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Difference between revisions of "MCL coexpression mm9:1019"

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|ontology_enrichment_uberon=UBERON:0001911!1.59e-13!2;UBERON:0000076!1.59e-13!2;UBERON:0005333!1.59e-13!2;UBERON:0008425!1.59e-13!2;UBERON:0005311!1.59e-13!2;UBERON:0001301!9.29e-09!3;UBERON:0006555!9.29e-09!3;UBERON:0005103!9.29e-09!3;UBERON:0000083!9.29e-09!3;UBERON:0009201!9.29e-09!3;UBERON:0004819!9.29e-09!3;UBERON:0006553!9.29e-09!3;UBERON:0003074!9.29e-09!3;UBERON:0003060!9.29e-09!3;UBERON:0005085!6.46e-08!13;UBERON:0000080!8.90e-07!4;UBERON:0005904!8.90e-07!4;UBERON:0006947!8.90e-07!4;UBERON:0002120!8.90e-07!4;UBERON:0004054!8.90e-07!4;UBERON:0004875!8.90e-07!4;UBERON:0004876!8.90e-07!4;UBERON:0005721!8.90e-07!4;UBERON:0005754!8.90e-07!4;UBERON:0007297!8.90e-07!4
 
|ontology_enrichment_uberon=UBERON:0001911!1.59e-13!2;UBERON:0000076!1.59e-13!2;UBERON:0005333!1.59e-13!2;UBERON:0008425!1.59e-13!2;UBERON:0005311!1.59e-13!2;UBERON:0001301!9.29e-09!3;UBERON:0006555!9.29e-09!3;UBERON:0005103!9.29e-09!3;UBERON:0000083!9.29e-09!3;UBERON:0009201!9.29e-09!3;UBERON:0004819!9.29e-09!3;UBERON:0006553!9.29e-09!3;UBERON:0003074!9.29e-09!3;UBERON:0003060!9.29e-09!3;UBERON:0005085!6.46e-08!13;UBERON:0000080!8.90e-07!4;UBERON:0005904!8.90e-07!4;UBERON:0006947!8.90e-07!4;UBERON:0002120!8.90e-07!4;UBERON:0004054!8.90e-07!4;UBERON:0004875!8.90e-07!4;UBERON:0004876!8.90e-07!4;UBERON:0005721!8.90e-07!4;UBERON:0005754!8.90e-07!4;UBERON:0007297!8.90e-07!4
 
|tfbs_overrepresentation_for_novel_motifs=0.438063,1.02534,0.411716,0.480627,0.299217,0.495263,0.587291,0.206208,0.215218,0.219671,0.542749,0.575086,0.206435,0.599731,0.315771,0,0.795315,0.291368,1.06769,0.112498,0.978328,0.27937,0.598814,0.80655,0.419327,0.62766,1.0368,0.516511,0.344372,0.446946,0.50223,0.897561,0.289148,0.498917,0.316253,0.0235321,0.279977,0.57142,1.32199,0.230656,0.295233,0.507468,0.258106,0.851774,0.0275764,0.469348,0.714592,0.532496,0.219744,0.347313,0.777641,0.654933,0.139618,1.04034,1.0579,0.606984,1.67322,0.56214,0.522357,0.604914,0.877332,0.664501,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,1.14464,0.0869413,1.09164,0.17012,0.159969,0.498755,0.703064,0.859987,0.98764,0.610783,0.812889,0.663039,1.09903,0.975495,0.0369809,0.042613,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.668513,0.589174,0.913319,0.71485,0.127063,0.280055,0.897279,1.02279,0.778243,0.777175,1.26443,0.837607,1.30996,0.383871,0.376549,0.430942,1.02459,1.75621,1.35148,1.27206,0.293461,0.418498,0.484437,0.796633,0.276329,1.09707,0.745011,1.52304,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.275843,0.446555,1.26843,1.24438,2.07659,1.67603,1.19971,0.641722,2.09861,0.770616,0.507927,0.717753,2.03691,2.9597,0.300961,0.147909,0.0736236,1.04192,0.681896,1.5029,1.12411,1.57831,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,1.48714,0.278874,0.573477,0.705627
 
