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MCL coexpression mm9:1088: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9|coexpression_dpi_cluster_scores_mean=-0.0445388769378857,1.00902908567553,0.994658329975428,0.983654850874348,0.978576671700264,0.374549153712998,0.373487358473112,-0.134765288684817,-0.0855429007547897,-0.0844208718962267,-0.139442408395463,-0.132388773365856,-0.0894587585639179,-0.144964910709592,-0.079267316844302,-0.0499256109988985,-0.00536434988405293,-0.0511769997256259,-0.0692674855268637,-0.0467732430733024,0.589348614794138,-0.0123764923040409,0.0454394536460239,0.618354142832819,0.651454192797606,1.04648352978412,0.949980507316525,0.820536736385956,0.976549780175116,1.03788989562624,0.608837578994293,0.0142945556342142,0.0136513592133931,-0.00217029469952185,0.19422818113706,0.199745345012713,0.134666485853802,0.118799960932114,0.103918570952323,0.084782853021055,0.156405121879302,0.144322248560069,0.0441397427743113,-0.0255658940424163,-0.0338455614483861,-0.0271502937666914,-0.107715685022407,-0.0422826819689087,-0.0545686249602861,-0.00985190118868053,-0.0676135955148006,-0.13448767120239,-0.0329885276102114,-0.114451574639109,-0.0823564293301703,-0.0565527659366329,-0.0644353352637771,-0.0617940243158269,-0.105744953404681,-0.121670544318649,-0.0994908089019906,-0.182318693544694,-0.13789650214838,-0.131601606834329,-0.10794115850457,-0.107638915054159,-0.0871789704187199,-0.111525760545243,-0.138687895918954,-0.123052201210198,-0.145461898995752,-0.038590347613335,0.0147221774260955,-0.116959954574897,-0.133587179364487,-0.122819339590088,0.0603752728190349,0.0320902973184617,0.0451190517135596,-0.120017121369845,-0.0720443055501084,-0.104372385228084,0.0274615332111673,0.0365451907558258,0.014165804689207,0.0175054608278149,0.0406567698436976,-0.0436902178087328,-0.0291460931379155,0.057283553936965,-0.0529802215909127,0.849063351540238,0.858882465797443,0.77074160125546,0.993114386072716,1.020695603804,0.793963587197552,-0.0158346144551691,-0.0182026054869687,-0.0373216243251561,-0.0957692679421603,-0.120566833219244,-0.13995730407116,-0.218527307613735,-0.0272760425646324,-0.0817579499214437,-0.0814102373582894,1.19987048448807,0.0200985561245021,-0.0484020124366993,-0.113019978167725,-0.0925340576619071,-0.0229548677620495,0.00670685961823794,0.0461813745687737,0.018751246542187,0.321651915624989,0.217621506045712,-0.025727093241655,-0.0823193082578326,-0.0598548616073939,-0.0918837598504687,0.514507976993501,0.0618012499149191,0.0441622424292101,0.996504966147347,0.0731477891789457,0.0270275635400436,0.0864500135167201,0.0530117015342174,0.0234841566762196,-0.082449355584795,0.0496306188011306,0.0223522662216735,0.0394951542143579,0.063202221148765,0.0561133932818913,0.142802912214372,0.29628556386129,0.142493684756371,-0.0106876997141647,-0.0237948842369392,-0.0467415581218699,0.0109959379936088,-0.00112182397444729,0.0334120157535734,-0.0105963553890197,0.131238256401643,-0.127171829858738,-0.1106928482927,-0.0751455766649808,-0.0843813062017733,-0.0757086996979651,-0.0356512484540848,-0.0395700551805347,0.0338970319282121,0.136839169408614,0.0718084674590887,0.0988360502080063,0.0241650327543917,0.0789171959554676,0.0952745667184277,0.125548779806105,0.125925160645465,0.125817327017401,0.123627797632239,0.0995887519841259,0.129223169690206,0.118013711455329,0.13607054279337,0.119507711582523,0.123994340762052,0.14632510922624,0.123572507194389,0.0321294216257583,-0.0513063441439554,1.26206259152512,0.862055546147956,-0.0257383898206727,0.0222859639354304,0.198323729746828,0.577828861399686,0.700174043128483,0.803581152901226,0.917147604306536,1.05605336166515,0.768929648109034,0.851382951050785,0.720281862009547,0.840613324842366,0.971027520698706,1.06246013847