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MCL coexpression mm9:378: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9|coexpression_dpi_cluster_scores_mean=-0.00371303316172685,0.0141115515555087,0.00431408514176789,0.00745074175861323,0.016924379024344,0.00017392759541507,-0.0103191526780621,-0.028630679327724,-0.000653952431277371,0.00826258727859355,-0.038434289389626,-0.042083694433304,-0.0328659079508987,-0.0282669914649897,0.0149483539023763,0.01332398952906,-0.0048020498778337,-0.00641284205608869,-0.000295325285470817,-0.00272382356164153,0.118821966017111,0.00378528104731555,-0.0236067638073801,0.00382311679456085,0.0174039895298491,-0.0157377530911342,-0.0162478905461677,-0.0116876378182839,0.00212258023648323,-0.0075709649537413,-0.0109613418521017,0.0159871435649889,-0.0051759602013017,-0.0452980620384934,-0.017747331620333,-0.0194751533966395,-0.00754960286503858,0.0287749328419783,0.0127484308044009,0.0152864980200819,0.0244828630589304,0.0331259885547956,0.0273834373216146,-0.0021905902789892,0.00409480814830011,0.00217046994890253,0.0408225942793287,0.0072278272727062,0.0434271281623375,0.0740640838125283,0.0107264669639655,-0.0259506023720265,-0.0322786069008215,-0.0334540488138138,-0.0166777147992396,0.0103931915460973,0.00116891973494956,0.0214870422988631,-0.0276198100246628,-0.0360778158798439,-0.0346377000744707,0.00142031208193755,-0.00235597840003845,0.032550628036878,-0.00667349621415785,0.0193384389168692,-0.0225022349226589,0.00996058739326996,-0.0367286710219184,-0.0351640638039208,-0.0370078630255162,-0.0151210394836889,-0.0133139608904153,-0.0357817688037042,-0.0395024142682775,-0.0311418377310755,-0.0200248417903877,-0.0143972132196625,0.0266380691025239,-0.0203170206276025,-0.0241917096229444,-0.0361928381458573,0.0264811420879828,0.0165325159905678,0.0238041510774916,-0.0203308147078134,-0.0210082426464021,-0.0309946225290902,-0.00691459879742665,-0.0123332658950667,0.00196848429518763,0.0640280451442774,0.0110274057562526,0.0477579570259052,0.0486736168641182,0.0541122523366233,0.286469444100333,0.0222112468714109,0.0218222839987035,0.0191233843778319,-0.00761969668824837,0.0442126866447136,-0.0177985607985923,-0.0452980620384934,-0.0223633161227461,-0.0167812815013595,-0.0186448903146963,0.153000185653522,0.103220284180322,0.306077457424893,-0.0088280046554277,0.052207466207824,0.0425299002508617,0.051331708887973,0.0201215098740809,0.55698593700182,0.0398312026438027,1.09127935305809,0.118992799278581,0.0803033044412903,0.0793518066701965,0.131279019354813,0.126375133502943,-0.0185601722869176,-8.71378349720058e-06,0.0271128310038753,-0.009122468088741,-0.00253306565493079,-0.0305461355062964,0.0264923408147328,0.00393159246038647,-0.0378595860199216,-0.0157853955739557,-0.00913133477750619,0.0273668647623461,0.0224308368355069,-0.0118196551905426,0.225470575372724,0.0314194268390858,1.17482709358766,-0.00540304739516578,-0.0266439025227058,-0.0256452249653326,0.0143239364730441,-0.00730130726526849,0.000428449791337638,-0.00486344178064218,0.609023961392664,-0.0145571078592338,-0.0210523387897456,-0.00724156247