0.0339407523590761
GO:0045120pronucleus0.0359335298015824
GO:0065007biological regulation0.0388170245174001
GO:0000096sulfur amino acid metabolic process0.0390459646284324
GO:0042168heme metabolic process0.0390459646284324
GO:0050790regulation of catalytic activity0.0390459646284324
GO:0022403cell cycle phase0.0390459646284324
GO:0009069serine family amino acid metabolic process0.0390459646284324
GO:0051899membrane depolarization0.0390459646284324
GO:0033013tetrapyrrole metabolic process0.0400006848200994
GO:0006778porphyrin metabolic process0.0400006848200994
GO:0046873metal ion transmembrane transporter activity0.0400006848200994
GO:0006749glutathione metabolic process0.0411607496894537
GO:0048477oogenesis0.0448395069175333
GO:0065009regulation of a molecular function0.0456768811291409
GO:0006839mitochondrial transport0.0456938762583261



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)
MA0003.10.416392
MA0004.10.943038
MA0006.10.0915448
MA0007.10.0693451
MA0009.10.356735
MA0014.10.00558589
MA0017.10.11299
MA0019.10.221321
MA0024.10.322453
MA0025.10.553002
MA0027.11.91746
MA0028.10.0230932
MA0029.10.305809
MA0030.10.31081
MA0031.10.284004
MA0038.10.150331
MA0040.10.366712
MA0041.10.397031
MA0042.11.02922
MA0043.10.435645
MA0046.10.385571
MA0048.10.227772
MA0050.10.0934518
MA0051.10.155655
MA0052.10.974861
MA0055.12.01431
MA0056.10
MA0057.10.0493412
MA0058.10.358248
MA0059.10.168372
MA0060.10.00783438
MA0061.10.0572065
MA0063.10
MA0066.14.27173
MA0067.10.652366
MA0068.10.0532285
MA0069.10.373449
MA0070.10.365675
MA0071.10.310039
MA0072.10.358914
MA0073.10.000387491
MA0074.10.123701
MA0076.10.0318933
MA0077.10.341791
MA0078.10.521853
MA0081.10.192641
MA0083.11.10972
MA0084.10.958921
MA0087.11.03221
MA0088.10.269089
MA0089.10
MA0090.10.221633
MA0091.11.46918
MA0092.10.482591
MA0093.11.13914
MA0095.10
MA0098.10
MA0100.10.117472
MA0101.10.177595
MA0103.10.537896
MA0105.10.355784
MA0106.10.533809
MA0107.10.0280799
MA0108.20.237143
MA0109.10
MA0111.10.512045
MA0113.10.490789
MA0114.10.150918
MA0115.10.437985
MA0116.10.708546
MA0117.10.411186
MA0119.10.178209
MA0122.11.09377
MA0124.10.604388
MA0125.10.538769
MA0130.10
MA0131.10.218222
MA0132.10
MA0133.10
MA0135.10.466327
MA0136.10.419326
MA0139.10.180641
MA0140.10.117411
MA0141.10.327475
MA0142.10.27329
MA0143.10.515613
MA0144.11.1282
MA0145.10.451873
MA0146.10.0233321
MA0147.10.172105
MA0148.10.59177
MA0149.10.723587
MA0062.20.117118
MA0035.20.119926
MA0039.20.000458716
MA0138.20.212837
MA0002.20.336369
MA0137.20.322137
MA0104.20.379989
MA0047.20.149878
MA0112.20.451845
MA0065.20.310259
MA0150.10.522782
MA0151.10
MA0152.10.457674
MA0153.10.480495
MA0154.10.354879
MA0155.10.14685
MA0156.10.128979
MA0157.10.697652
MA0158.10
MA0159.10.0719173
MA0160.10.598518
MA0161.10
MA0162.10.111166
MA0163.10.0905096
MA0164.10.134941
MA0080.20.282578
MA0018.20.140467
MA0099.20.208596
MA0079.25.04018e-08
MA0102.21.0092
MA0258.10.273872
MA0259.10.0586005
MA0442.10
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