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MCL coexpression mm9:587: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9|coexpression_dpi_cluster_scores_mean=-0.0182557535656054,0.554884356397868,0.545386510887868,0.699366899745335,0.734112498534438,0.275765845336689,0.210802239160514,0.416263632565416,0.291132394344294,0.296982956256377,-0.0172657390506706,-0.00466450559237501,0.451729058454837,0.451860970976969,0.0107290987451011,0.0792746727232861,-0.0106373143403589,0.30189636437285,0.3257931884998,0.321612142725812,-0.0217798301945207,0.0549102586899326,0.0298241914922605,0.234403723970632,0.249858401535458,0.409148283640683,0.391216535864156,0.316171392386697,0.28668854509049,0.303703138407981,0.204542285811427,-0.105706234011838,-0.18720963249889,-0.817846801120991,0.0137075944420822,-0.0612707742111438,0.00549334045939258,0.720348490997695,0.55889980598926,0.600572448435705,0.727152370360891,0.737219273047524,0.685993246547052,-0.12261540663784,-0.0921297364788462,-0.0880029028722686,-0.113777361939236,-0.332965259261789,-0.290175358185521,-0.23976248499843,-0.25667621560261,-0.333684255312676,0.410557026910037,0.424453257161894,0.392529645495829,-0.0930386092459126,-0.0168198194208641,-0.0183046545773539,-0.186746718507745,-0.229050866252251,-0.293457802354706,-0.312672116508515,-0.407812889108679,-0.056019571364592,-0.0280937410570295,-0.0400584980155603,-0.186778810929508,-0.204533594292639,-0.0947984798011123,-0.122358131676519,-0.127229476205359,-0.207002219890668,-0.250680248180066,-0.13850020696671,-0.162550418898135,-0.177187348290578,-0.206756496560703,-0.113720460914814,-0.110689984799711,-0.119235667073639,-0.147445953095405,-0.121341090249533,-0.0845722712047182,-0.124551568294277,-0.0715579608613375,-0.188188791191332,-0.15051186479668,-0.12000499475921,-0.10586031082999,-0.0846028746499471,0.181564606308244,-0.00881493772167809,-0.179529069795268,0.0223998640631921,0.0425821429126424,-0.0207730402543422,0.0224872725085144,-0.175463681175864,-0.278228913973445,-0.235121393465999,-0.018660588800959,-0.0862041669733706,-0.114996574706865,-0.287360589096326,-0.0496479920605941,-0.0612295857542399,-0.0678604219294652,0.100069495089754,0.368057868306471,0.0638974758086472,-0.166921398594357,-0.125772035857037,-0.041447231023592,-0.0488151297329332,0.046587934752243,0.0499001051519461,0.14402344264211,0.0684470094763495,0.196071894856281,-0.0711108940997713,0.0529630795233403,0.0846112497395959,0.253847426894298,0.0639384576858233,0.0635204222396115,0.35668242444962,0.0850935425523772,-0.0120444899464463,0.0343198317665723,-0.0199358954125599,-0.00367929592952348,-0.085591055885691,0.0187448206790603,0.0249401252215921,-0.0251096429494814,0.012932905862483,-0.104951490650551,0.115139196828979,0.0370246709143799,0.144788621918494,-0.206592276302222,-0.172697914358182,-0.151890995270955,-0.0821538443891538,-0.0279572915143628,-0.0302615937670102,-0.0100549960368596,0.119599511385419,-0.239370970253963,-0.139575637484441,-0.0942838449948727,-0.142246839942849,-0.0365161534782043,0.0169723002492023,-0.0711366585123811,-0.143194829399348,0.0206339982165484,-0.0385814196187565,0.0558869410141338,-0.17038870064355,-0.141269437032017,-0.149564995810879,-0.110858460491529,-0.117670638577838,-0.119888360511399,-0.109307841649048,-0.13193604841397,-0.0490623941275183,-0.064237141602923,-0.0372766243050282,-0.0177792393947468,-0.0403977161297057,-0.0445748795761325,0.00706047973183155,0.0142648790043089,-0.0645082781464623,0.55758195866179,0.265167