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MCL coexpression mm9:3349: Difference between revisions

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{{MCL_coexpression_mm9
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activity;0.00690297485344875;110173!GO:0048488;synaptic vesicle endocytosis;0.0172508185679887;227801!GO:0006516;glycoprotein catabolic process;0.0172508185679887;110173!GO:0017124;SH3 domain binding;0.0172508185679887;227801!GO:0015923;mannosidase activity;0.0172508185679887;110173!GO:0030665;clathrin coated vesicle membrane;0.0172508185679887;227801!GO:0048489;synaptic vesicle transport;0.0224193037463458;227801!GO:0030662;coated vesicle membrane;0.0224193037463458;227801!GO:0030659;cytoplasmic vesicle membrane;0.0280618538186314;227801!GO:0030425;dendrite;0.0280618538186314;227801!GO:0044433;cytoplasmic vesicle part;0.0280618538186314;227801!GO:0019904;protein domain specific binding;0.0280618538186314;227801!GO:0012506;vesicle membrane;0.0280618538186314;227801!GO:0043025;cell soma;0.0280618538186314;227801!GO:0030136;clathrin-coated vesicle;0.0339865740550138;227801!GO:0030135;coated vesicle;0.0352437618835035;227801!GO:0004553;hydrolase activity, hydrolyzing O-glycosyl compounds;0.0352437618835035;110173!GO:0009100;glycoprotein metabolic process;0.0374829962895571;110173!GO:0016798;hydrolase activity, acting on glycosyl bonds;0.0391229485738048;110173!GO:0043005;neuron projection;0.0399111231992233;227801!GO:0010324;membrane invagination;0.0486697011754536;227801!GO:0006897;endocytosis;0.0486697011754536;227801!GO:0005764;lysosome;0.0486697011754536;110173!GO:0000323;lytic vacuole;0.0486697011754536;110173!GO:0016023;cytoplasmic membrane-bound vesicle;0.0493369173761718;227801!GO:0005773;vacuole;0.0493369173761718;110173!GO:0031988;membrane-bound 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|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004119!3.98e-09!118;UBERON:0000925!3.98e-09!118;UBERON:0006595!3.98e-09!118;UBERON:0009854!9.04e-09!23;UBERON:0009856!9.04e-09!23;UBERON:0005177!1.14e-08!79;UBERON:0004921!1.23e-08!114;UBERON:0002107!1.39e-08!22;UBERON:0007499!1.39e-08!22;UBERON:0006925!1.39e-08!22;UBERON:0009497!1.39e-08!22;UBERON:0000015!1.39e-08!22;UBERON:0002423!1.39e-08!22;UBERON:0006235!1.39e-08!22;UBERON:0008835!1.39e-08!22;UBERON:0003894!1.39e-08!22;UBERON:0004161!1.39e-08!22;UBERON:0008836!1.39e-08!22;UBERON:0005911!1.43e-08!69;UBERON:0001007!2.51e-08!116;UBERON:0001555!2.51e-08!116;UBERON:0007026!2.51e-08!116;UBERON:0002365!4.44e-08!25;UBERON:0002330!4.44e-08!25;UBERON:0009569!1.48e-07!66;UBERON:0001041!1.53e-07!80;UBERON:0005172!2.57e-07!49;UBERON:0005173!2.57e-07!49;UBERON:0002417!2.57e-07!49;UBERON:0000916!2.57e-07!49;UBERON:0002100!4.02e-07!90
|tfbs_overrepresentation_for_novel_motifs=0.752782,1.68931,0.722405,0.801166,0.587814,0.81763,0.919454,2.05228,0.479531,0.235304,0.870507,0.906098,1.18012,0.933025,0.608226,0,1.14208,0.578045,0.448066,1.57636,0.679146,0.756749,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,1.55113,0.380786,0.825437,1.24901,0.575271,1.05917,0.608816,0.144706,1.38481,0.902078,0.536514,0.50014,0.582863,1.94114,0.261619,0.610669,0.922882,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,3.02035,1.44925,1.07031,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,1.02517,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.928366,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,1.79445,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.751419,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.999018,3.74474,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.833542
}}

