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MCL coexpression mm9:307: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9|coexpression_dpi_cluster_scores_mean=-0.0101983267681984,0.113123663834835,0.163059802126933,0.141932453041888,0.156903938289338,0.0711526359658242,0.0406902673902325,-0.0490687390070629,-0.0801284152067659,-0.0751900412744649,-0.0856750966601278,-0.0743237028315169,-0.043554302347487,-0.0525189686121226,-0.0585391278961279,-0.0560697350278539,-0.061730735568492,-0.049194508862299,-0.0585527902418529,-0.0762918699192337,0.652042745384369,-0.0142695557561331,-0.00356882616650696,0.120768156988619,0.115368878332657,0.133229238684521,0.117075429170466,0.123237835277076,0.0873950438384803,0.0708964239346404,0.0252379482390246,-0.0243040319525333,-0.0366137640388468,-0.0875643446051177,0.0767638965983776,0.0716749243389868,0.0734186915157111,0.0077745208806533,0.0123019560238881,0.0163547460981689,0.0130720491356651,0.0272939799364953,0.0133829586305188,0.00114153739817245,0.00265887347288704,0.0249608611814166,0.0243324271296325,-0.0057914349320966,0.0087544868431216,0.0367505424266524,0.00362996781277136,-0.0153077435815578,-0.0735999404317017,-0.0697368704301822,-0.0593554657500406,-0.00365201193504438,0.00482909184980954,-0.00109074447657704,-0.0613515218691094,-0.0634298195835995,-0.0770242813334371,-0.036607131929252,-0.0398525378830164,-0.0262454738233747,-0.046184618962926,-0.0241518650691992,-0.0193336868466468,0.0134351233994571,-0.0746318532880196,-0.06801019402931,-0.0664821385903839,-0.023284156424808,-0.0102437141266998,-0.0661799552990188,-0.0684727608776788,-0.0612751215418875,-0.0692166976622555,0.0123073227754634,-0.00550372656980392,-0.0818068017005417,-0.0692746949590677,-0.0726518841268214,0.00712173051359271,-0.00223357278521052,0.0162791253067482,-0.0174354923674793,-0.0244686022280763,-0.0630237806936083,-0.0437504893095461,-0.00713647441661004,0.0930684652853074,1.11793762360426,0.978292103028542,1.27781880952816,1.3114076569278,1.31550953633187,0.90434867798195,0.0412424705878547,0.0040819474866214,0.00464331327138213,0.00376375194621283,-0.0299789434533966,-0.0175111696698516,0.00375035273554271,0.0045829635962368,-0.0226844309998027,0.0023998108367436,0.986000293057483,0.010905947883797,0.0905887691605531,-0.00938152119082012,0.00626999202022517,0.0262534794811742,0.0192030259126311,0.0332603978701845,0.126599496813877,0.14644534696436,0.192930117843829,-0.00431041937483006,0.0105447826159312,0.0629082250901257,0.0024631806417955,0.0373264375807595,0.0285135508292688,-0.00518151597033061,0.0987503833453748,-0.0287834506803815,0.00290646949361316,-0.0288906720346513,0.0111525953444664,-0.00643491967826852,-0.0794581789662473,0.00163476521714725,-0.00422564578929424,0.026437762715338,0.00342701530431572,0.0256719215019161,0.0959860106775526,0.235046335570446,0.105909631779107,-0.0123284136830741,-0.0211261667232025,-0.0017553779720505,0.0189197704304422,-0.0222232340842152,-0.00524869930694696,-0.0218372938324546,0.0720476166892111,-0.0185883725021753,-0.01641763431688,-0.0220278786210958,-0.0252633216360045,-0.024695211644684,-0.0215466047948163,-0.00190854771337336,0.0187071076459046,-0.0124051657964797,0.00232903799940732,-0.000224945453024907,0.0252590992428812,0.027996271624328,0.0141