078695,-0.0135193729095757,-0.0111792961664077,0.0184292668644498,0.0386342051689924,0.00261649381298134,-0.00163294445278257,-0.00893998738941109,0.00106315738492004,-0.00896535868394142,-0.00146208823129269,0.00216540688442676,0.0108780349358485,-0.00861869598633493,0.00667018508748933,0.0343330989079777,0.00867767441401599,0.0263750119222709,0.0410111385608857,0.180254817358435,0.174587406558154,0.145607087820237,0.282017156139185,0.242100747289861,0.000602124002337605,-0.0290112042809128,0.0731624406265792,0.019153034062197,0.0119682385627046,0.000737675293881955,-0.00898977015320202,0.00914093791747035,0.011301685418083,0.0116119518149611,0.0567270315276868,0.00496665745649664,0.0455115833806311,0.0132078423999311,0.0387336283628465,0.112046542202881,0.0577117729907123,0.0669730911573264,-0.00264466881907064,0.0110116949665542,0.00386943062818685,0.0222556359478574,0.017034499956686,-0.000476473189204625,0.0632612469986086,0.146602787794784,0.201993879482231,0.176326801715809,0.0480786630225501,-0.0139318728859204,-0.00978772292752036,0.0194557867261668,-0.0180855939661907,-0.00120199171568538,0.0149301362782767,0.0166755707753018,0.0199587752869293,0.0213092863966207,0.0777573302487907,0.0352245684039065,0.0294243842584631,0.0137182301710169,0.0456705687627938,0.0264573570794476,0.129888768601104,-0.0112362492187558,-0.0182767722743109,-0.00260564304989258,0.013393488382741,0.0189273795873035,0.0483968559238687,0.0453182759361849,0.0477591557404261,0.0353554536180685,0.0623578328892063,0.182609077190727,0.228878678975825,0.151452797535155,-0.00536681815390766,-0.0293134991441772,0.358216952994477,0.407556803266796,0.0272424641985551,0.036587530294336,-0.0300195907612634,0.397800713324752,-0.0308350665555495,-0.00087743560589776,-0.0275662722281154,-0.014340655767362,-0.0246751330314848,-0.0398854339778126,-0.0206540532266394,-0.0241684383497054,-0.0174742009981169,-0.00766671107877266,0.275637506982294,-0.0115017282884043,-0.00420348768234536,0.00982833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lipid biosynthetic process;0.00449241220621267;14712!GO:0016843;amine-lyase activity;0.00449241220621267;71881!GO:0016844;strictosidine synthase activity;0.00449241220621267;71881!GO:0016287;glycerone-phosphate O-acyltransferase activity;0.00449241220621267;14712!GO:0046485;ether lipid metabolic process;0.00449241220621267;14712!GO:0004075;biotin carboxylase activity;0.00842142699329734;107476!GO:0005782;peroxisomal matrix;0.00842142699329734;14712!GO:0003989;acetyl-CoA carboxylase activity;0.00842142699329734;107476!GO:0009374;biotin binding;0.00898187114488589;107476!GO:0016413;O-acetyltransferase activity;0.00898187114488589;14712!GO:0008610;lipid biosynthetic process;0.0105996946032502;14712,107476!GO:0016421;CoA carboxylase activity;0.0105996946032502;107476!GO:0016840;carbon-nitrogen lyase activity;0.0105996946032502;71881!GO:0016885;ligase activity, forming carbon-carbon bonds;0.0105996946032502;107476!GO:0046504;glycerol ether biosynthetic process;0.0105996946032502;14712!GO:0045017;glycerolipid biosynthetic process;0.0105996946032502;14712!GO:0009058;biosynthetic