439265787,-0.144436614327024,-0.153522394244638,-0.0544361909025176,0.0359043996880036,0.0783517782175305,0.113801875869261,0.262696154780679,0.111779890844938,0.20661231490534,0.202144989231603,0.206424996009292,0.267021545895662,0.318401512499396,0.368604547164247,-0.249354878174872,-0.114811614759092,-0.0428406512211899,-0.111551689589943,-0.0401569621444203,-0.0047187526831869,0.0594975103852191,0.0951051944913985,0.0638204561532176,0.125594748359724,0.00481133800116702,-0.143114006760921,-0.113209757740489,-0.0950961519126162,-0.058798186781097,-0.0296012023525696,-0.0121061695906275,0.061242467592432,-1.97344198088027e-05,-0.0561888300919237,0.00929879980307887,-0.00476188371441318,-0.0264693227666007,-0.00929523752921388,-0.0429617846052855,0.00974784143189389,0.147849415249081,-0.204044404045887,-0.104075934611532,-0.11287375178259,-0.0748487255190367,0.0246445073591261,0.0191794725131299,0.132188515713433,0.0530132164369612,0.0175664327012654,0.131078688163203,0.150167320482454,0.155645584814247,0.141181569639764,0.0110922448995007,0.113111214382489,0.0587355943283826,0.0952243542502503,0.00852405398791019,0.014301113968532,-0.367986892610873,-0.0369528831758147,-0.0772204509413384,-0.0717793290876535,-0.031863236133665,0.0176374981669307,0.00515884494892648,-0.000350858970572989,-0.0417569784108631,-0.0190189021684581,0.0134891776651207,0.107737735686092,0.0610440447232068,-0.186680841385093,-0.0619684497640259,0.0593461550915296,0.0950252943960665,-0.166305216454654,-0.102671860941268,-0.021842775767287,-0.0275308244208736,0.0621144088017601,0.09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nucleotide binding;0.000581269972159091;68556,320795,98314,76295,27403,56480!GO:0017076;purine nucleotide binding;0.000999727131268797;68556,320795,98314,76295,27403,56480!GO:0000166;nucleotide binding;0.00137670865549461;68556,320795,98314,76295,27403,56480!GO:0005524;ATP binding;0.00243065589320011;68556,320795,76295,27403,56480!GO:0032559;adenyl ribonucleotide binding;0.00243065589320011;68556,320795,76295,27403,56480!GO:0032553;ribonucleotide binding;0.00499779722893616;68556,320795,76295,27403,56480!GO:0032555;purine ribonucleotide binding;0.00499779722893616;68556,320795,76295,27403,56480!GO:0051990;(R)-2-hydroxyglutarate dehydrogenase activity;0.0076699720593875;98314!GO:0032025;response to cobalt ion;0.0076699720593875;98314!GO:0010042;response to manganese ion;0.0076699720593875;98314!GO:0010043;response to zinc ion;0.0139427295764083;98314!GO:0006972;hyperosmotic response;0.0255518688309197;320795!GO:0004849;uridine kinase activity;0.0294772723990682;68556!GO:0005677;chromatin silencing complex;0.0437696187419012;209011!GO:0010038;response to metal ion;0.045218395249302;98314!GO:0016301;kinase activity;0.045218395249302;68556,320795,56480!GO:0006970;response to osmotic stress;0.045218395249302;320795!GO:0019206;nucleoside kinase activity;0.045218395249302;68556!GO:0016887;ATPase activity;0.045218395249302;76295,27403!GO:0010035;response to inorganic substance;0.045218395249302;98314!GO:0006342;chromatin silencing;0.045218395249302;209011!GO:0031507;heterochromatin formation;0.045218395249302;209011!GO:0045814;negative regulation of gene expression, epigenetic;0.0476710522172964;209011!GO:0004697;protein kinase C activity;0.0476710522172964;320795!GO:0016772;transferase activity, transferring phosphorus-containing groups;0.0476710522172964;68556,320795,56480!GO:0016787;hydrolase activity;0.0481444912763527;209011,320795,76295,27403!GO:0001565;phorbol