383478807441,0.0195040830846012,0.0336344143292902,0.037691692267245,0.0215386937728627,0.0303571319040361,0.0596271999004726,0.0502348548604918,0.0924535394093758,0.128505452130311,0.153961447711509,0.132600971611625,0.138628344061304,-0.00767168292076387,-0.0552931679285549,0.198182596945802,0.11515448988983,-0.0122094797081197,-0.0182825216633785,0.041010392736189,0.131430083806444,0.154603131308182,0.213844914342216,0.124947272757545,0.168909163158238,0.191782941222884,0.175613801137303,0.168499420437417,0.113826389567538,0.115214337479399,0.151644184596938,0.0573396179872509,0.128778585941408,0.362190233065046,0.431074547530753,0.562098889967514,0.609689382713853,0.871791353149531,1.21599976375347,1.311914779065,1.28835346088318,1.21293049515639,0.0276779978193825,0.0495582135760702,0.117210840322535,0.146500554287441,0.24700799475873,0.271863297050745,0.37827500392018,0.360278004298793,0.5986693215815,0.77081024035363,0.801256303926869,0.858864604193266,1.02037167006575,1.15731636201719,1.0684062846629,0.0426477549403426,-0.0126731534303162,0.0104386986618012,-0.00815997774219346,0.0144147100892889,0.0231964017966774,0.0199713937078955,0.0142922879991157,0.0198008431711449,0.0128775666193348,0.0193492035235291,0.0244955641564197,0.0395874926695423,0.0340230337344928,-0.0396366617969746,-0.0264452893475618,0.0742558480372032,0.0288559049254194,0.0494009508451351,0.0165645796017854,-0.0294363862761165,0.140011447789664,0.0113968475355343,-0.0164818938851475,-0.0235119990282554,-0.0107780501923583,-0.00964358914017372,-0.0263715499026208,-0.00140356160775488,-0.0215637241759339,0.00185781979017815,-0.00241192592941624,0.0635819071728851,0.0220413313643927,0.00780836146281027,0.012827082636797,0.0202712397011832,-0.003098894164983,-0.00880718360767576,0.0165650930245109,0.03056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activity;0.0316660275023284;15233,76187,110265,13109,216454!GO:0016740;transferase activity;0.0316660275023284;102448,16150,14858,64697,22017,192136,223337!GO:0050093;methanol dehydrogenase activity;0.0316660275023284;76187!GO:0004411;homogentisate 1,2-dioxygenase activity;0.0316660275023284;15233!GO:0008119;thiopurine S-methyltransferase activity;0.0316660275023284;22017!GO:0004856;xylulokinase activity;0.0316660275023284;102448!GO:0008113;peptide-methionine-(S)-S-oxide reductase activity;0.0474574142287016;110265!GO:0005506;iron ion binding;0.0474574142287016;15233,76187,13109!GO:0047961;glycine N-acyltransferase activity;0.0474574142287016;64697!GO:0007252;I-kappaB phosphorylation;0.0474574142287016;16150!GO:0008384;IkappaB kinase activity;0.0474574142287016;16150!GO:0042732;D-xylose metabolic 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|gostat_on_MCL_coexpression=GO:0016491;oxidoreductase activity;0.0316660275023284;15233,76187,110265,13109,216454!GO:0016740;transferase activity;0.0316660275023284;102448,16150,14858,64697,22017,192136,223337!GO:0050093;methanol dehydrogenase activity;0.0316660275023284;76187!GO:0004411;homogentisate 1,2-dioxygenase activity;0.0316660275023284;15233!GO:0008119;thiopurine S-methyltransferase activity;0.0316660275023284;22017!GO:0004856;xylulokinase activity;0.0316660275023284;102448!GO:0008113;peptide-methionine-(S)-S-oxide reductase activity;0.0474574142287016;110265!GO:0005506;iron ion binding;0.0474574142287016;15233,76187,13109!GO:0047961;glycine N-acyltransferase activity;0.0474574142287016;64697!GO:0007252;I-kappaB phosphorylation;0.0474574142287016;16150!GO:0008384;IkappaB kinase activity;0.0474574142287016;16150!GO:0042732;D-xylose metabolic process;0.0474574142287016;102448!