process;0.0105996946032502;14712,107476,71881!GO:0031903;microbody membrane;0.0200624266775967;14712!GO:0005778;peroxisomal membrane;0.0200624266775967;14712!GO:0044439;peroxisomal part;0.0202827699919549;14712!GO:0044438;microbody part;0.0202827699919549;14712!GO:0046486;glycerolipid metabolic process;0.0247882917154048;14712!GO:0006662;glycerol ether metabolic process;0.0247882917154048;14712!GO:0044255;cellular lipid metabolic process;0.0247882917154048;14712,107476!GO:0008374;O-acyltransferase activity;0.0268689504028476;14712!GO:0006629;lipid metabolic process;0.030024142586548;14712,107476!GO:0016407;acetyltransferase 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|ontology_enrichment_uberon=
|tfbs_overrepresentation_for_novel_motifs=0.138811,0.281131,0.388927,0.165951,1.28425,0.521151,0.240519,0.517797,0.298763,0.0803725,0.208344,0.231566,0.0278964,0.249744,0.910023,0,0.405853,0.0601435,0.470006,0.601422,1.12967,0.247808,0.249061,0.489432,0.798169,1.36729,0.721038,0.556066,0.289627,0.158048,0.532548,1.23631,0.0591615,0.945587,0.534808,0.475036,0.0551797,0.228897,0.701925,0.142999,0.834652,0.183887,1.3621,0.0723454,0.265696,0.479224,0.339166,0.201138,1.14619,0.612305,0.39102,0.291819,0.507638,0.621761,0.63782,0.709407,0.634897,0.222181,0.680997,0.253617,0.476165,0.299289,0.323654,0.381514,0.26368,0.41591,0.765078,1.10104,0.472057,0.958179,0.111851,0.291401,0.00332225,0.66884,0.0802546,0.18496,1.72503,0.878887,0.461106,0.339733,0.293881,0.420719,0.807577,0.0259741,0.563042,0.241331,0.434902,0.158281,0.343187,1.25993,1.94089,0.56755,0.505205,0.0663617,0.0448178,0.0383905,0.509793,0.507703,0.339375,0.259155,0.779402,0.493598,0.605777,1.01513,0.390631,0.183584,0.44182,0.198293,0.346967,0.102757,0.418563,1.47672,1.14987,0.608615,0.837889,0.828183,0.217615,0.168461,0.406964,0.0536296,0.673855,0.363969,0.272218,0.329142,0.889642,0.464341,0.246642,0.499188,0.763646,0.881568,0.590261,0.941762,0.735806,0.265613,0.858504,1.13687,0.144091,0.5435,0.811653,1.62404,1.22863,0.769526,0.281588,0.50313,0.385159,0.184199,0.341725,1.58469,0.145585,0.855605,0.546569,0.00215267,0.623204,0.647468,0.264901,0.698893,0.292614,0.266327,0.137279,0.143914,0.820693,0.562267,0.464731,0.415022,0.382373,0.259222,0.201311,0.230394,0.0282494
|tfbs_overrepresentation_jaspar=MA0003.1;0.210739,MA0004.1;0.166273,MA0006.1;0.0693118,MA0007.1;0.473814,MA0009.1;0.517357,MA0014.1;0.000608625,MA0017.1;0.991585,MA0019.1;0.359884,MA0024.1;0.47854,MA0025.1;0.731571,MA0027.1;2.12059,MA0028.1;0.258067,MA0029.1;0.459477,MA0030.1;0.465221,MA0031.1;0.434261,MA0038.1;0.745228,MA0040.1;0.528552,MA0041.1;0.118772,MA0042.1;0.11115,MA0043.1;0.604858,MA0046.1;0.549602,MA0048.1;0.126821,MA0050.1;0.562435,MA0051.1;0.277682,MA0052.1;0.535783,MA0055.1;0.163189,MA0056.1;0,MA0057.1;0.0072309,MA0058.1;0.348173,MA0059.1;0.73982,MA0060.1;0.0366148,MA0061.1;0.0476315,MA0063.1;0,MA0066.1;0.262291,MA0067.1;0.836675,MA0068.1;0.0077798,MA0069.1;0.536088,MA0070.1;0.52739,MA0071.1;1.06732,MA0072.1;1.29166,MA0073.1;0.00133951,MA0074.1;0.235223,MA0076.1;0.636542,MA0077.1;0.500504,MA0078.1;0.303693,MA0081