368,0.0460464603343164,0.366167617765666,0.587242045043393,0.70571947598683,0.76208198630312,0.938228666801671,0.843784104621657,1.3514233810626,1.35774297542219,1.67006124751096,1.06917578309171,-0.00382622568017367,0.0193852552327133,0.0683278319772383,0.165398977593924,0.293600749662646,0.373921084753071,0.465115986698044,1.00135550510673,0.762177043003633,0.985201368200236,1.04226761604071,0.963987176495804,1.01382729926375,0.900811058723959,1.22500515456782,0.202125350361177,-0.0639223532141831,0.0129986976033581,0.0038898995480571,-0.00764726564455247,0.0759545447531791,0.07787897957257,0.0176354369250565,0.0776103453917138,0.0150407250224965,0.0126845538620367,0.0753031869210932,0.0422652506052958,0.127325372585489,0.0306036205835821,0.0885386974780511,0.213763540504147,0.170619200505814,0.0747418752439939,0.0832046533312531,-0.0355834740710456,-0.0122317498990938,-0.0842951944465333,-0.0861346725988754,-0.0395908869984372,-0.0973518182222573,-0.0956720253931061,-0.0794798583514004,-0.149871668840229,-0.0994768315544494,-0.0882804640278607,0.019037419532569,0.0353235449034053,-0.0697748824175112,-0.0334024095092329,0.155926613866901,-0.113704273883313,-0.048468817550482,-0.079592463125054,-0.091774508854764,-0.132941477276827,-0.0751436692017049,0.467513032708596,-0.104134846619828,-0.0648921594658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family amino acid catabolic process;0.00291129926721968;11484!GO:0006533;aspartate catabolic process;0.00291129926721968;11484!GO:0006083;acetate metabolic process;0.00291129926721968;11484!GO:0017067;tyrosine-ester sulfotransferase activity;0.00291129926721968;53315!GO:0019807;aspartoacylase activity;0.00291129926721968;11484!GO:0004370;glycerol kinase activity;0.00291129926721968;14933!GO:0006531;aspartate metabolic process;0.00291129926721968;11484!GO:0004046;aminoacylase activity;0.00370488396178192;11484!GO:0004062;aryl sulfotransferase activity;0.00370488396178192;53315!GO:0006791;sulfur utilization;0.00370488396178192;53315!GO:0000103;sulfate assimilation;0.00370488396178192;53315!GO:0006072;glycerol-3-phosphate metabolic process;0.00509365721805264;14933!GO:0009066;aspartate family amino acid metabolic process;0.0109661455256367;11484!GO:0006071;glycerol metabolic process;0.0135726686781398;14933!GO:0019751;polyol metabolic process;0.0135726686781398;14933!GO:0008146;sulfotransferase activity;0.0270918119405119;53315!GO:0009063;amino acid catabolic process;0.0270918119405119;11484!GO:0016811;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides;0.0270918119405119;11484!GO:0016782;transferase activity, transferring sulfur-containing groups;0.0270918119405119;53315!GO:0009310;amine catabolic process;0.0270918119405119;11484!GO:0044270;nitrogen compound catabolic process;0.0270918119405119;11484!GO:0006790;sulfur metabolic process;0.0277014569550259;53315!GO:0016810;hydrolase activity, acting on carbon-nitrogen (but not peptide) 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|gostat_on_MCL_coexpression=GO:0009068;aspartate family amino acid catabolic process;0.00291129926721968;11484!GO:0006533;aspartate catabolic process;0.00291129926721968;11484!GO:0006083;acetate metabolic process;0.00291129926721968;11484!GO:0017067;tyrosine-ester sulfotransferase activity;0.00291129926721968;53315!GO:0019807;aspartoacylase activity;0.00291129926721968;11484!GO:0004370;glycerol kinase activity;0.00291129926721968;14933!GO:0006531;aspartate metabolic process;0.00291129926721968;11484!GO:0004046;aminoacylase activity;0.00370488396178192;11484!GO:0004062;aryl sulfotransferase activity;0.00370488396178192;53315!GO:0006791;sulfur utilization;0.00370488396178192;53315!GO:0000103;sulfate assimilation;0.00370488396178192;53315!GO:0006072;glycerol-3-phosphate metabolic