Latest revision as of 19:58, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr2:38142694..38142715,-p2@Dennd1a
Mm9::chr2:38142729..38142745,-p3@Dennd1a
Mm9::chr3:135148569..135148632,+p1@Manba


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:0004567beta-mannosidase activity0.00690297485344875
GO:0048488synaptic vesicle endocytosis0.0172508185679887
GO:0006516glycoprotein catabolic process0.0172508185679887
GO:0017124SH3 domain binding0.0172508185679887
GO:0015923mannosidase activity0.0172508185679887
GO:0030665clathrin coated vesicle membrane0.0172508185679887
GO:0048489synaptic vesicle transport0.0224193037463458
GO:0030662coated vesicle membrane0.0224193037463458
GO:0030659cytoplasmic vesicle membrane0.0280618538186314
GO:0030425dendrite0.0280618538186314
GO:0044433cytoplasmic vesicle part0.0280618538186314
GO:0019904protein domain specific binding0.0280618538186314
GO:0012506vesicle membrane0.0280618538186314
GO:0043025cell soma0.0280618538186314
GO:0030136clathrin-coated vesicle0.0339865740550138
GO:0030135coated vesicle0.0352437618835035
GO:0004553hydrolase activity, hydrolyzing O-glycosyl compounds0.0352437618835035
GO:0009100glycoprotein metabolic process0.0374829962895571
GO:0016798hydrolase activity, acting on glycosyl bonds0.0391229485738048
GO:0043005neuron projection0.0399111231992233
GO:0010324membrane invagination0.0486697011754536
GO:0006897endocytosis0.0486697011754536
GO:0005764lysosome0.0486697011754536
GO:0000323lytic vacuole0.0486697011754536
GO:0016023cytoplasmic membrane-bound vesicle0.0493369173761718
GO:0005773vacuole0.0493369173761718
GO:0031988membrane-bound vesicle0.0493369173761718



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
endoderm-derived structure3.98e-09118
endoderm3.98e-09118
presumptive endoderm3.98e-09118
digestive tract diverticulum9.04e-0923
sac9.04e-0923
trunk region element1.14e-0879
subdivision of digestive tract1.23e-08114
liver1.39e-0822
epithelial sac1.39e-0822
digestive gland1.39e-0822
epithelium of foregut-midgut junction1.39e-0822
anatomical boundary1.39e-0822
hepatobiliary system1.39e-0822
foregut-midgut junction1.39e-0822
hepatic diverticulum1.39e-0822
liver primordium1.39e-0822
septum transversum1.39e-0822
liver bud1.39e-0822
endo-epithelium1.43e-0869
digestive system2.51e-08116
digestive tract2.51e-08116
primitive gut2.51e-08116
exocrine gland4.44e-0825
exocrine system4.44e-0825
subdivision of trunk1.48e-0766
foregut1.53e-0780
abdomen element2.57e-0749
abdominal segment element2.57e-0749
abdominal segment of trunk2.57e-0749
abdomen2.57e-0749
trunk4.02e-0790


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)
MA0003.13.77865
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
MA0048.10.932001
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.13.14815
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
MA0073.10.0430758
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.11.40099
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
MA0116.10.602598
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
MA0136.10.933582
MA0139.11.16863
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.11.33779
MA0145.11.44606
MA0146.12.07553
MA0147.11.37022
MA0148.10.820161
MA0149.12.8784
MA0062.20.412742
MA0035.20.903829
MA0039.21.10518
MA0138.21.07027
MA0002.20.466067
MA0137.21.60348
MA0104.20.48458
MA0047.20.962424
MA0112.21.44603
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
MA0162.12.19629
MA0163.12.84458
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.24.46976
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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