.1;0.402057,MA0083.1;1.46984,MA0084.1;1.15371,MA0087.1;0.564877,MA0088.1;0.257644,MA0089.1;0,MA0090.1;0.144081,MA0091.1;0.175078,MA0092.1;0.871078,MA0093.1;0.269439,MA0095.1;0,MA0098.1;0,MA0100.1;0.643107,MA0101.1;0.119531,MA0103.1;0.0877522,MA0105.1;1.27717,MA0106.1;0.309901,MA0107.1;0.286884,MA0108.2;0.987584,MA0109.1;0,MA0111.1;0.465601,MA0113.1;0.287528,MA0114.1;1.08747,MA0115.1;0.60742,MA0116.1;0.243718,MA0117.1;0.577975,MA0119.1;0.381144,MA0122.1;0.596061,MA0124.1;0.786128,MA0125.1;0.716372,MA0130.1;0,MA0131.1;0.356119,MA0132.1;0,MA0133.1;0,MA0135.1;0.638323,MA0136.1;0.250125,MA0139.1;0.0266907,MA0140.1;0.226598,MA0141.1;0.665563,MA0142.1;0.421761,MA0143.1;0.300449,MA0144.1;0.71596,MA0145.1;0.0688972,MA0146.1;0.697456,MA0147.1;0.433894,MA0148.1;0.524837,MA0149.1;0.12279,MA0062.2;0.950195,MA0035.2;0.230058,MA0039.2;0.00326808,MA0138.2;0.349554,MA0002.2;1.61998,MA0137.2;0.319762,MA0104.2;0.561984,MA0047.2;0.270154,MA0112.2;0.287479,MA0065.2;1.62743,MA0150.1;0.156344,MA0151.1;0,MA0152.1;0.270237,MA0153.1;0.653688,MA0154.1;0.68796,MA0155.1;0.5414,MA0156.1;0.306246,MA0157.1;0.394402,MA0158.1;0,MA0159.1;0.208462,MA0160.1;1.60899,MA0161.1;0,MA0162.1;0.000212795,MA0163.1;0.169249,MA0164.1;1.29154,MA0080.2;0.288132,MA0018.2;0.257759,MA0099.2;0.344363,MA0079.2;8.58856e-08,MA0102.2;1.20505,MA0258.1;0.658099,MA0259.1;0.40921,MA0442.1;0
}}

Latest revision as of 15:12, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:25018083..25018119,-p@chr10:25018083..25018119
-
Mm9::chr10:25156813..25156838,+p@chr10:25156813..25156838
+
Mm9::chr11:78008044..78008065,+p3@Proca1
Mm9::chr11:83986974..83986996,+p5@Acaca
Mm9::chr13:37575274..37575296,+p@chr13:37575274..37575296
+
Mm9::chr15:84015494..84015535,-p@chr15:84015494..84015535
-
Mm9::chr17:10689280..10689294,+p3@ENSMUST00000161274
Mm9::chr17:10689300..10689307,+p4@ENSMUST00000161274
Mm9::chr19:3972322..3972345,+p4@Aldh3b2
Mm9::chr19:8915055..8915067,+p9@Bscl2
Mm9::chr2:150426133..150426149,-p4@2310001A20Rik
Mm9::chr2:150426151..150426199,-p2@2310001A20Rik
Mm9::chr2:26465321..26465332,+p@chr2:26465321..26465332
+
Mm9::chr3:97503099..97503129,-p@chr3:97503099..97503129
-
Mm9::chr6:115312361..115312378,+p@chr6:115312361..115312378
+
Mm9::chr8:127387001..127387014,+p3@Gnpat
Mm9::chr8:127387091..127387127,+p2@Gnpat
Mm9::chr8:18606895..18606902,+p@chr8:18606895..18606902
+
Mm9::chr9:65248675..65248686,+p@chr9:65248675..65248686
+
Mm9::chr9:65248704..65248719,+p@chr9:65248704..65248719
+


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:0008611ether lipid biosynthetic process0.00449241220621267
GO:0016843amine-lyase activity0.00449241220621267
GO:0016844strictosidine synthase activity0.00449241220621267
GO:0016287glycerone-phosphate O-acyltransferase activity0.00449241220621267
GO:0046485ether lipid metabolic process0.00449241220621267
GO:0004075biotin carboxylase activity0.00842142699329734
GO:0005782peroxisomal matrix0.00842142699329734
GO:0003989acetyl-CoA carboxylase activity0.00842142699329734
GO:0009374biotin binding0.00898187114488589
GO:0016413O-acetyltransferase activity0.00898187114488589