process;0.00509365721805264;14933!GO:0009066;aspartate family amino acid metabolic process;0.0109661455256367;11484!GO:0006071;glycerol metabolic process;0.0135726686781398;14933!GO:0019751;polyol metabolic process;0.0135726686781398;14933!GO:0008146;sulfotransferase activity;0.0270918119405119;53315!GO:0009063;amino acid catabolic process;0.0270918119405119;11484!GO:0016811;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides;0.0270918119405119;11484!GO:0016782;transferase activity, transferring sulfur-containing groups;0.0270918119405119;53315!GO:0009310;amine catabolic process;0.0270918119405119;11484!GO:0044270;nitrogen compound catabolic process;0.0270918119405119;11484!GO:0006790;sulfur metabolic process;0.0277014569550259;53315!GO:0016810;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds;0.0396802049783122;11484!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000160!5.95e-17!31;UBERON:0005409!2.43e-15!47;UBERON:0009854!1.29e-12!23;UBERON:0009856!1.29e-12!23;UBERON:0001007!1.49e-12!116;UBERON:0001555!1.49e-12!116;UBERON:0007026!1.49e-12!116;UBERON:0004119!1.50e-12!118;UBERON:0000925!1.50e-12!118;UBERON:0006595!1.50e-12!118;UBERON:0002107!4.65e-12!22;UBERON:0007499!4.65e-12!22;UBERON:0006925!4.65e-12!22;UBERON:0009497!4.65e-12!22;UBERON:0000015!4.65e-12!22;UBERON:0002423!4.65e-12!22;UBERON:0006235!4.65e-12!22;UBERON:0008835!4.65e-12!22;UBERON:0003894!4.65e-12!22;UBERON:0004161!4.65e-12!22;UBERON:0008836!4.65e-12!22;UBERON:0004921!1.45e-11!114;UBERON:0005172!1.57e-10!49;UBERON:0005173!1.57e-10!49;UBERON:0002417!1.57e-10!49;UBERON:0000916!1.57e-10!49;UBERON:0002365!9.15e-10!25;UBERON:0002330!9.15e-10!25;UBERON:0000344!1.45e-08!15;UBERON:0009569!1.47e-07!66;UBERON:0001242!2.52e-07!13;UBERON:0000060!2.52e-07!13;UBERON:0001262!2.52e-07!13;UBERON:0004786!2.52e-07!13
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.161863,0.411716,1.20801,0.810002,1.23933,0.587291,0.594722,0.616096,0.478312,0.542749,1.40872,0.206435,0.599731,0.847296,0,0.795315,0.291368,0.19222,0.112498,0.374752,0.27937,0.598814,0.80655,0.419327,0.62766,0.184473,0.516511,0.344372,0.145661,1.25421,0.897561,0.78719,0.166577,0.316253,0.0235321,1.40094,0.57142,0.258564,0.230656,0.800988,0.507468,0.258106,0.851774,0.277561,0.469348,0.714592,0.532496,0.219744,0.917701,0.777641,0.654933,0.139618,1.04034,1.0579,0.606984,0.356236,0.56214,0.522357,0.604914,0.877332,0.664501,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,1.79967,0.608073,0.293368,1.09164,1.55661,0.159969,0.498755,0.703064,0.859987,0.378988,0.610783,0.812889,0.663039,0.200155,0.975495,0.146394,0.042613,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,0.203879,0.913319,0.71485,0.399703,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,1.10097,1.02459,0.380122,1.35148,1.27206,0.293461,0.418498,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.275843,1.13474,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.147909,0.545091,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,2.40184,0.227149
}}

Latest revision as of 16:22, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:73139974..73139980,-p2@Aspa
Mm9::chr5:87995134..87995144,-p@chr5:87995134..87995144
-
Mm9::chr5:87997964..87997976,-p3@Sult1d1
Mm9::chr5:87997991..87998003,-p4@Sult1d1
Mm9::chr5:87998007..87998027,-p2@Sult1d1
Mm9::chrX:83021894..83021919,-p2@Gyk
Mm9::chrX:83021945..83021982,-p1@Gyk


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:0009068aspartate family amino acid catabolic process0.00291129926721968
GO:0006533aspartate catabolic process0.00291129926721968
GO:0006083acetate metabolic process0.00291129926721968
GO:0017067tyrosine-ester sulfotransferase activity0.00291129926721968
GO:0019807aspartoacylase activity0.00291129926721968
GO:0004370glycerol kinase activity0.00291129926721968
