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MCL coexpression mm9:591: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9|coexpression_dpi_cluster_scores_mean=-0.0219703373568861,0.338963233250829,0.204871732039902,0.260697048863155,0.267584467582778,0.0461326477217104,0.0824013891886329,-0.0149722766579764,0.0294805695578613,0.0283923519308008,-0.0325133492269151,-0.0433212325731179,-0.0382351735943261,-0.0366896994559693,-0.0339503663708653,0.00292489175940136,-0.0311624894009398,-0.0246062469904088,-0.0535328483067282,-0.0405931211038451,0.127812986287308,0.0188920444965074,-0.015797970053924,0.164928800057179,0.11934392413034,0.204002893452689,0.170862718056882,0.14839618527029,0.150434780166647,0.0366962719746743,0.105580757965958,0.041020564365224,0.0213857884422674,-0.0628335436647921,-0.00729479732290132,0.00188176136101687,0.0155144025609413,0.0139217282472149,-0.00788033644028482,0.0149484357495373,-0.00928679825320765,0.0125317407057454,0.010839253003923,0.015078717454264,0.00351838254529023,-0.00815792376002596,0.0227234915532443,0.0201629527035724,0.0423321352641734,0.0127731707350319,0.0151681753593913,0.00165798855676432,-0.0411344517686722,-0.0628335436647921,-0.0375981632115473,-0.00959752084452221,0.054700185974755,0.0472436492607391,-0.0628335436647921,-0.0474664667337096,-0.0450662737247542,-0.0212676447332466,-0.016783588940094,-0.0396059871547191,-0.0379497434433684,-0.0239805387158561,-0.0193655918415038,-0.0157653476033579,-0.0524426558517645,-0.0495997173242445,-0.0432177884841696,-0.0240784973740643,-0.016749117008206,-0.0401804488508408,-0.0503744738864985,-0.0250769314088345,0.0177811759690011,0.0352956674926126,0.0246052442676832,-0.0305558845545232,-0.0508880410313023,-0.0476581705103987,0.047341914542346,-0.0305180416749597,0.0454177387885803,-0.00445528313837068,-0.00698641943003168,-0.0202423449460093,0.00722683946770447,-0.0133229316275071,0.0178194992319522,0.0282715456541835,0.00956148968085467,0.00325209702648236,0.118459294425118,0.0611470449349806,0.269193774929289,-0.0167002290432014,-0.0219027782560475,-0.0325369883053042,-0.0339065179004014,-0.0628335436647921,-0.0628335436647921,-0.0628335436647921,-0.0498134803296003,-0.0293812124094213,-0.0332189084161287,0.139262533645873,-0.0253626697475584,0.14586020863327,-0.046263893880911,0.00803957333840254,-0.0225666927804361,-0.0143879422861055,-0.0209189809010421,0.407811152012727,0.0698910619640056,1.07431360377401,0.161612437086486,0.109219682452906,0.184302643573731,0.138884525246169,0.0514065863948497,0.0560194658441148,0.0611297514617659,0.205955141864913,-0.0261376912667963,-0.0628335436647921,6.47577481005573e-05,0.0716579905317871,-0.0256853940997949,-0.0250452695929812,0.00614701365236434,0.0223210729861792,0.07991252133723,0.0641464972159212,-0.0140302055937177,0.157867691340799,-0.00800619514032882,0.169155030048289,-0.0456082913849784,-0.041653113991862,-0.0517019947566081,-0.0293629589564127,-0.038515022365586,-0.0279361742011563,-0.0329859188467552,0.209696495806553,-0.0368867266352781,-0.0449554872268555,-0.0399917609880361,-0.0353315465786314,-0.0268935698454945,-0.0328897019940921,-0.0175662226686994,-0.0441368723326664,-0.0628335436647921,-0.0395184696227429,-0.030836706194207,0.0840338585101548,0.114685335101371,0.0898692646288201,0.15019657595057,0.163640819931304,0.210021478860414,0.299450631195985,0.328584171117204,0.37701917465562,0.412746684727593,0.615345490105735,0.780137401617265,0.807871666365039,0.801975296273184,0.869546273239062,0.00347939824970998,-0.0320198689151463,0.335465165822708,0.2532561620573,-0.0167100335822817,-0.0414689102890192,-0.00261847760005303,0.0810601794523124,0.110208509056404,0.127191224938953,0.169594506401814,0.140418198921942,0.093405058052797,0.127257200971