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MCL coexpression mm9:644: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9|coexpression_dpi_cluster_scores_mean=0.0214443332014508,0.0170069940881833,-0.00499125124717515,0.0985357134003776,0.0497268618724858,-0.0105806854394472,0.00854642632255628,0.00101811718544078,0.0542251247105188,0.0709983995922835,-0.000823805157460953,0.0319199380500305,0.0350117881066458,-0.0060934584308285,0.529681834821089,0.741606863746065,0.857926682079149,0.0106010154498948,-0.0142104107222659,0.0915884017865523,0.0537402174047015,0.0488535423541397,0.0171775281198669,0.0091978773313028,0.0238717618009017,-0.0343308586052193,0.0128276869757073,0.0253962871328329,0.0148299081979941,-0.0120410351207981,-0.00740030180959514,0.374317003748317,0.179147211022748,1.24558971032318,0.0200419153644334,-0.0137264853703112,0.0163698771712766,0.019208704710909,-0.0417292569129259,-0.0312790051840153,-0.0645243191930986,-0.0439701507284065,-0.017649132948345,0.00944100301824691,0.00106352645298307,-0.0188159190985435,0.0177791589686715,-0.00598605239354561,0.0351637256956455,0.0207124526504986,0.0154599345419392,0.0184900548163728,0.0092010188542343,-0.0214551801942637,-0.0255550906601071,0.0256966924328065,-0.00654022350421791,-0.0111936851500804,0.0668436746224487,0.101398705980613,0.0368195401126756,0.0110581221697608,0.00239526564491684,-0.00920796415165782,0.0258111403723492,0.00604102152663212,0.0208749322988678,0.0595079243994695,0.0276973951297179,0.0455572666097063,0.0221212339919879,0.0499803514489331,0.0548859630666436,0.00923359453767775,0.0135829038140089,0.0375697829193581,-0.0185730096510882,0.0423585130094006,0.0302759735549328,0.0757399299420532,0.0309213915572971,0.0802583528776539,0.0516310760982341,0.0117929508087176,0.0316368459058518,0.0245641976881409,0.0441390406106148,0.0683067671920751,0.0411929498891262,0.0282447991043636,-0.00602691704843966,-0.0250057517974546,-0.0306241871637489,-0.00671716049903981,-0.0249924844046875,-0.0352922053828888,0.0926323433151026,0.00390269755116593,0.0272692799574178,0.00852708900970252,0.0492092322034062,0.0508718971178328,-0.0645243191930986,0.0181171874076655,-0.002696638743381,0.0100069568161694,0.0156502290655988,0.00797436132694289,0.0166897596498854,0.000668034172717745,0.104621627095101,0.0948818831847143,0.0695834513840727,0.0323213340260055,0.0598309275738922,0.0105932672752978,0.00468832195232579,0.032949903571897,0.405312853926574,0.147578248413049,0.433030455655153,0.432482845454922,0.0798923510323131,0.0437819061970675,0.0875448946522929,0.0506287836267212,0.0500347341310399,-0.0459703573992037,0.0317309548147825,0.0240855958192665,-0.0239990651221925,0.0302352551732716,0.0612325226727403,0.0448543629808439,0.0606718509181239,0.0507158932796132,-0.0117197772050565,0.292218227935318,-0.0191948925276966,0.0144469701853945,0.0280318509470516,0.0385799473586996,0.0355883671463616,0.0365933171356029,0.0371764790720309,-0.00389580994129613,0.0471698946432053,0.0235637675919521,0.0285248867969533,0.0175180296842626,0.0109340051041001,-0.00360308936374077,0.0179257298983193,-0.0173348185263203,0.0223442785222144,-0.00394776093345096,-0.0197706038722078,-0.00474403827717899,0.0102317327042846,0.103195920394443,0.0210999500836532,-0.0162254206427026,0.0420054391642571,0.00936985625074715,0.00284377361338831,0.0216234147628173,0.0443579799487211,0.0263172401713545,0.0105609479358968,0.0455553537880118,0.0405055194886076,0.0540784115577189,0.0797033758868808,0.0502501273611903,0.0576171408068523,0.0341876718142275,0.129106666738688,0.0326457268