|tfbs_overrepresentation_for_novel_motifs=0.438063,1.02534,0.411716,0.480627,0.299217,0.495263,0.587291,0.206208,0.215218,0.219671,0.542749,0.575086,0.206435,0.599731,0.315771,0,0.795315,0.291368,1.06769,0.112498,0.978328,0.27937,0.598814,0.80655,0.419327,0.62766,1.0368,0.516511,0.344372,0.446946,0.50223,0.897561,0.289148,0.498917,0.316253,0.0235321,0.279977,0.57142,1.32199,0.230656,0.295233,0.507468,0.258106,0.851774,0.0275764,0.469348,0.714592,0.532496,0.219744,0.347313,0.777641,0.654933,0.139618,1.04034,1.0579,0.606984,1.67322,0.56214,0.522357,0.604914,0.877332,0.664501,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,1.14464,0.0869413,1.09164,0.17012,0.159969,0.498755,0.703064,0.859987,0.98764,0.610783,0.812889,0.663039,1.09903,0.975495,0.0369809,0.042613,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.668513,0.589174,0.913319,0.71485,0.127063,0.280055,0.897279,1.02279,0.778243,0.777175,1.26443,0.837607,1.30996,0.383871,0.376549,0.430942,1.02459,1.75621,1.35148,1.27206,0.293461,0.418498,0.484437,0.796633,0.276329,1.09707,0.745011,1.52304,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.275843,0.446555,1.26843,1.24438,2.07659,1.67603,1.19971,0.641722,2.09861,0.770616,0.507927,0.717753,2.03691,2.9597,0.300961,0.147909,0.0736236,1.04192,0.681896,1.5029,1.12411,1.57831,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,1.48714,0.278874,0.573477,0.705627
 +
|tfbs_overrepresentation_jaspar=MA0003.1;0.188259,MA0004.1;0.481116,MA0006.1;0.311391,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;0.0886247,MA0017.1;0.337808,MA0019.1;0.740036,MA0024.1;0.880057,MA0025.1;1.15921,MA0027.1;2.57545,MA0028.1;0.860672,MA0029.1;0.858105,MA0030.1;0.864739,MA0031.1;0.828781,MA0038.1;0.62758,MA0040.1;0.936879,MA0041.1;0.404721,MA0042.1;0.391504,MA0043.1;1.02178,MA0046.1;0.960497,MA0048.1;0.128106,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;0.157978,MA0056.1;0,MA0057.1;0.117936,MA0058.1;0.384683,MA0059.1;0.397033,MA0060.1;0.232592,MA0061.1;0.261749,MA0063.1;0,MA0066.1;0.616444,MA0067.1;1.27078,MA0068.1;0.385183,MA0069.1;0.945354,MA0070.1;0.93557,MA0071.1;0.519509,MA0072.1;0.927016,MA0073.1;0.0210304,MA0074.1;0.580087,MA0076.1;0.356883,MA0077.1;0.905143,MA0078.1;0.670113,MA0081.1;1.07783,MA0083.1;2.32874,MA0084.1;1.59945,MA0087.1;0.977537,MA0088.1;0.285759,MA0089.1;0,MA0090.1;1.1347,MA0091.1;0.494398,MA0092.1;0.446857,MA0093.1;0.329976,MA0095.1;0,MA0098.1;0,MA0100.1;0.568369,MA0101.1;0.406019,MA0103.1;0.920496,MA0105.1;0.162418,MA0106.1;0.677988,MA0107.1;0.342432,MA0108.2;0.763162,MA0109.1;0,MA0111.1;0.460823,MA0113.1;0.649407,MA0114.1;1.32534,MA0115.1;1.0246,MA0116.1;0.836994,MA0117.1;0.992087,MA0119.1;0.40661,MA0122.1;1.01209,MA0124.1;1.21735,MA0125.1;1.14291,MA0130.1;0,MA0131.1;0.735438,MA0132.1;0,MA0133.1;0,MA0135.1;1.05845,MA0136.1;0.600242,MA0139.1;0.202522,MA0140.1;0.568252,MA0141.1;0.368264,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.262477,MA0145.1;0.631666,MA0146.1;0.0256827,MA0147.1;0.274511,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.167299,MA0035.2;0.573016,MA0039.2;0.219063,MA0138.2;0.727395,MA0002.2;0.205289,MA0137.2;0.365364,MA0104.2;0.218974,MA0047.2;0.626803,MA0112.2;0.0910939,MA0065.2;2.14244,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.792589,MA0155.1;0.687925,MA0156.1;0.356017,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.776527,MA0160.1;0.50056,MA0161.1;0,MA0162.1;0.0312493,MA0163.1;0.28052,MA0164.1;0.600609,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;0.00352098,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;0.26402,MA0442.1;0
 
}}
 
}}

Revision as of 03:41, 23 January 2013


Phase1 CAGE Peaks

  Short description
Mm9::chr10:29030794..29030801,+ p@chr10:29030794..29030801
+
Mm9::chr16:23268489..23268505,+ p@chr16:23268489..23268505
+
Mm9::chr16:23268536..23268552,+ p@chr16:23268536..23268552
+
Mm9::chr16:23268568..23268612,+ p@chr16:23268568..23268612
+
Mm9::chr17:34745931..34745934,+ p17@Agpat1
Mm9::chr17:34745942..34745966,+ p4@Agpat1
Mm9::chr7:148477887..148477932,+ p1@Drd4