GO:0006531aspartate metabolic process0.00291129926721968
GO:0004046aminoacylase activity0.00370488396178192
GO:0004062aryl sulfotransferase activity0.00370488396178192
GO:0006791sulfur utilization0.00370488396178192
GO:0000103sulfate assimilation0.00370488396178192
GO:0006072glycerol-3-phosphate metabolic process0.00509365721805264
GO:0009066aspartate family amino acid metabolic process0.0109661455256367
GO:0006071glycerol metabolic process0.0135726686781398
GO:0019751polyol metabolic process0.0135726686781398
GO:0008146sulfotransferase activity0.0270918119405119
GO:0009063amino acid catabolic process0.0270918119405119
GO:0016811hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides0.0270918119405119
GO:0016782transferase activity, transferring sulfur-containing groups0.0270918119405119
GO:0009310amine catabolic process0.0270918119405119
GO:0044270nitrogen compound catabolic process0.0270918119405119
GO:0006790sulfur metabolic process0.0277014569550259
GO:0016810hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds0.0396802049783122



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
intestine5.95e-1731
gastrointestinal system2.43e-1547
digestive tract diverticulum1.29e-1223
sac1.29e-1223
digestive system1.49e-12116
digestive tract1.49e-12116
primitive gut1.49e-12116
endoderm-derived structure1.50e-12118
endoderm1.50e-12118
presumptive endoderm1.50e-12118
liver4.65e-1222
epithelial sac4.65e-1222
digestive gland4.65e-1222
epithelium of foregut-midgut junction4.65e-1222
anatomical boundary4.65e-1222
hepatobiliary system4.65e-1222
foregut-midgut junction4.65e-1222
hepatic diverticulum4.65e-1222
liver primordium4.65e-1222
septum transversum4.65e-1222
liver bud4.65e-1222
subdivision of digestive tract1.45e-11114
abdomen element1.57e-1049
abdominal segment element1.57e-1049
abdominal segment of trunk1.57e-1049
abdomen1.57e-1049
exocrine gland9.15e-1025
exocrine system9.15e-1025
mucosa1.45e-0815
subdivision of trunk1.47e-0766
intestinal mucosa2.52e-0713
anatomical wall2.52e-0713
wall of intestine2.52e-0713
gastrointestinal system mucosa2.52e-0713


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)
MA0003.10.0861444
MA0004.11.20906
MA0006.10.837454
MA0007.10.465969
MA0009.10.92425
MA0014.10.425579
MA0017.10.337808
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.321735
MA0029.10.858105
MA0030.10.864739
MA0031.11.93597
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.11.79544
MA0043.11.02178
MA0046.18.51378
MA0048.10.128106
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.0406078
MA0056.10
MA0057.10.117936
MA0058.11.00014
MA0059.11.02718
MA0060.11.22438
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.121435
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.14.19963e-05
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.0841779
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.11.58083
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.162418
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.11.16549
MA0113.10.649407
MA0114.10.259463
MA0115.11.0246
MA0116.10.311187
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
MA0145.10.0910975
MA0146.10.493711
MA0147.10.274511
MA0148.11.24416
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.20.790799
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.20.218974
MA0047.21.51738
MA0112.20.304722
MA0065.20.305574
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.15.63571
MA0154.11.29007
MA0155.10.102995
MA0156.10.356017
MA0157.11.83902
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.10.127623
MA0163.10.0280055
MA0164.11.46244
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.20.00878868
MA0102.21.65195
MA0258.10.246285
MA0259.10.26402
MA0442.10
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