773828,-0.0172694779866644,0.0496833562216074,0.025927861223844,0.048978652142463,-0.000673739227491103,0.026758959888276,0.0694489455595987,-0.0204654396607645,-0.0032698407185225,0.042934070379305,0.0112128364738296,0.00140979965876226,0.0451636162877557,0.0388319850796701,0.0274070203581459,0.0365155994234093,0.0792247544372177,0.000458462611892755,0.0147163819908765,0.0240879922337423,0.0417371792065671,0.0179462313712454,0.0444856975396123,0.0263201544675842,0.0236125629224408,0.495481551966577,0.503632602729803,0.593072116769172,0.532853462669329,0.554047954020815,0.591052106528664,0.471959735771895,0.356946409260682,0.338613793760398,0.213921117969955,0.0986276389935123,-0.000373016070925836,-0.0217063853058998,0.0127116864119411,-0.000522966827171517,-0.000957505096432145,-0.0020639983490903,-0.00869642997078893,-0.000206118814130117,-0.000694507365008447,-0.00265491112644184,-0.0348170516137254,0.014854893587938,0.025312618627955,0.0517128552908035,0.00440688654841063,0.033151620947651,0.0360794174284638,0.0186120123121331,0.00807794241523914,-0.0354614775670691,0.000260074875635957,0.0392929669582272,0.0306386849810933,0.0575329851960924,0.0232515299374441,0.0838175462083062,0.0752728620164426,0.0652953656694614,0.0428946368760013,0.0574784687728185,0.0258554078152574,0.0282491543950665,0.0606371881289668,0.0729558477679778,0.00492998999366152,0.0684062773495475,0.00854851275067226,0.0222445176283014,0.0271458224619889,0.0119734954776456,-0.0311715357334186,0.0769664404139067,0.042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endopeptidase activity;0.035451443793266;73218!GO:0016772;transferase activity, transferring phosphorus-containing groups;0.035451443793266;23970,15258,74080!GO:0000309;nicotinamide-nucleotide adenylyltransferase activity;0.035451443793266;74080!GO:0045806;negative regulation of endocytosis;0.035451443793266;23970!GO:0043388;positive regulation of DNA binding;0.035451443793266;15258!GO:0051099;positive regulation of binding;0.035451443793266;15258!GO:0009435;NAD biosynthetic process;0.035451443793266;74080!GO:0019674;NAD metabolic process;0.035451443793266;74080!GO:0042771;DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis;0.035451443793266;15258!GO:0051101;regulation of DNA binding;0.035451443793266;15258!GO:0019363;pyridine nucleotide biosynthetic process;0.035451443793266;74080!GO:0016605;PML body;0.035451443793266;15258!GO:0030330;DNA damage response, signal transduction by p53 class mediator;0.035451443793266;15258!GO:0016740;transferase activity;0.035451443793266;23970,15258,74080!GO:0008630;DNA damage response, signal transduction resulting in induction of apoptosis;0.035451443793266;15258!GO:0042364;water-soluble vitamin biosynthetic process;0.035451443793266;74080!GO:0051051;negative regulation of transport;0.035451443793266;23970!GO:0009110;vitamin biosynthetic process;0.035451443793266;74080!GO:0004190;aspartic-type endopeptidase activity;0.035451443793266;73218!GO:0051098;regulation of binding;0.0374148170020494;15258!GO:0006769;nicotinamide metabolic process;0.0391900315242104;74080!GO:0019362;pyridine nucleotide metabolic process;0.0408027456076468;74080!GO:0007224;smoothened signaling pathway;0.0455185289494597;15258!GO:0008629;induction of apoptosis by intracellular signals;0.0467300915721629;15258!GO:0006733;oxidoreduction coenzyme metabolic process;0.0478437468235302;74080!GO:0030100;regulation of endocytosis;0.048440920128482;23970!GO:0042770;DNA damage response, signal 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|gostat_on_MCL_coexpression=GO:0008717;D-alanyl-D-alanine