529,0.038186742123577,0.195813146849351,0.210917921619234,0.244327002682253,-0.0386948239628744,-0.0302030568313681,-0.0355182699610809,-0.00206568666003433,0.00762558415532638,0.0466918308366444,0.0528111925125532,0.205952570284156,0.218615748191576,0.28009886491039,0.0587361132064304,-0.0259853686642336,-0.00098488172008146,0.00106617787710325,0.0163835337231004,0.0142741053593231,-0.038204985663294,0.0265161484217875,0.0248649946477362,0.0334527243327008,0.0984068988812024,0.0302342907249184,0.0280550658863927,0.00597158620809919,0.130392229811402,0.211790089908595,0.0714722703158867,-0.0111605829911356,-0.0228135640543725,-0.0373588375344974,-0.0273479969840257,0.0277535435861684,0.0515031497599661,0.0104995164830466,0.0498457114992351,0.050174868644082,0.03539837031637,0.16857924836728,0.187855904668427,0.130905343009242,-0.0628335436647921,-0.0313967493237558,0.152606806550086,0.167348001473465,0.14556298466749,0.110841147124938,-0.0277088023932929,0.524211986389553,-0.028804087364716,-0.0168594228761311,-0.0377311513623487,-0.033185474041504,-0.0236917563523112,-0.0375763132474204,-0.0413678999779275,-0.0202385920871397,-0.0417508227139142,0.00334241505030733,0.0273721137528811,-0.0109712678814295,-0.00871451874829406,0.00177916276921818,0.0452195449858636,-0.0225416619212601,-0.0628335436647921,-0.020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activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor;5.29291857872747e-05;18597,18293!GO:0005739;mitochondrion;0.000224485943461562;12908,18597,18293,102103!GO:0016903;oxidoreductase activity, acting on the aldehyde or oxo group of donors;0.00048344881914575;18597,18293!GO:0006096;glycolysis;0.00048344881914575;18597,18293!GO:0006007;glucose catabolic process;0.00048344881914575;18597,18293!GO:0046365;monosaccharide catabolic process;0.00048344881914575;18597,18293!GO:0019320;hexose catabolic process;0.00048344881914575;18597,18293!GO:0046164;alcohol catabolic process;0.00048344881914575;18597,18293!GO:0044275;cellular carbohydrate catabolic process;0.000598117729282579;18597,18293!GO:0016052;carbohydrate catabolic process;0.000641168179667001;18597,18293!GO:0006006;glucose metabolic process;0.00105982972717645;18597,18293!GO:0004092;carnitine O-acetyltransferase activity;0.00117999570144423;12908!GO:0050164;oxoglutarate dehydrogenase (NADP+) activity;0.00117999570144423;18293!GO:0019318;hexose metabolic process;0.00148344954783774;18597,18293!GO:0005996;monosaccharide metabolic process;0.00148344954783774;18597,18293!GO:0004591;oxoglutarate dehydrogenase (succinyl-transferring) activity;0.00191733542995084;18293!GO:0004738;pyruvate dehydrogenase activity;0.00242169834513759;18597!GO:0030976;thiamin pyrophosphate binding;0.00242169834513759;18293!GO:0004739;pyruvate dehydrogenase (acetyl-transferring) activity;0.00242169834513759;18597!GO:0044444;cytoplasmic part;0.00275277858356794;12908,18597,18293,102103!GO:0016413;O-acetyltransferase activity;0.00284126494223344;12908!GO:0044265;cellular macromolecule catabolic process;0.00284126494223344;18597,18293!GO:0044262;cellular carbohydrate metabolic process;0.00329753507447477;18597,18293!GO:0006066;alcohol metabolic process;0.00331374989964021;18597,18293!GO:0016406;carnitine O-acyltransferase activity;0.00368007399453356;12908!GO:0009057;macromolecule catabolic process;0.00403332330099428;18597,18293!GO:0005975;carbohydrate metabolic process;0.00546562014632149;18597,18293!GO:0044248;cellular catabolic process;0.00725663534467636;18597,18293!GO:0009056;catabolic process;0.0115500949709336;18597,18293!GO:0016620;oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor;0.0147945239064525;18293!GO:0008374;O-acyltransferase activity;0.0148097630336227;12908!GO:0005737;cytoplasm;0.0157018038464137;12908,18597,18293,102103!GO:0016491;oxidoreductase