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005172!2.68e-19!49;UBERON:0005173!2.68e-19!49;UBERON:0002417!2.68e-19!49;UBERON:0000916!2.68e-19!49;UBERON:0002107!1.25e-18!22;UBERON:0007499!1.25e-18!22;UBERON:0006925!1.25e-18!22;UBERON:0009497!1.25e-18!22;UBERON:0000015!1.25e-18!22;UBERON:0002423!1.25e-18!22;UBERON:0006235!1.25e-18!22;UBERON:0008835!1.25e-18!22;UBERON:0003894!1.25e-18!22;UBERON:0004161!1.25e-18!22;UBERON:0008836!1.25e-18!22;UBERON:0009854!1.61e-17!23;UBERON:0009856!1.61e-17!23;UBERON:0002365!1.41e-15!25;UBERON:0002330!1.41e-15!25;UBERON:0003104!2.98e-14!61;UBERON:0009142!2.98e-14!61;UBERON:0009569!1.35e-11!66;UBERON:0003914!2.15e-09!47;UBERON:0005256!4.00e-09!45;UBERON:0002113!4.68e-09!14;UBERON:0003918!4.68e-09!14;UBERON:0011143!4.68e-09!14;UBERON:0005095!4.68e-09!14;UBERON:0007687!4.68e-09!14;UBERON:0005177!4.32e-08!79
|tfbs_overrepresentation_for_novel_motifs=0.621914,0.939777,0.560725,0.723709,0.319585,0.378043,0.515388,0.311893,0.169209,0.116705,0.145866,0.496525,0.0119064,0.181267,0.35264,0,0.859737,0.0315235,0.473812,0.505759,0.477574,0.898706,0.180675,0.577208,0.274696,0.579011,0.123116,1.31807,0.411918,0.487905,0.122529,0.403236,0.0308777,0.859556,0.635392,1.51528,0.028285,0.490894,1.48987,0.378664,0.132316,0.395563,1.04718,0.640187,0.335833,0.104823,0.260475,0.432194,0.461946,0.418159,0.307679,0.218134,0.458035,0.524674,0.540069,0.185973,0.197567,0.157588,0.412631,1.03741,0.386651,0.224758,0.187517,0.298968,0.564065,0.330595,0.662968,0.992392,0.382806,0.851665,0.517607,0.16386,0.0215499,0.569888,0.390163,0.815322,0.593339,0.252107,0.372571,1.7719,0.33001,0.33504,0.223742,0.295929,0.468641,0.148278,0.00317853,0.302729,0.264106,1.14963,0.72731,0.472928,1.06401,0.600223,0.0949249,0.0808213,0.789568,0.416272,0.260664,0.0165281,0.117729,0.403003,0.509378,0.308141,0.828295,0.394918,0.354606,0.841739,1.29373,0.221421,0.605231,0.510939,0.225717,0.149001,0.733862,0.130578,0.0814819,1.20371,0.322341,0.27556,0.574718,0.282956,0.20086,0.251444,0.784453,0.375593,0.528274,0.408257,0.661578,0.0365982,1.23783,0.705817,1.53364,0.195077,0.753996,0.883015,0.310556,0.126256,0.708276,1.51166,1.11861,0.667289,0.60159,0.411967,0.302305,0.125712,0.726958,1.47245,0.647594,0.323022,0.076247,0.0140779,0.526055,1.0037,0.194455,0.598868,0.218838,0.0430997,0.0878751,0.0931012,0.717087,0.467905,0.980978,0.599911,0.811218,0.1895,0.116624,0.1646,0.588393
|tfbs_overrepresentation_jaspar=MA0003.1;0.410361,MA0004.1;0.724898,MA0006.1;0.62004,MA0007.1;0.688271,MA0009.1;0.425374,MA0014.1;0.316742,MA0017.1;1.08641,MA0019.1;0.764645,MA0024.1;0.388875,MA0025.1;0.630472,MA0027.1;2.00714,MA0028.1;0.364782,MA0029.1;0.371051,MA0030.1;0.376415,MA0031.1;0.918306,MA0038.1;0.199569,MA0040.1;1.11181,MA0041.1;0.256066,MA0042.1;0.514842,MA0043.1;0.5085,MA0046.1;7.69685,MA0048.1;0.242961,MA0050.1;0.132769,MA0051.1;0.205659,MA0052.1;0.442788,MA0055.1;0.101897,MA0056.1;0,MA0057.1;0.108538,MA0058.1;0.858935,MA0059.1;0.527296,MA0060.1;0.3841,MA0