endopeptidase activity;0.035451443793266;73218!GO:0016772;transferase activity, transferring phosphorus-containing groups;0.035451443793266;23970,15258,74080!GO:0000309;nicotinamide-nucleotide adenylyltransferase activity;0.035451443793266;74080!GO:0045806;negative regulation of endocytosis;0.035451443793266;23970!GO:0043388;positive regulation of DNA binding;0.035451443793266;15258!GO:0051099;positive regulation of binding;0.035451443793266;15258!GO:0009435;NAD biosynthetic process;0.035451443793266;74080!GO:0019674;NAD metabolic process;0.035451443793266;74080!GO:0042771;DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis;0.035451443793266;15258!GO:0051101;regulation of DNA binding;0.035451443793266;15258!GO:0019363;pyridine nucleotide biosynthetic process;0.035451443793266;74080!GO:0016605;PML body;0.035451443793266;15258!GO:0030330;DNA damage response, signal transduction by p53 class mediator;0.035451443793266;15258!GO:0016740;transferase activity;0.035451443793266;23970,15258,74080!GO:0008630;DNA damage response, signal transduction resulting in induction of apoptosis;0.035451443793266;15258!GO:0042364;water-soluble vitamin biosynthetic process;0.035451443793266;74080!GO:0051051;negative regulation of transport;0.035451443793266;23970!GO:0009110;vitamin biosynthetic process;0.035451443793266;74080!GO:0004190;aspartic-type endopeptidase activity;0.035451443793266;73218!GO:0051098;regulation of binding;0.0374148170020494;15258!GO:0006769;nicotinamide metabolic process;0.0391900315242104;74080!GO:0019362;pyridine nucleotide metabolic process;0.0408027456076468;74080!GO:0007224;smoothened signaling pathway;0.0455185289494597;15258!GO:0008629;induction of apoptosis by intracellular signals;0.0467300915721629;15258!GO:0006733;oxidoreduction coenzyme metabolic process;0.0478437468235302;74080!GO:0030100;regulation of endocytosis;0.048440920128482;23970!GO:0042770;DNA damage response, signal transduction;0.048440920128482;15258!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005172!2.03e-09!49;UBERON:0005173!2.03e-09!49;UBERON:0002417!2.03e-09!49;UBERON:0000916!2.03e-09!49;UBERON:0002106!1.48e-08!6;UBERON:0004457!1.48e-08!6;UBERON:0000042!1.48e-08!6;UBERON:0004854!1.48e-08!6;UBERON:0009034!1.48e-08!6;UBERON:0002095!1.48e-08!6;UBERON:0004782!1.48e-08!6;UBERON:0003281!1.48e-08!6;UBERON:0009664!1.48e-08!6;UBERON:0002296!1.48e-08!6;UBERON:0005602!1.48e-08!6;UBERON:0001179!1.48e-08!6;UBERON:0006293!1.48e-08!6
|tfbs_overrepresentation_for_novel_motifs=0.795069,0.490989,0.269904,0.329881,0.52369,0.907763,1.08973,0.345089,0.362206,0.401738,0.385334,0.414631,0.345518,0.437133,0.555819,0,0.619876,0.508485,0.318616,0.387499,0.238546,0.831639,0.436294,0.520732,0.758244,0.4628,0.630402,0.361771,0.213277,0.500344,0.921513,0.717576,0.168723,0.270473,1.6721,0.308746,0.94339,0.411296,0.144953,0.391645,0.51597,0.931853,0.104243,0.559697,0.351346,0.319944,0.543674,0.376103,0.401883,0.61724,0.603113,0.488021,0.479906,0.855661,0.87275,0.443782,0.223087,1.03993,0.60268,0.441884,0.698157,0.496904,0.383763,0.592318,0.45416,0.631188,1.00675,1.3527,0.693631,1.20659,0.706068,0.110167,1.25712,0.905636,0.0810502,0.932285,0.270351,0.532872,0.681539,0.679143,0.724739,0.636582,0.495545,0.101814,0.792744,0.256335,0.4982,0.231893,0.548334,1.51408,1.07554,0.797601,0.730003,0.535058,0.141946,0.129056,0.104462,0.732731,0.543917,0.197581,0.161581,1.70591,0.838603,0.603683,0.602672,0.930972,0.660145,0.973236,0.246223,0.67437,0.286453,0.840348,0.243062,1.01194,1.0825,0.512539,0.170188,0.333247,0.621127,0.479408,0.910937,0.572279,0.464505,0.532013,1.13603,0.685116,1.10612,0.723425,1.00525,0.540802,0.821997,0.323373,0.976125,0.456508,1.10385,0.0275241,0.300001,0.35497,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,1.45372,0.354106,0.546641,1.84176,0.302077,0.178088,0.235808,1.11868,0.857198,0.133365,0.455644,0.93735,0.488969,0.199652,0.290467,0.299755,1.06466,0.791909,0.685546,0.776587,0.593295,0.448733,0.484323,1.06237,0.148813
