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MCL coexpression mm9:1230: Difference between revisions

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{{MCL_coexpression_mm9
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transport;0.00633946670214681;224674!GO:0015168;glycerol transmembrane transporter activity;0.00633946670214681;224674!GO:0015665;alcohol transmembrane transporter activity;0.00633946670214681;224674!GO:0015793;glycerol transport;0.00633946670214681;224674!GO:0015169;glycerol-3-phosphate transmembrane transporter activity;0.00633946670214681;224674!GO:0015166;polyol transmembrane transporter activity;0.00633946670214681;224674!GO:0006127;glycerophosphate shuttle;0.00633946670214681;224674!GO:0021995;neuropore closure;0.00887428085907578;234366!GO:0015791;polyol transport;0.00887428085907578;224674!GO:0021506;anterior neuropore closure;0.00887428085907578;234366!GO:0001842;neural fold formation;0.0120999660568884;234366!GO:0010172;embryonic body morphogenesis;0.0147872268848731;234366!GO:0010171;body morphogenesis;0.0170603152436236;234366!GO:0006072;glycerol-3-phosphate metabolic process;0.0190079824906938;224674!GO:0007205;protein kinase C activation;0.0332421055492497;13139!GO:0004143;diacylglycerol kinase activity;0.0332421055492497;13139!GO:0006071;glycerol metabolic process;0.049204409131596;224674!GO:0019751;polyol metabolic 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|gostat_on_MCL_coexpression=GO:0015794;glycerol-3-phosphate transport;0.00633946670214681;224674!GO:0015168;glycerol transmembrane transporter activity;0.00633946670214681;224674!GO:0015665;alcohol transmembrane transporter activity;0.00633946670214681;224674!GO:0015793;glycerol transport;0.00633946670214681;224674!GO:0015169;glycerol-3-phosphate transmembrane transporter activity;0.00633946670214681;224674!GO:0015166;polyol transmembrane transporter activity;0.00633946670214681;224674!GO:0006127;glycerophosphate shuttle;0.00633946670214681;224674!GO:0021995;neuropore closure;0.00887428085907578;234366!GO:0015791;polyol transport;0.00887428085907578;224674!GO:0021506;anterior neuropore closure;0.00887428085907578;234366!GO:0001842;neural fold formation;0.0120999660568884;234366!GO:0010172;embryonic body morphogenesis;0.0147872268848731;234366!GO:0010171;body morphogenesis;0.0170603152436236;234366!GO:0006072;glycerol-3-phosphate metabolic process;0.0190079824906938;224674!GO:0007205;protein kinase C activation;0.0332421055492497;13139!GO:0004143;diacylglycerol kinase activity;0.0332421055492497;13139!GO:0006071;glycerol metabolic process;0.049204409131596;224674!GO:0019751;polyol metabolic process;0.049204409131596;224674!
|ontology_enrichment_celltype=CL:0000838!1.02e-07!12;CL:0000084!2.97e-07!11;CL:0000827!2.97e-07!11;CL:0000791!7.67e-07!9;CL:0000789!7.67e-07!9;CL:0002420!7.67e-07!9;CL:0002419!7.67e-07!9;CL:0000790!7.67e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004119!2.70e-23!118;UBERON:0000925!2.70e-23!118;UBERON:0006595!2.70e-23!118;UBERON:0001007!7.99e-23!116;UBERON:0001555!7.99e-23!116;UBERON:0007026!7.99e-23!116;UBERON:0004921!1.20e-21!114;UBERON:0005409!4.93e-14!47;UBERON:0000160!7.78e-14!31;UBERON:0005911!4.49e-11!69;UBERON:0003929!1.18e-10!55;UBERON:0004923!4.36e-10!24;UBERON:0000344!5.72e-10!15;UBERON:0001242!6.29e-09!13;UBERON:0000060!6.29e-09!13;UBERON:0001262!6.29e-09!13;UBERON:0004786!6.29e-09!13;UBERON:0001041!1.71e-08!80;UBERON:0000490!2.06e-08!66;UBERON:0000077!7.70e-08!35;UBERON:0002193!4.26e-07!48;UBERON:0002405!4.26e-07!48;UBERON:0004177!7.47e-07!29;UBERON:0005057!7.47e-07!29
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.473747,1.17362,0.535892,0.346849,0.550971,0.645383,0.247459,0.257202,1.48899,0.599767,0.632897,0.692139,0.6581,0.364314,0,0.856992,0.338549,0.656199,0.442204,0.426133,0.108444,0.657163,0.345236,0.472505,0.686615,0.223823,0.572827,0.394364,0.534301,0.558142,0.960397,3.34545,0.589948,1.70316,0.144368,0.871288,0.629145,0.303703,0.27383,0.342638,1.38433,0.671603,0.366415,1.9448,0.524258,0.77511,1.43855,0.284064,0.397446,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.614918,0.663395,0.939962,0.724164,0.269393,1.93338,1.62226,0.869046,1.2599,1.61148,0.935192,1.46355,1.1311,0.253541,3.09546,1.156,3.30442,0.57254,0.204132,0.763395,0.922432,1.92862,0.254777,0.874787,0.722675,0.240896,1.03903,4.79811,0.479018,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,0.244935,0.976308,0.775372,0.483322,0.326561,0.960112,1.08669,0.839694,0.838613,2.36799,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,1.35637,0.53982,1.99662,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,1.25097,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.920761,1.03315,2.88524,1.10596,0.287383,0.678689,1.18867,0.71546,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,1.21135,0.82857,0.671017,0.325308,0.63125,4.01447
|tfbs_overrepresentation_jaspar=MA0003.1;2.22936,MA0004.1;0.536396,MA0006.1;0.945134,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;0.558098,MA0017.1;1.00628,MA0019.1;0.800946,MA0024.1;0.942716,MA0025.1;1.22395,MA0027.1;2.64231,MA0028.1;0.969171,MA0029.1;0.920529,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;0.486223,MA0050.1;0.57678,MA0051.1;1.66123,MA0052.1;1.00829,MA0055.1;0.0585191,MA0056.1;0,MA0057.1;0.149949,MA0058.1;0.436487,MA0059.1;0.449345,MA0060.1;0.275911,MA0061.1;0.307097,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;0.153907,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;0.00638767,MA0074.1;0.638014,MA0076.1;1.04996,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;0.358337,MA0089.1;0,MA0090.1;0.500693,MA0091.1;0.55008,MA0092.1;0.501022,MA0093.1;0.379257,MA0095.1;0,MA0098.1;0,MA0100.1;0.626021,MA0101.1;0.458688,MA0103.1;1.03097,MA0105.1;0.57901,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;2.02544,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;0.682297,MA0140.1;0.625902,MA0141.1;0.419361,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;0.829535,MA0145.1;3.15794,MA0146.1;1.89206,MA0147.1;0.320675,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;2.47808,MA0035.2;0.630778,MA0039.2;0.769467,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;0.416331,MA0104.2;1.33199,MA0047.2;0.685741,MA0112.2;0.37938,MA0065.2;0.763394,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.933846,MA0155.1;0.822245,MA0156.1;1.04798,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.331229,MA0160.1;0.556423,MA0161.1;0,MA0162.1;1.53386,MA0163.1;1.4645,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;0.31703,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.833237,MA0442.1;0
}}

