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MCL coexpression mm9:3172: Difference between revisions

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{{MCL_coexpression_mm9
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transaminase activity;0.0101585527374333;14719!GO:0044429;mitochondrial part;0.0101585527374333;14719,94063!GO:0000315;organellar large ribosomal subunit;0.0270649807712208;94063!GO:0005762;mitochondrial large ribosomal subunit;0.0270649807712208;94063!GO:0005739;mitochondrion;0.0270649807712208;14719,94063!GO:0008483;transaminase activity;0.0270649807712208;14719!GO:0015934;large ribosomal subunit;0.0270649807712208;94063!GO:0016769;transferase activity, transferring nitrogenous groups;0.0270649807712208;14719!GO:0009058;biosynthetic process;0.0270649807712208;14719,94063!GO:0000313;organellar ribosome;0.0270649807712208;94063!GO:0005761;mitochondrial ribosome;0.0270649807712208;94063!GO:0030170;pyridoxal phosphate binding;0.0281665330698366;14719!GO:0031980;mitochondrial lumen;0.0281665330698366;94063!GO:0005759;mitochondrial matrix;0.0281665330698366;94063!GO:0033279;ribosomal subunit;0.0307453010775401;94063!GO:0006869;lipid transport;0.0343911761270973;14719!GO:0019842;vitamin 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|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003914!1.42e-16!47;UBERON:0000025!1.74e-13!114;UBERON:0004111!3.29e-13!122;UBERON:0009854!6.69e-11!23;UBERON:0009856!6.69e-11!23;UBERON:0003103!7.61e-11!43;UBERON:0002107!7.66e-11!22;UBERON:0007499!7.66e-11!22;UBERON:0006925!7.66e-11!22;UBERON:0009497!7.66e-11!22;UBERON:0000015!7.66e-11!22;UBERON:0002423!7.66e-11!22;UBERON:0006235!7.66e-11!22;UBERON:0008835!7.66e-11!22;UBERON:0003894!7.66e-11!22;UBERON:0004161!7.66e-11!22;UBERON:0008836!7.66e-11!22;UBERON:0003104!2.83e-10!61;UBERON:0009142!2.83e-10!61;UBERON:0005172!4.48e-09!49;UBERON:0005173!4.48e-09!49;UBERON:0002417!4.48e-09!49;UBERON:0000916!4.48e-09!49;UBERON:0002365!1.60e-08!25;UBERON:0002330!1.60e-08!25;UBERON:0010314!2.03e-08!92;UBERON:0005256!7.34e-08!45;UBERON:0007100!2.05e-07!18;UBERON:0000948!2.05e-07!18;UBERON:0005498!2.05e-07!18;UBERON:0004140!2.05e-07!18;UBERON:0009881!2.05e-07!18;UBERON:0004141!2.05e-07!18;UBERON:0003084!2.05e-07!18;UBERON:0007005!2.05e-07!18;UBERON:0004139!2.05e-07!18;UBERON:0004291!2.05e-07!18;UBERON:0000073!8.04e-07!54
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.564138,0.722405,0.801166,0.587814,0.81763,0.919454,1.17946,0.479531,0.235304,0.870507,0.906098,2.05331,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,0.756749,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,2.79074,0.575271,0.411696,0.608816,0.144706,0.563758,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,0.156582,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,1.23806,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,2.81128,1.03818,1.05896,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.181575,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,1.17262,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,2.74838,2.94913,1.38039,0.685481,0.876299,1.63327,0.580657,1.79445,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,1.77018,0.260379,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.135528
|tfbs_overrepresentation_jaspar=MA0003.1;0.245953,MA0004.1;0.801718,MA0006.1;0.60285,MA0007.1;0.784593,MA0009.1;1.27673,MA0014.1;0.416365,MA0017.1;0.635031,MA0019.1;1.08369,MA0024.1;1.23079,MA0025.1;1.51835,MA0027.1;2.9431,MA0028.1;0.61552,MA0029.1;1.20789,MA0030.1;1.21482,MA0031.1;1.17722,MA0038.1;0.963265,MA0040.1;1.28983,MA0041.1;0.714279,MA0042.1;0.69885,MA0043.1;1.3775,MA0046.1;1.31428,MA0048.1;0.353763,MA0050.1;0.845669,MA0051.1;0.973068,MA0052.1;1.29825,MA0055.1;0.190475,MA0056.1;0,MA0057.1;0.337566,MA0058.1;0.690848,MA0059.1;0.705317,MA0060.1;0.502699,MA0061.1;0.5406,MA0063.1;0,MA0066.1;0.951196,MA0067.1;1.63197,MA0068.1;0.343188,MA0069.1;1.29861,MA0070.1;1.28847,MA0071.1;0.844726,MA0072.1;1.2796,MA0073.1;0.00834468,MA0074.1;0.911576,MA0076.1;0.657929,MA0077.1;1.2569,MA0078.1;1.0091,MA0081.1;0.732313,MA0083.1;1.37668,MA0084.1;1.96428,MA0087.1;1.33189,MA0088.1;0.766354,MA0089.1;0,MA0090.1;0.762482,MA0091.1;0.816659,MA0092.1;0.762845,MA0093.1;0.62555,MA0095.1;0,MA0098.1;0,MA0100.1;0.89873,MA0101.1;0.71579,MA0103.1;0.647985,MA0105.1;0.405648,MA0106.1;1.01755,MA0107.1;0.640607,MA0108.2;1.10817,MA0109.1;0,MA0111.1;0.778753,MA0113.1;0.986839,MA0114.1;0.537669,MA0115.1;1.38041,MA0116.1;1.46662,MA0117.1;1.34691,MA0119.1;0.716476,MA0122.1;1.36752,MA0124.1;1.57762,MA0125.1;1.5017,MA0130.1;0,MA0131.1;1.07881,MA0132.1;0,MA0133.1;0,MA0135.1;1.4152,MA0136.1;2.15063,MA0139.1;1.16863,MA0140.1;0.898603,MA0141.1;0.671467,MA0142.1;1.16183,MA0143.1;1.00467,MA0144.1;0.541532,MA0145.1;0.292366,MA0146.1;0.46063,MA0147.1;0.556853,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;1.06145,MA0035.2;0.903829,MA0039.2;0.40695,MA0138.2;1.07027,MA0002.2;0.466067,MA0137.2;0.668025,MA0104.2;0.48458,MA0047.2;0.962424,MA0112.2;0.29236,MA0065.2;0.292912,MA0150.1;0.784464,MA0151.1;0,MA0152.1;0.962542,MA0153.1;1.43238,MA0154.1;0.925147,MA0155.1;0.312898,MA0156.1;0.656895,MA0157.1;1.12772,MA0158.1;0,MA0159.1;0.569393,MA0160.1;0.823568,MA0161.1;0,MA0162.1;0.499274,MA0163.1;0.157796,MA0164.1;2.15144,MA0080.2;1.54848,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;0.00137444,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;0.543506,MA0442.1;0
}}