|tfbs_overrepresentation_jaspar=MA0003.1;1.2787,MA0004.1;0.879856,MA0006.1;1.65004,MA0007.1;0.316976,MA0009.1;0.743257,MA0014.1;0.44164,MA0017.1;0.598706,MA0019.1;0.567591,MA0024.1;0.70077,MA0025.1;0.971686,MA0027.1;2.37948,MA0028.1;0.194782,MA0029.1;0.679737,MA0030.1;0.686088,MA0031.1;0.651724,MA0038.1;0.462726,MA0040.1;0.755433,MA0041.1;0.263922,MA0042.1;0.252679,MA0043.1;0.837621,MA0046.1;0.778239,MA0048.1;0.769903,MA0050.1;0.95731,MA0051.1;0.471092,MA0052.1;0.76328,MA0055.1;1.39853,MA0056.1;0,MA0057.1;0.181039,MA0058.1;1.27846,MA0059.1;0.714494,MA0060.1;0.395347,MA0061.1;0.147394,MA0063.1;0,MA0066.1;0.452472,MA0067.1;1.08124,MA0068.1;0.187364,MA0069.1;0.76361,MA0070.1;0.75417,MA0071.1;0.364454,MA0072.1;0.745922,MA0073.1;0.0394021,MA0074.1;0.419185,MA0076.1;0.635923,MA0077.1;0.724865,MA0078.1;0.502121,MA0081.1;0.277253,MA0083.1;0.836845,MA0084.1;1.4063,MA0087.1;0.794721,MA0088.1;0.12124,MA0089.1;0,MA0090.1;0.811744,MA0091.1;0.342071,MA0092.1;0.300264,MA0093.1;1.10424,MA0095.1;0,MA0098.1;0,MA0100.1;0.408523,MA0101.1;0.265031,MA0103.1;0.619698,MA0105.1;0.94454,MA0106.1;0.509454,MA0107.1;0.211681,MA0108.2;0.589413,MA0109.1;0,MA0111.1;0.312463,MA0113.1;0.482899,MA0114.1;0.446898,MA0115.1;0.84036,MA0116.1;0.186271,MA0117.1;0.808813,MA0119.1;0.265536,MA0122.1;0.828211,MA0124.1;1.02871,MA0125.1;0.955734,MA0130.1;0,MA0131.1;0.563262,MA0132.1;0,MA0133.1;0,MA0135.1;0.873285,MA0136.1;0.437601,MA0139.1;1.67615,MA0140.1;2.77212,MA0141.1;0.658164,MA0142.1;0.63775,MA0143.1;0.49828,MA0144.1;0.88666,MA0145.1;0.3137,MA0146.1;0.331601,MA0147.1;1.48109,MA0148.1;0.344843,MA0149.1;0.269772,MA0062.2;0.271822,MA0035.2;1.06146,MA0039.2;0.35217,MA0138.2;0.555696,MA0002.2;0.105469,MA0137.2;0.652494,MA0104.2;2.41329,MA0047.2;0.46201,MA0112.2;0.57262,MA0065.2;1.30208,MA0150.1;1.53423,MA0151.1;0,MA0152.1;0.46211,MA0153.1;0.889592,MA0154.1;0.434137,MA0155.1;0.637282,MA0156.1;0.222905,MA0157.1;0.606944,MA0158.1;0,MA0159.1;0.957875,MA0160.1;0.347545,MA0161.1;0,MA0162.1;0.609924,MA0163.1;0.563751,MA0164.1;0.437937,MA0080.2;0.212408,MA0018.2;0.446948,MA0099.2;0.549696,MA0079.2;0.0308303,MA0102.2;1.45844,MA0258.1;0.833943,MA0259.1;0.891672,MA0442.1;0
}}

Latest revision as of 15:39, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:80318068..80318083,+p2@3110056O03Rik
Mm9::chr11:102217808..102217820,-p@chr11:102217808..102217820
-
Mm9::chr15:83254210..83254223,-p@chr15:83254210..83254223
-
Mm9::chr1:75233328..75233336,+p10@Dnajb2
Mm9::chr4:122959994..122960005,+p3@LOC100503296
p3@Pabpc4
Mm9::chr6:28374572..28374589,+p@chr6:28374572..28374589
+
Mm9::chr6:38826531..38826540,-p9@Hipk2
Mm9::chr6:86055182..86055186,+p@chr6:86055182..86055186
+
Mm9::chr7:25162358..25162371,+p@chr7:25162358..25162371
+
Mm9::chr9:121361587..121361593,-p@chr9:121361587..121361593
-
Mm9::chr9:98197322..98197331,+p6@Nmnat3


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:0008717D-alanyl-D-alanine endopeptidase activity0.035451443793266
GO:0016772transferase activity, transferring phosphorus-containing groups0.035451443793266
GO:0000309nicotinamide-nucleotide adenylyltransferase activity0.035451443793266
GO:0045806negative regulation of endocytosis0.035451443793266