Latest revision as of 16:36, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:128181040..128181051,-p6@Dgka
Mm9::chr12:4914035..4914063,-p3@Ubxn2a
Mm9::chr13:39052367..39052408,-p1@Slc35b3
Mm9::chr14:47896665..47896684,+p2@Socs4
Mm9::chr17:31433136..31433198,+p1@Slc37a1
Mm9::chr8:72519989..72520007,-p5@Gatad2a


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:0015794glycerol-3-phosphate transport0.00633946670214681
GO:0015168glycerol transmembrane transporter activity0.00633946670214681
GO:0015665alcohol transmembrane transporter activity0.00633946670214681
GO:0015793glycerol transport0.00633946670214681
GO:0015169glycerol-3-phosphate transmembrane transporter activity0.00633946670214681
GO:0015166polyol transmembrane transporter activity0.00633946670214681
GO:0006127glycerophosphate shuttle0.00633946670214681
GO:0021995neuropore closure0.00887428085907578
GO:0015791polyol transport0.00887428085907578
GO:0021506anterior neuropore closure0.00887428085907578
GO:0001842neural fold formation0.0120999660568884
GO:0010172embryonic body morphogenesis0.0147872268848731
GO:0010171body morphogenesis0.0170603152436236
GO:0006072glycerol-3-phosphate metabolic process0.0190079824906938
GO:0007205protein kinase C activation0.0332421055492497
GO:0004143diacylglycerol kinase activity0.0332421055492497
GO:0006071glycerol metabolic process0.049204409131596
GO:0019751polyol metabolic process0.049204409131596



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
lymphoid lineage restricted progenitor cell1.02e-0712
T cell2.97e-0711
pro-T cell2.97e-0711
mature alpha-beta T cell7.67e-079
alpha-beta T cell7.67e-079
immature T cell7.67e-079
mature T cell7.67e-079
immature alpha-beta T cell7.67e-079

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.70e-23118
endoderm2.70e-23118
presumptive endoderm2.70e-23118
digestive system7.99e-23116
digestive tract7.99e-23116
primitive gut7.99e-23116
subdivision of digestive tract1.20e-21114
gastrointestinal system4.93e-1447
intestine7.78e-1431
endo-epithelium4.49e-1169
gut epithelium1.18e-1055
organ component layer4.36e-1024
mucosa5.72e-1015
intestinal mucosa6.29e-0913
anatomical wall6.29e-0913
wall of intestine6.29e-0913
gastrointestinal system mucosa6.29e-0913
foregut1.71e-0880
unilaminar epithelium2.06e-0866
mixed endoderm/mesoderm-derived structure7.70e-0835
hemolymphoid system4.26e-0748
immune system4.26e-0748
hemopoietic organ7.47e-0729
immune organ7.47e-0729


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)
MA0003.12.22936
MA0004.10.536396
MA0006.10.945134
MA0007.10.52077
MA0009.10.987341
MA0014.10.558098
MA0017.11.00628
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.969171
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.486223
MA0050.10.57678
MA0051.11.66123
MA0052.11.00829
MA0055.10.0585191
MA0056.10
MA0057.10.149949
MA0058.10.436487
MA0059.10.449345
MA0060.10.275911
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.153907
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.00638767
MA0074.10.638014
MA0076.11.04996
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.358337
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.11.03097
MA0105.10.57901
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
MA0119.12.02544
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.682297
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.829535
MA0145.13.15794
MA0146.11.89206
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.22.47808
MA0035.20.630778
MA0039.20.769467
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.21.33199
MA0047.20.685741
MA0112.20.37938
MA0065.20.763394
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.933846
MA0155.10.822245
MA0156.11.04798
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.11.53386
MA0163.11.4645
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.20.31703
MA0102.21.7182
MA0258.10.290587
MA0259.10.833237
MA0442.10
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