ester receptor 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|gostat_on_MCL_coexpression=GO:0030554;adenyl nucleotide binding;0.000581269972159091;68556,320795,98314,76295,27403,56480!GO:0017076;purine nucleotide binding;0.000999727131268797;68556,320795,98314,76295,27403,56480!GO:0000166;nucleotide binding;0.00137670865549461;68556,320795,98314,76295,27403,56480!GO:0005524;ATP binding;0.00243065589320011;68556,320795,76295,27403,56480!GO:0032559;adenyl ribonucleotide binding;0.00243065589320011;68556,320795,76295,27403,56480!GO:0032553;ribonucleotide binding;0.00499779722893616;68556,320795,76295,27403,56480!GO:0032555;purine ribonucleotide binding;0.00499779722893616;68556,320795,76295,27403,56480!GO:0051990;(R)-2-hydroxyglutarate dehydrogenase activity;0.0076699720593875;98314!GO:0032025;response to cobalt ion;0.0076699720593875;98314!GO:0010042;response to manganese ion;0.0076699720593875;98314!GO:0010043;response to zinc ion;0.0139427295764083;98314!GO:0006972;hyperosmotic response;0.0255518688309197;320795!GO:0004849;uridine kinase activity;0.0294772723990682;68556!GO:0005677;chromatin silencing complex;0.0437696187419012;209011!GO:0010038;response to metal ion;0.045218395249302;98314!GO:0016301;kinase activity;0.045218395249302;68556,320795,56480!GO:0006970;response to osmotic stress;0.045218395249302;320795!GO:0019206;nucleoside kinase activity;0.045218395249302;68556!GO:0016887;ATPase activity;0.045218395249302;76295,27403!GO:0010035;response to inorganic substance;0.045218395249302;98314!GO:0006342;chromatin silencing;0.045218395249302;209011!GO:0031507;heterochromatin formation;0.045218395249302;209011!GO:0045814;negative regulation of gene expression, epigenetic;0.0476710522172964;209011!GO:0004697;protein kinase C activity;0.0476710522172964;320795!GO:0016772;transferase activity, transferring phosphorus-containing groups;0.0476710522172964;68556,320795,56480!GO:0016787;hydrolase activity;0.0481444912763527;209011,320795,76295,27403!GO:0001565;phorbol ester receptor activity;0.0481444912763527;320795!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004119!5.47e-13!118;UBERON:0000925!5.47e-13!118;UBERON:0006595!5.47e-13!118;UBERON:0001007!1.96e-12!116;UBERON:0001555!1.96e-12!116;UBERON:0007026!1.96e-12!116;UBERON:0004921!1.25e-11!114;UBERON:0005409!1.57e-09!47;UBERON:0000160!1.59e-09!31;UBERON:0007023!1.48e-08!51;UBERON:0004923!6.64e-08!24;UBERON:0000344!7.76e-07!15
}}

Latest revision as of 15:33, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:121023786..121023859,-p1@Tbk1
Mm9::chr10:79459200..79459220,+p2@Abca7
Mm9::chr11:120486287..120486312,-p1@Sirt7
Mm9::chr11:69224513..69224543,-p@chr11:69224513..69224543
-
Mm9::chr1:95721847..95721882,+p2@D2hgdh
Mm9::chr2:181316679..181316695,-p1@Uckl1
Mm9::chr3:35653043..35653057,+p1@Atp11b
Mm9::chr4:134479531..134479543,+p1@D4Wsu53e
Mm9::chr4:154998962..154999038,+p1@Cdk11b
Mm9::chr6:56664885..56664945,+p1@Avl9
Mm9::chr8:86222994..86223105,-p1@Pkn1
Mm9::chr9:96531906..96531973,-p1@Rasa2


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:0030554adenyl nucleotide binding0.000581269972159091
GO:0017076purine nucleotide binding0.000999727131268797
GO:0000166nucleotide binding0.00137670865549461
GO:0005524ATP binding0.00243065589320011
GO:0032559adenyl ribonucleotide binding0.00243065589320011
GO:0032553ribonucleotide binding0.00499779722893616
GO:0032555purine ribonucleotide binding0.00499779722893616
GO:0051990(R)-2-hydroxyglutarate dehydrogenase activity0.0076699720593875