activity;0.0206757213662636;18597,18293!GO:0016407;acetyltransferase activity;0.0255988472166892;12908!GO:0043231;intracellular membrane-bound organelle;0.0260679889230526;12908,18597,18293,102103!GO:0043227;membrane-bound organelle;0.0260679889230526;12908,18597,18293,102103!GO:0042579;microbody;0.0352708844022384;12908!GO:0005777;peroxisome;0.0352708844022384;12908!GO:0043229;intracellular organelle;0.0385290791314264;12908,18597,18293,102103!GO:0043226;organelle;0.0385290791314264;12908,18597,18293,102103!GO:0019842;vitamin binding;0.038950713132341;18293!GO:0050662;coenzyme 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|gostat_on_MCL_coexpression=GO:0016624;oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor;5.29291857872747e-05;18597,18293!GO:0005739;mitochondrion;0.000224485943461562;12908,18597,18293,102103!GO:0016903;oxidoreductase activity, acting on the aldehyde or oxo group of donors;0.00048344881914575;18597,18293!GO:0006096;glycolysis;0.00048344881914575;18597,18293!GO:0006007;glucose catabolic process;0.00048344881914575;18597,18293!GO:0046365;monosaccharide catabolic process;0.00048344881914575;18597,18293!GO:0019320;hexose catabolic process;0.00048344881914575;18597,18293!GO:0046164;alcohol catabolic process;0.00048344881914575;18597,18293!GO:0044275;cellular carbohydrate catabolic process;0.000598117729282579;18597,18293!GO:0016052;carbohydrate catabolic process;0.000641168179667001;18597,18293!GO:0006006;glucose metabolic process;0.00105982972717645;18597,18293!GO:0004092;carnitine O-acetyltransferase activity;0.00117999570144423;12908!GO:0050164;oxoglutarate dehydrogenase (NADP+) activity;0.00117999570144423;18293!GO:0019318;hexose metabolic process;0.00148344954783774;18597,18293!GO:0005996;monosaccharide metabolic process;0.00148344954783774;18597,18293!GO:0004591;oxoglutarate dehydrogenase (succinyl-transferring) activity;0.00191733542995084;18293!GO:0004738;pyruvate dehydrogenase activity;0.00242169834513759;18597!GO:0030976;thiamin pyrophosphate binding;0.00242169834513759;18293!GO:0004739;pyruvate dehydrogenase (acetyl-transferring) activity;0.00242169834513759;18597!GO:0044444;cytoplasmic part;0.00275277858356794;12908,18597,18293,102103!GO:0016413;O-acetyltransferase activity;0.00284126494223344;12908!GO:0044265;cellular macromolecule catabolic process;0.00284126494223344;18597,18293!GO:0044262;cellular carbohydrate metabolic process;0.00329753507447477;18597,18293!GO:0006066;alcohol metabolic process;0.00331374989964021;18597,18293!GO:0016406;carnitine O-acyltransferase activity;0.00368007399453356;12908!GO:0009057;macromolecule catabolic process;0.00403332330099428;18597,18293!GO:0005975;carbohydrate metabolic process;0.00546562014632149;18597,18293!GO:0044248;cellular catabolic process;0.00725663534467636;18597,18293!GO:0009056;catabolic process;0.0115500949709336;18597,18293!GO:0016620;oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor;0.0147945239064525;18293!GO:0008374;O-acyltransferase activity;0.0148097630336227;12908!GO:0005737;cytoplasm;0.0157018038464137;12908,18597,18293,102103!GO:0016491;oxidoreductase activity;0.0206757213662636;18597,18293!GO:0016407;acetyltransferase activity;0.0255988472166892;12908!GO:0043231;intracellular membrane-bound organelle;0.0260679889230526;12908,18597,18293,102103!GO:0043227;membrane-bound organelle;0.0260679889230526;12908,18597,18293,102103!GO:0042579;microbody;0.0352708844022384;12908!GO:0005777;peroxisome;0.0352708844022384;12908!GO:0043229;intracellular organelle;0.0385290791314264;12908,18597,18293,102103!GO:0043226;organelle;0.0385290791314264;12908,18597,18293,102103!GO:0019842;vitamin binding;0.038950713132341;18293!GO:0050662;coenzyme binding;0.041968713804469;18293!