Latest revision as of 19:41, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr19:11844847..11844896,+p1@Mrpl16
Mm9::chr8:98412264..98412275,-p2@Got2
Mm9::chr8:98412277..98412315,-p1@Got2


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:0004069aspartate transaminase activity0.0101585527374333
GO:0044429mitochondrial part0.0101585527374333
GO:0000315organellar large ribosomal subunit0.0270649807712208
GO:0005762mitochondrial large ribosomal subunit0.0270649807712208
GO:0005739mitochondrion0.0270649807712208
GO:0008483transaminase activity0.0270649807712208
GO:0015934large ribosomal subunit0.0270649807712208
GO:0016769transferase activity, transferring nitrogenous groups0.0270649807712208
GO:0009058biosynthetic process0.0270649807712208
GO:0000313organellar ribosome0.0270649807712208
GO:0005761mitochondrial ribosome0.0270649807712208
GO:0030170pyridoxal phosphate binding0.0281665330698366
GO:0031980mitochondrial lumen0.0281665330698366
GO:0005759mitochondrial matrix0.0281665330698366
GO:0033279ribosomal subunit0.0307453010775401
GO:0006869lipid transport0.0343911761270973
GO:0019842vitamin binding0.0458887217228312



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>

Uber Anatomy
Ontology termp-valuen
epithelial tube1.42e-1647
tube1.74e-13114
anatomical conduit3.29e-13122
digestive tract diverticulum6.69e-1123
sac6.69e-1123
compound organ7.61e-1143
liver7.66e-1122
epithelial sac7.66e-1122
digestive gland7.66e-1122
epithelium of foregut-midgut junction7.66e-1122
anatomical boundary7.66e-1122
hepatobiliary system7.66e-1122
foregut-midgut junction7.66e-1122
hepatic diverticulum7.66e-1122
liver primordium7.66e-1122
septum transversum7.66e-1122
liver bud7.66e-1122
mesenchyme2.83e-1061
entire embryonic mesenchyme2.83e-1061
abdomen element4.48e-0949
abdominal segment element4.48e-0949
abdominal segment of trunk4.48e-0949
abdomen4.48e-0949
exocrine gland1.60e-0825
exocrine system1.60e-0825
structure with developmental contribution from neural crest2.03e-0892
trunk mesenchyme7.34e-0845
primary circulatory organ2.05e-0718
heart2.05e-0718
primitive heart tube2.05e-0718
primary heart field2.05e-0718
anterior lateral plate mesoderm2.05e-0718
heart tube2.05e-0718
heart primordium2.05e-0718
cardiac mesoderm2.05e-0718
cardiogenic plate2.05e-0718
heart rudiment2.05e-0718
regional part of nervous system8.04e-0754


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)
MA0003.10.245953
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.10.416365
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.10.61552
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.353763
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.190475
MA0056.10
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.00834468
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.766354
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.10.62555
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.10.405648
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.10.537669
MA0115.11.38041
MA0116.11.46662
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.12.15063
MA0139.11.16863
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.292366
MA0146.10.46063
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.21.06145
MA0035.20.903829
MA0039.20.40695
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.925147
MA0155.10.312898
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.499274
MA0163.10.157796
MA0164.12.15144
MA0080.21.54848
MA0018.20.944669
MA0099.21.06348
MA0079.20.00137444
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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