GO:0043388positive regulation of DNA binding0.035451443793266
GO:0051099positive regulation of binding0.035451443793266
GO:0009435NAD biosynthetic process0.035451443793266
GO:0019674NAD metabolic process0.035451443793266
GO:0042771DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis0.035451443793266
GO:0051101regulation of DNA binding0.035451443793266
GO:0019363pyridine nucleotide biosynthetic process0.035451443793266
GO:0016605PML body0.035451443793266
GO:0030330DNA damage response, signal transduction by p53 class mediator0.035451443793266
GO:0016740transferase activity0.035451443793266
GO:0008630DNA damage response, signal transduction resulting in induction of apoptosis0.035451443793266
GO:0042364water-soluble vitamin biosynthetic process0.035451443793266
GO:0051051negative regulation of transport0.035451443793266
GO:0009110vitamin biosynthetic process0.035451443793266
GO:0004190aspartic-type endopeptidase activity0.035451443793266
GO:0051098regulation of binding0.0374148170020494
GO:0006769nicotinamide metabolic process0.0391900315242104
GO:0019362pyridine nucleotide metabolic process0.0408027456076468
GO:0007224smoothened signaling pathway0.0455185289494597
GO:0008629induction of apoptosis by intracellular signals0.0467300915721629
GO:0006733oxidoreduction coenzyme metabolic process0.0478437468235302
GO:0030100regulation of endocytosis0.048440920128482
GO:0042770DNA damage response, signal transduction0.048440920128482



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>


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)
MA0003.11.2787
MA0004.10.879856
MA0006.11.65004
MA0007.10.316976
MA0009.10.743257
MA0014.10.44164
MA0017.10.598706
MA0019.10.567591
MA0024.10.70077
MA0025.10.971686
MA0027.12.37948
MA0028.10.194782
MA0029.10.679737
MA0030.10.686088
MA0031.10.651724
MA0038.10.462726
MA0040.10.755433
MA0041.10.263922
MA0042.10.252679
MA0043.10.837621
MA0046.10.778239
MA0048.10.769903
MA0050.10.95731
MA0051.10.471092
MA0052.10.76328
MA0055.11.39853
MA0056.10
MA0057.10.181039
MA0058.11.27846
MA0059.10.714494
MA0060.10.395347
MA0061.10.147394
MA0063.10
MA0066.10.452472
MA0067.11.08124
MA0068.10.187364
MA0069.10.76361
MA0070.10.75417
MA0071.10.364454
MA0072.10.745922
MA0073.10.0394021
MA0074.10.419185
MA0076.10.635923
MA0077.10.724865
MA0078.10.502121
MA0081.10.277253
MA0083.10.836845
MA0084.11.4063
MA0087.10.794721
MA0088.10.12124
MA0089.10
MA0090.10.811744
MA0091.10.342071
MA0092.10.300264
MA0093.11.10424
MA0095.10
MA0098.10
MA0100.10.408523
MA0101.10.265031
MA0103.10.619698
MA0105.10.94454
MA0106.10.509454
MA0107.10.211681
MA0108.20.589413
MA0109.10
MA0111.10.312463
MA0113.10.482899
MA0114.10.446898
MA0115.10.84036
MA0116.10.186271
MA0117.10.808813
MA0119.10.265536
MA0122.10.828211
MA0124.11.02871
MA0125.10.955734
MA0130.10
MA0131.10.563262
MA0132.10
MA0133.10
MA0135.10.873285
MA0136.10.437601
MA0139.11.67615
MA0140.12.77212
MA0141.10.658164
MA0142.10.63775
MA0143.10.49828
MA0144.10.88666
MA0145.10.3137
MA0146.10.331601
MA0147.11.48109
MA0148.10.344843
MA0149.10.269772
MA0062.20.271822
MA0035.21.06146
MA0039.20.35217
MA0138.20.555696
MA0002.20.105469
MA0137.20.652494
MA0104.22.41329
MA0047.20.46201
MA0112.20.57262
MA0065.21.30208
MA0150.11.53423
MA0151.10
MA0152.10.46211
MA0153.10.889592
MA0154.10.434137
MA0155.10.637282
MA0156.10.222905
MA0157.10.606944
MA0158.10
MA0159.10.957875
MA0160.10.347545
MA0161.10
MA0162.10.609924
MA0163.10.563751
MA0164.10.437937
MA0080.20.212408
MA0018.20.446948
MA0099.20.549696
MA0079.20.0308303
MA0102.21.45844
MA0258.10.833943
MA0259.10.891672
MA0442.10
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