}}

Latest revision as of 15:34, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:22063208..22063220,+p@chr10:22063208..22063220
+
Mm9::chr11:6192633..6192653,+p8@Ogdh
Mm9::chr11:6192671..6192695,+p4@Ogdh
Mm9::chr11:6192857..6192873,+p@chr11:6192857..6192873
+
Mm9::chr11:6192879..6192901,+p@chr11:6192879..6192901
+
Mm9::chr11:95686449..95686463,+p@chr11:95686449..95686463
+
Mm9::chr1:74063293..74063302,-p@chr1:74063293..74063302
-
Mm9::chr1:74063339..74063352,-p@chr1:74063339..74063352
-
Mm9::chr1:74154930..74154944,-p@chr1:74154930..74154944
-
Mm9::chr2:30270958..30270969,-p9@Crat
Mm9::chr8:42102103..42102121,-p7@Mtus1
Mm9::chrX:156576256..156576268,-p3@Pdha1


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:0016624oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor5.29291857872747e-05
GO:0005739mitochondrion0.000224485943461562
GO:0016903oxidoreductase activity, acting on the aldehyde or oxo group of donors0.00048344881914575
GO:0006096glycolysis0.00048344881914575
GO:0006007glucose catabolic process0.00048344881914575
GO:0046365monosaccharide catabolic process0.00048344881914575
GO:0019320hexose catabolic process0.00048344881914575
GO:0046164alcohol catabolic process0.00048344881914575
GO:0044275cellular carbohydrate catabolic process0.000598117729282579
GO:0016052carbohydrate catabolic process0.000641168179667001
GO:0006006glucose metabolic process0.00105982972717645
GO:0004092carnitine O-acetyltransferase activity0.00117999570144423
GO:0050164oxoglutarate dehydrogenase (NADP+) activity0.00117999570144423
GO:0019318hexose metabolic process0.00148344954783774
GO:0005996monosaccharide metabolic process0.00148344954783774
GO:0004591oxoglutarate dehydrogenase (succinyl-transferring) activity0.00191733542995084
GO:0004738pyruvate dehydrogenase activity0.00242169834513759
GO:0030976thiamin pyrophosphate binding0.00242169834513759
GO:0004739pyruvate dehydrogenase (acetyl-transferring) activity0.00242169834513759
GO:0044444cytoplasmic part0.00275277858356794
GO:0016413O-acetyltransferase activity0.00284126494223344
GO:0044265cellular macromolecule catabolic process0.00284126494223344
GO:0044262cellular carbohydrate metabolic process0.00329753507447477
GO:0006066alcohol metabolic process0.00331374989964021
GO:0016406carnitine O-acyltransferase activity0.00368007399453356
GO:0009057macromolecule catabolic process0.00403332330099428
GO:0005975carbohydrate metabolic process0.00546562014632149
GO:0044248cellular catabolic process0.00725663534467636
GO:0009056catabolic process0.0115500949709336
GO:0016620oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor0.0147945239064525
GO:0008374O-acyltransferase activity0.0148097630336227
GO:0005737cytoplasm0.0157018038464137
GO:0016491oxidoreductase activity0.0206757213662636
GO:0016407acetyltransferase activity0.0255988472166892
GO:0043231intracellular membrane-bound organelle0.0260679889230526