GO:0008610lipid biosynthetic process0.0105996946032502
GO:0016421CoA carboxylase activity0.0105996946032502
GO:0016840carbon-nitrogen lyase activity0.0105996946032502
GO:0016885ligase activity, forming carbon-carbon bonds0.0105996946032502
GO:0046504glycerol ether biosynthetic process0.0105996946032502
GO:0045017glycerolipid biosynthetic process0.0105996946032502
GO:0009058biosynthetic process0.0105996946032502
GO:0031903microbody membrane0.0200624266775967
GO:0005778peroxisomal membrane0.0200624266775967
GO:0044439peroxisomal part0.0202827699919549
GO:0044438microbody part0.0202827699919549
GO:0046486glycerolipid metabolic process0.0247882917154048
GO:0006662glycerol ether metabolic process0.0247882917154048
GO:0044255cellular lipid metabolic process0.0247882917154048
GO:0008374O-acyltransferase activity0.0268689504028476
GO:0006629lipid metabolic process0.030024142586548
GO:0016407acetyltransferase activity0.0471297987841342



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><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)
MA0003.10.210739
MA0004.10.166273
MA0006.10.0693118
MA0007.10.473814
MA0009.10.517357
MA0014.10.000608625
MA0017.10.991585
MA0019.10.359884
MA0024.10.47854
MA0025.10.731571
MA0027.12.12059
MA0028.10.258067
MA0029.10.459477
MA0030.10.465221
MA0031.10.434261
MA0038.10.745228
MA0040.10.528552
MA0041.10.118772
MA0042.10.11115
MA0043.10.604858
MA0046.10.549602
MA0048.10.126821
MA0050.10.562435
MA0051.10.277682
MA0052.10.535783
MA0055.10.163189
MA0056.10
MA0057.10.0072309
MA0058.10.348173
MA0059.10.73982
MA0060.10.0366148
MA0061.10.0476315
MA0063.10
MA0066.10.262291
MA0067.10.836675
MA0068.10.0077798
MA0069.10.536088
MA0070.10.52739
MA0071.11.06732
MA0072.11.29166
MA0073.10.00133951
MA0074.10.235223
MA0076.10.636542
MA0077.10.500504
MA0078.10.303693
MA0081.10.402057
MA0083.11.46984
MA0084.11.15371
MA0087.10.564877
MA0088.10.257644
MA0089.10
MA0090.10.144081
MA0091.10.175078
MA0092.10.871078
MA0093.10.269439
MA0095.10
MA0098.10
MA0100.10.643107
MA0101.10.119531
MA0103.10.0877522
MA0105.11.27717
MA0106.10.309901
MA0107.10.286884
MA0108.20.987584
MA0109.10
MA0111.10.465601
MA0113.10.287528
MA0114.11.08747
MA0115.10.60742
MA0116.10.243718
MA0117.10.577975
MA0119.10.381144
MA0122.10.596061
MA0124.10.786128
MA0125.10.716372
MA0130.10
MA0131.10.356119
MA0132.10
MA0133.10
MA0135.10.638323
MA0136.10.250125
MA0139.10.0266907
MA0140.10.226598
MA0141.10.665563
MA0142.10.421761
MA0143.10.300449
MA0144.10.71596
MA0145.10.0688972
MA0146.10.697456
MA0147.10.433894
MA0148.10.524837
MA0149.10.12279
MA0062.20.950195
MA0035.20.230058
MA0039.20.00326808
MA0138.20.349554
MA0002.21.61998
MA0137.20.319762
MA0104.20.561984
MA0047.20.270154
MA0112.20.287479
MA0065.21.62743
MA0150.10.156344
MA0151.10
MA0152.10.270237
MA0153.10.653688
MA0154.10.68796
MA0155.10.5414
MA0156.10.306246
MA0157.10.394402
MA0158.10
MA0159.10.208462
MA0160.11.60899
MA0161.10
MA0162.10.000212795
MA0163.10.169249
MA0164.11.29154
MA0080.20.288132
MA0018.20.257759
MA0099.20.344363
MA0079.28.58856e-08
MA0102.21.20505
MA0258.10.658099
MA0259.10.40921
MA0442.10
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