GO:0032025response to cobalt ion0.0076699720593875
GO:0010042response to manganese ion0.0076699720593875
GO:0010043response to zinc ion0.0139427295764083
GO:0006972hyperosmotic response0.0255518688309197
GO:0004849uridine kinase activity0.0294772723990682
GO:0005677chromatin silencing complex0.0437696187419012
GO:0010038response to metal ion0.045218395249302
GO:0016301kinase activity0.045218395249302
GO:0006970response to osmotic stress0.045218395249302
GO:0019206nucleoside kinase activity0.045218395249302
GO:0016887ATPase activity0.045218395249302
GO:0010035response to inorganic substance0.045218395249302
GO:0006342chromatin silencing0.045218395249302
GO:0031507heterochromatin formation0.045218395249302
GO:0045814negative regulation of gene expression, epigenetic0.0476710522172964
GO:0004697protein kinase C activity0.0476710522172964
GO:0016772transferase activity, transferring phosphorus-containing groups0.0476710522172964
GO:0016787hydrolase activity0.0481444912763527
GO:0001565phorbol ester receptor activity0.0481444912763527



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 structure5.47e-13118
endoderm5.47e-13118
presumptive endoderm5.47e-13118
digestive system1.96e-12116
digestive tract1.96e-12116
primitive gut1.96e-12116
subdivision of digestive tract1.25e-11114
gastrointestinal system1.57e-0947
intestine1.59e-0931
adult organism1.48e-0851
organ component layer6.64e-0824
mucosa7.76e-0715


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)
MA0003.13.0268
MA0004.10.819913
MA0006.10.496735
MA0007.10.290695
MA0009.10.709264
MA0014.12.06593
MA0017.10.546298
MA0019.10.535691
MA0024.10.667197
MA0025.10.936082
MA0027.12.34178
MA0028.12.24825
MA0029.10.64639
MA0030.11.57146
MA0031.10.618697
MA0038.10.432665
MA0040.10.721328
MA0041.11.25077
MA0042.11.20982
MA0043.10.802848
MA0046.10.743934
MA0048.11.05335
MA0050.10.337476
MA0051.10.440863
MA0052.10.729105
MA0055.10.624457
MA0056.10
MA0057.10.630087
MA0058.11.18867
MA0059.10.658541
MA0060.10.108526
MA0061.10.40468
MA0063.10
MA0066.10.422624
MA0067.11.04514
MA0068.10.0405002
MA0069.10.729433
MA0070.10.720077
MA0071.10.336739
MA0072.10.711905
MA0073.10.0207592
MA0074.10.390075
MA0076.13.24198
MA0077.10.691048
MA0078.10.471303
MA0081.10.252371
MA0083.10.802078
MA0084.11.3693
MA0087.10.760279
MA0088.10.459114
MA0089.10
MA0090.10.27428
MA0091.10.315003
MA0092.10.274547
MA0093.10.531567
MA0095.10
MA0098.10
MA0100.10.989129
MA0101.10.240622
MA0103.10.566591
MA0105.10.226879
MA0106.10.478503
MA0107.10.189625
MA0108.20.557195
MA0109.10
MA0111.10.78079
MA0113.10.452439
MA0114.10.797973
MA0115.10.805567
MA0116.10.165534
MA0117.10.774259
MA0119.10.241106
MA0122.10.793507
MA0124.10.992825
MA0125.10.920215
MA0130.10
MA0131.10.531427
MA0132.10
MA0133.10
MA0135.10.838263
MA0136.10.408073
MA0139.10.297344
MA0140.10.379562
MA0141.10.210047
MA0142.10.604892
MA0143.10.467531
MA0144.10.129525
MA0145.12.04353
MA0146.15.38581
MA0147.10.138228
MA0148.10.317692
MA0149.10.245177
MA0062.23.69627
MA0035.20.383789
MA0039.24.16319
MA0138.20.523978
MA0002.20.627335
MA0137.20.207733
MA0104.20.670538
MA0047.20.431964
MA0112.20.109037
MA0065.20.4963
MA0150.10.290598
MA0151.10
MA0152.10.432062
MA0153.10.854464
MA0154.10.16541
MA0155.10.555224
MA0156.10.580656
MA0157.10.574484
MA0158.10
MA0159.10.446593
MA0160.10.320315
MA0161.10
MA0162.11.72487
MA0163.12.43096
MA0164.10.408402
MA0080.20.190316
MA0018.20.417217
MA0099.20.518072
MA0079.21.92054
MA0102.21.42135
MA0258.10.376353
MA0259.10.408856
MA0442.10
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