GO:0043227membrane-bound organelle0.0260679889230526
GO:0042579microbody0.0352708844022384
GO:0005777peroxisome0.0352708844022384
GO:0043229intracellular organelle0.0385290791314264
GO:0043226organelle0.0385290791314264
GO:0019842vitamin binding0.038950713132341
GO:0050662coenzyme binding0.041968713804469



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
primary circulatory organ4.67e-0818
heart4.67e-0818
primitive heart tube4.67e-0818
primary heart field4.67e-0818
anterior lateral plate mesoderm4.67e-0818
heart tube4.67e-0818
heart primordium4.67e-0818
cardiac mesoderm4.67e-0818
cardiogenic plate4.67e-0818
heart rudiment4.67e-0818
cardiovascular system6.38e-0723
circulatory system6.38e-0723


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)
MA0003.10.195227
MA0004.11.48666
MA0006.10.496735
MA0007.10.290695
MA0009.10.709264
MA0014.10.0136923
MA0017.11.04297
MA0019.10.535691
MA0024.10.667197
MA0025.10.936082
MA0027.12.34178
MA0028.10.173587
MA0029.10.64639
MA0030.10.65267
MA0031.10.618697
MA0038.10.432665
MA0040.10.721328
MA0041.10.239557
MA0042.10.228771
MA0043.10.802848
MA0046.10.743934
MA0048.10.0440103
MA0050.10.337476
MA0051.10.440863
MA0052.12.90016
MA0055.10.0370218
MA0056.10
MA0057.10.151898
MA0058.11.18867
MA0059.11.22696
MA0060.10.108526
MA0061.10.129002
MA0063.10
MA0066.10.422624
MA0067.11.04514
MA0068.10.0405002
MA0069.10.729433
MA0070.10.720077
MA0071.10.336739
MA0072.10.711905
MA0073.10.000670495
MA0074.14.73969
MA0076.10.200996
MA0077.10.691048
MA0078.10.471303
MA0081.10.702944
MA0083.10.802078
MA0084.11.3693
MA0087.10.760279
MA0088.10.24301
MA0089.10
MA0090.10.27428
MA0091.10.845572
MA0092.10.274547
MA0093.11.61312
MA0095.10
MA0098.10
MA0100.10.379666
MA0101.10.240622
MA0103.10.19444
MA0105.10.491577
MA0106.10.478503
MA0107.10.189625
MA0108.20.557195
MA0109.10
MA0111.10.78079
MA0113.10.452439
MA0114.11.29784
MA0115.10.805567
MA0116.10.959944
MA0117.10.774259
MA0119.10.676816
MA0122.10.793507
MA0124.10.992825
MA0125.10.920215
MA0130.10
MA0131.13.33243
MA0132.10
MA0133.10
MA0135.10.838263
MA0136.10.408073
MA0139.10.0883913
MA0140.10.379562
MA0141.11.13771
MA0142.10.604892
MA0143.10.467531
MA0144.10.129525
MA0145.10.0257706
MA0146.10.651503
MA0147.11.36583
MA0148.10.317692
MA0149.11.27195
MA0062.20.0662974
MA0035.20.998181
MA0039.20.701947
MA0138.20.523978
MA0002.20.302282
MA0137.20.207733
MA0104.21.1126
MA0047.20.431964
MA0112.20.109037
MA0065.21.15835
MA0150.10.290598
MA0151.10
MA0152.11.1034
MA0153.10.854464
MA0154.10.376318
MA0155.10.30272
MA0156.10.580656
MA0157.10.574484
MA0158.10
MA0159.10.145521
MA0160.11.5465
MA0161.10
MA0162.10.00450899
MA0163.10.287849
MA0164.10.408402
MA0080.20.556674
MA0018.21.88337
MA0099.20.518072
MA0079.21.19135e-05
MA0102.21.42135
MA0258.10.376353
MA0259.10.408856
MA0442.10
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