061.1;0.755956,MA0063.1;0,MA0066.1;0.192176,MA0067.1;0.732677,MA0068.1;1.38289,MA0069.1;0.443076,MA0070.1;0.434849,MA0071.1;0.81947,MA0072.1;1.09391,MA0073.1;0.0392123,MA0074.1;0.504232,MA0076.1;0.438642,MA0077.1;0.409496,MA0078.1;0.228674,MA0081.1;0.0806296,MA0083.1;0.507806,MA0084.1;1.04444,MA0087.1;0.470385,MA0088.1;0.113219,MA0089.1;0,MA0090.1;0.310535,MA0091.1;0.118208,MA0092.1;1.07169,MA0093.1;0.679147,MA0095.1;0,MA0098.1;0,MA0100.1;0.486222,MA0101.1;0.0741335,MA0103.1;0.739353,MA0105.1;0.0937205,MA0106.1;0.234207,MA0107.1;0.407817,MA0108.2;0.296634,MA0109.1;0,MA0111.1;0.675922,MA0113.1;0.614015,MA0114.1;2.44998,MA0115.1;0.51095,MA0116.1;0.14839,MA0117.1;1.21278,MA0119.1;0.933065,MA0122.1;1.24966,MA0124.1;0.683426,MA0125.1;0.615761,MA0130.1;0,MA0131.1;0.27582,MA0132.1;0,MA0133.1;0,MA0135.1;0.540552,MA0136.1;0.181597,MA0139.1;0.513965,MA0140.1;0.161354,MA0141.1;0.463338,MA0142.1;0.336004,MA0143.1;0.22579,MA0144.1;0.470408,MA0145.1;0.763719,MA0146.1;0.923333,MA0147.1;0.506337,MA0148.1;0.381264,MA0149.1;0.0766295,MA0062.2;0.0999405,MA0035.2;0.164312,MA0039.2;1.03284,MA0138.2;0.269868,MA0002.2;0.153717,MA0137.2;0.794546,MA0104.2;0.346318,MA0047.2;0.199051,MA0112.2;1.01252,MA0065.2;0.766847,MA0150.1;0.687997,MA0151.1;0,MA0152.1;0.577815,MA0153.1;2.34269,MA0154.1;0.59291,MA0155.1;0.0821086,MA0156.1;0.197316,MA0157.1;0.836088,MA0158.1;0,MA0159.1;0.29096,MA0160.1;1.26102,MA0161.1;0,MA0162.1;0.112743,MA0163.1;0.623765,MA0164.1;0.181834,MA0080.2;0.182919,MA0018.2;0.551637,MA0099.2;0.732438,MA0079.2;0.289919,MA0102.2;1.09525,MA0258.1;1.40467,MA0259.1;0.47498,MA0442.1;0
}}

Latest revision as of 15:04, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:127303554..127303563,+p4@BC089597
Mm9::chr10:39744983..39745000,-p4@AI317395
Mm9::chr10:39745012..39745024,-p3@AI317395
Mm9::chr11:113570266..113570286,-p2@Cpsf4l
Mm9::chr13:17786563..17786620,-p1@5033411D12Rik
Mm9::chr13:23931270..23931311,+p2@Slc17a3
Mm9::chr13:34129460..34129474,+p2@Bphl
Mm9::chr13:47138485..47138555,-p1@Tpmt
Mm9::chr14:56194642..56194689,+p@chr14:56194642..56194689
+
Mm9::chr14:56194692..56194703,+p@chr14:56194692..56194703
+
Mm9::chr14:65059685..65059700,-p2@Msra
Mm9::chr15:9265320..9265378,+p1@Ugt3a2
Mm9::chr16:37580223..37580237,+p4@Hgd
Mm9::chr19:12770273..12770299,+p1@Keg1
Mm9::chr1:13650535..13650550,-p2@Lactb2
Mm9::chr1:13650557..13650635,-p1@Lactb2
Mm9::chr1:9538195..9538206,+p2@Adhfe1
Mm9::chr4:96330803..96330853,-p1@Cyp2j5
Mm9::chr6:3938967..3938987,-p@chr6:3938967..3938987
-
Mm9::chr7:126669716..126669732,+p3@Acsm5
Mm9::chr8:129965075..129965087,-p@chr8:129965075..129965087
-
Mm9::chr8:129965091..129965127,-p@chr8:129965091..129965127
-
Mm9::chr8:23804533..23804553,-p2@Ikbkb
Mm9::chr9:119266661..119266682,+p2@Xylb
Mm9::chr9:65478877..65478895,+p@chr9:65478877..65478895
+
Mm9::chr9:78194969..78194997,-p2@Gsta2


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:0016491oxidoreductase activity0.0316660275023284
GO:0016740transferase activity0.0316660275023284
GO:0050093methanol dehydrogenase activity0.0316660275023284
GO:0004411homogentisate 1,2-dioxygenase activity0.0316660275023284
GO:0008119thiopurine S-methyltransferase activity0.0316660275023284
GO:0004856xylulokinase activity0.0316660275023284
GO:0008113peptide-methionine-(S)-S-oxide reductase activity0.0474574142287016