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0001593dopamine D4 receptor activity0.00677000561866695
GO:0060081membrane hyperpolarization0.00677000561866695
GO:0060080regulation of inhibitory postsynaptic membrane potential0.00677000561866695
GO:0001591dopamine D2 receptor-like receptor activity0.00677000561866695
GO:0007195dopamine receptor, adenylate cyclase inhibiting pathway0.00677000561866695
GO:0004952dopamine receptor activity0.00677000561866695
GO:0035240dopamine binding0.00677000561866695
GO:0042053regulation of dopamine metabolic process0.00677000561866695
GO:0042069regulation of catecholamine metabolic process0.00677000561866695
GO:0048148behavioral response to cocaine0.00677000561866695
GO:0014075response to amine stimulus0.00677000561866695
GO:00038411-acylglycerol-3-phosphate O-acyltransferase activity0.00677000561866695
GO:0042220response to cocaine0.00677000561866695
GO:0014073response to tropane0.00677000561866695
GO:0001975response to amphetamine0.00677000561866695
GO:0060078regulation of postsynaptic membrane potential0.00796405778689728
GO:0007193G-protein signaling, adenylate cyclase inhibiting pathway0.00796405778689728
GO:0016411acylglycerol O-acyltransferase activity0.00814818768945032
GO:0042596fear response0.00890643765665583
GO:0014070response to organic cyclic substance0.00902494282549825
GO:0043279response to alkaloid0.00913213234335016
GO:0007212dopamine receptor signaling pathway0.00922954925352844
GO:0042417dopamine metabolic process0.00980864510055752
GO:0033555multicellular organismal response to stress0.0117483292008871
GO:0010033response to organic substance0.0120823395000664
GO:0006584catecholamine metabolic process0.0120823395000664
GO:0018958phenol metabolic process0.0120823395000664
GO:0008374O-acyltransferase activity0.0120823395000664
GO:0042133neurotransmitter metabolic process0.0143849442504756
GO:0008344adult locomotory behavior0.0151478667030246
GO:0042391regulation of membrane potential0.0151478667030246
GO:0008227amine receptor activity0.0151478667030246
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.01857576292548
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.01857576292548
GO:0008654phospholipid biosynthetic process0.01857576292548
GO:0019933cAMP-mediated signaling0.01857576292548
GO:0030534adult behavior0.01857576292548
GO:0019935cyclic-nucleotide-mediated signaling0.0186789159297366
GO:0046467membrane lipid biosynthetic process0.0202749573683329
GO:0006576biogenic amine metabolic process0.0202749573683329
GO:0006575amino acid derivative metabolic process0.0225178370794055
GO:0030594neurotransmitter receptor activity0.0225178370794055
GO:0001505regulation of neurotransmitter levels0.0225178370794055
GO:0042165neurotransmitter binding0.0225178370794055
GO:0006725aromatic compound metabolic process0.0282529866546731
GO:0006644phospholipid metabolic process0.0283702256005521
GO:0019932second-messenger-mediated signaling0.0294365110287574
GO:0055082cellular chemical homeostasis0.0334935527425336
GO:0006873cellular ion homeostasis0.0334935527425336
GO:0006643membrane lipid metabolic process0.0339431119605927
GO:0050801ion homeostasis0.0362431522515591
GO:0008415acyltransferase activity0.0362431522515591
GO:0016747transferase activity, transferring groups other than amino-acyl groups0.0362431522515591
GO:0016746transferase activity, transferring acyl groups0.0370210120705414
GO:0007268synaptic transmission0.0387855068118376
GO:0007626locomotory behavior0.0404853938843609
GO:0048878chemical homeostasis0.0408208277965453
GO:0019725cellular homeostasis0.0408208277965453
GO:0019226transmission of nerve impulse0.0427750273268692
GO:0008610lipid biosynthetic process0.0441051034305814
GO:0006066alcohol metabolic process0.0466676985301054



Relative expression of the co-expression cluster over median
Analyst:





Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset


uberon_data



TFBS overrepresentationSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs




JASPAR motifs


Motifs-log10(p-value)
MA0003.10.188259
MA0004.10.481116
MA0006.10.311391
MA0007.10.465969
MA0009.10.92425
MA0014.10.0886247
MA0017.10.337808
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.860672
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.10.128106
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.157978
MA0056.10
MA0057.10.117936
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.385183
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.0210304
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.11.07783
MA0083.12.32874
MA0084.11.59945
MA0087.10.977537
MA0088.10.285759
MA0089.10
MA0090.11.1347
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.920496
MA0105.10.162418
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.11.32534
MA0115.11.0246
MA0116.10.836994
MA0117.10.992087
MA0119.10.40661
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.10.202522
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.631666
MA0146.10.0256827
MA0147.10.274511
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.20.219063
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.20.218974
MA0047.20.626803
MA0112.20.0910939
MA0065.22.14244
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.792589
MA0155.10.687925
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.776527
MA0160.10.50056
MA0161.10
MA0162.10.0312493
MA0163.10.28052
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.20.00352098
MA0102.21.65195
MA0258.10.246285
MA0259.10.26402
MA0442.10