GO:0005506iron ion binding0.0474574142287016
GO:0047961glycine N-acyltransferase activity0.0474574142287016
GO:0007252I-kappaB phosphorylation0.0474574142287016
GO:0008384IkappaB kinase activity0.0474574142287016
GO:0042732D-xylose metabolic process0.0474574142287016



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
abdomen element2.68e-1949
abdominal segment element2.68e-1949
abdominal segment of trunk2.68e-1949
abdomen2.68e-1949
liver1.25e-1822
epithelial sac1.25e-1822
digestive gland1.25e-1822
epithelium of foregut-midgut junction1.25e-1822
anatomical boundary1.25e-1822
hepatobiliary system1.25e-1822
foregut-midgut junction1.25e-1822
hepatic diverticulum1.25e-1822
liver primordium1.25e-1822
septum transversum1.25e-1822
liver bud1.25e-1822
digestive tract diverticulum1.61e-1723
sac1.61e-1723
exocrine gland1.41e-1525
exocrine system1.41e-1525
mesenchyme2.98e-1461
entire embryonic mesenchyme2.98e-1461
subdivision of trunk1.35e-1166
epithelial tube2.15e-0947
trunk mesenchyme4.00e-0945
kidney4.68e-0914
kidney mesenchyme4.68e-0914
upper urinary tract4.68e-0914
kidney rudiment4.68e-0914
kidney field4.68e-0914
trunk region element4.32e-0879


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)
MA0003.10.410361
MA0004.10.724898
MA0006.10.62004
MA0007.10.688271
MA0009.10.425374
MA0014.10.316742
MA0017.11.08641
MA0019.10.764645
MA0024.10.388875
MA0025.10.630472
MA0027.12.00714
MA0028.10.364782
MA0029.10.371051
MA0030.10.376415
MA0031.10.918306
MA0038.10.199569
MA0040.11.11181
MA0041.10.256066
MA0042.10.514842
MA0043.10.5085
MA0046.17.69685
MA0048.10.242961
MA0050.10.132769
MA0051.10.205659
MA0052.10.442788
MA0055.10.101897
MA0056.10
MA0057.10.108538
MA0058.10.858935
MA0059.10.527296
MA0060.10.3841
MA0061.10.755956
MA0063.10
MA0066.10.192176
MA0067.10.732677
MA0068.11.38289
MA0069.10.443076
MA0070.10.434849
MA0071.10.81947
MA0072.11.09391
MA0073.10.0392123
MA0074.10.504232
MA0076.10.438642
MA0077.10.409496
MA0078.10.228674
MA0081.10.0806296
MA0083.10.507806
MA0084.11.04444
MA0087.10.470385
MA0088.10.113219
MA0089.10
MA0090.10.310535
MA0091.10.118208
MA0092.11.07169
MA0093.10.679147
MA0095.10
MA0098.10
MA0100.10.486222
MA0101.10.0741335
MA0103.10.739353
MA0105.10.0937205
MA0106.10.234207
MA0107.10.407817
MA0108.20.296634
MA0109.10
MA0111.10.675922
MA0113.10.614015
MA0114.12.44998
MA0115.10.51095
MA0116.10.14839
MA0117.11.21278
MA0119.10.933065
MA0122.11.24966
MA0124.10.683426
MA0125.10.615761
MA0130.10
MA0131.10.27582
MA0132.10
MA0133.10
MA0135.10.540552
MA0136.10.181597
MA0139.10.513965
MA0140.10.161354
MA0141.10.463338
MA0142.10.336004
MA0143.10.22579
MA0144.10.470408
MA0145.10.763719
MA0146.10.923333
MA0147.10.506337
MA0148.10.381264
MA0149.10.0766295
MA0062.20.0999405
MA0035.20.164312
MA0039.21.03284
MA0138.20.269868
MA0002.20.153717
MA0137.20.794546
MA0104.20.346318
MA0047.20.199051
MA0112.21.01252
MA0065.20.766847
MA0150.10.687997
MA0151.10
MA0152.10.577815
MA0153.12.34269
MA0154.10.59291
MA0155.10.0821086
MA0156.10.197316
MA0157.10.836088
MA0158.10
MA0159.10.29096
MA0160.11.26102
MA0161.10
MA0162.10.112743
MA0163.10.623765
MA0164.10.181834
MA0080.20.182919
MA0018.20.551637
MA0099.20.732438
MA0079.20.289919
MA0102.21.09525
MA0258.11.40467
MA0259.10.47498
MA0442.10
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