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MCL coexpression mm9:454: Difference between revisions

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{{MCL_coexpression_mm9
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I complex;0.009203966471265;17913!GO:0016461;unconventional myosin complex;0.0138051932993965;17913!GO:0032420;stereocilium;0.0230042431219055;17913!GO:0032421;stereocilium bundle;0.0230042431219055;17913!GO:0008022;protein C-terminus binding;0.0239224461872794;17913!GO:0005902;microvillus;0.0260664748441257;17913!GO:0005903;brush border;0.0275967712637765;17913!GO:0007623;circadian rhythm;0.0306555151069646;246691!GO:0045765;regulation of angiogenesis;0.0306555151069646;246691!GO:0000187;activation of MAPK activity;0.0331025101815151;246691!GO:0043406;positive regulation of MAP kinase activity;0.0342681020504265;246691!GO:0016459;myosin complex;0.0424111867249851;17913!GO:0043405;regulation of MAP kinase activity;0.0424111867249851;246691!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0002107!6.21e-22!22;UBERON:0007499!6.21e-22!22;UBERON:0006925!6.21e-22!22;UBERON:0009497!6.21e-22!22;UBERON:0000015!6.21e-22!22;UBERON:0002423!6.21e-22!22;UBERON:0006235!6.21e-22!22;UBERON:0008835!6.21e-22!22;UBERON:0003894!6.21e-22!22;UBERON:0004161!6.21e-22!22;UBERON:0008836!6.21e-22!22;UBERON:0009854!7.81e-21!23;UBERON:0009856!7.81e-21!23;UBERON:0002365!6.71e-19!25;UBERON:0002330!6.71e-19!25;UBERON:0005256!4.76e-09!45;UBERON:0003914!1.57e-08!47;UBERON:0005172!4.71e-08!49;UBERON:0005173!4.71e-08!49;UBERON:0002417!4.71e-08!49;UBERON:0000916!4.71e-08!49;UBERON:0003929!7.74e-07!55|tfbs_overrepresentation_for_novel_motifs=0.19013,0.0414522,0.171413,0.630846,0.325044,0.232532,0.305009,0.416085,0.439801,0.0241551,0.26934,0.295134,0.0498401,0.315149,1.17512,0,0.482714,0.645746,0.379612,0.359873,0.146132,0.242916,0.3144,0.663197,0.176763,0.338177,0.156743,0.694761,0.126301,0.490013,0.237846,0.574932,0.0927567,0.314034,0.108791,0.0161089,0.0875334,0.292182,0.262298,0.0613737,0.656409,0.241862,2.36871,0.71889,0.118148,0.213039,0.41191,0.723497,1.0034,0.128181,0.467043,0.360991,1.50697,0.7073,0.723811,0.321095,0.417292,0.284741,0.145788,0.319396,0.556492,0.369066,0.215066,0.456979,0.330403,0.493315,0.854035,1.19441,0.552202,1.05011,0.158281,0.19416,0.453542,0.755651,0.0343898,0.0305002,0.0329844,1.03797,0.540754,0.148967,0.433876,0.498379,1.71362,0.0470048,0.646739,0.00962,0.0019315,0.107772,0.416206,1.35441,0.92132,0.6514,0.586758,0.102076,1.39003,0.231057,0.183077,0.589355,0.412133,0.681961,0.0875773,0.574674,0.690844,0.467576,1.17798,0.241519,0.52055,0.25809,2.08444,0.147333,0.185018,0.692526,0.457145,0.273484,0.928143,0.315992,0.00275197,0.224335,0.483885,0.604422,0.760792,0.438354,0.900811,0.40118,0.980682,0.544138,0.311744,0.580495,0.852575,0.339019,0.67485,0.617809,0.824167,0.332514,0.949083,0.0397143,1.08375,0.24296,0.901468,1.71991,1.32292,0.85857,0.349901,0.584599,0.46084,0.242215,0.414644,1.68046,0.575158,0.0996378,0.110319,0.212292,0.708784,0.23951,0.331737,0.786435,0.361851,0.115836,0.551917,0.196072,0.910663,0.645939,0.544546,0.183389,0.457889,0.869172,0.293289,0.797827,0.0128525|tfbs_overrepresentation_jaspar=MA0003.1;0.0116141,MA0004.1;0.221835,MA0006.1;0.105852,MA0007.1;0.210531,MA0009.1;0.599391,MA0014.1;0.0122179,MA0017.1;0.774877,MA0019.1;0.434009,MA0024.1;0.558971,MA0025.1;0.819843,MA0027.1;2.21717,MA0028.1;0.112137,MA0029.1;0.53905,MA0030.1;4.57127,MA0031.1;3.24836,MA0038.1;0.33811,MA0040.1;0.611015,MA0041.1;0.964068,MA0042.1;0.926457,MA0043.1;0.689898,MA0046.1;2.59352,MA0048.1;0.0196258,MA0050.1;1.29684,MA0051.1;0.345658,MA0052.1;0.618515,MA0055.1;0.0964477,MA0056.1;0,MA0057.1;0.195768,MA0058.1;0.152805,MA0059.1;0.48573,MA0060.1;0.485984,MA0061.1;0.0774738,MA0063.1;0,MA0066.1;0.328887,MA0067.1;0.92691,MA0068.1;2.22212,MA0069.1;0.618831,MA0070.1;0.609808,MA0071.1;2.79721,MA0072.1;1.46522,MA0073.1;0.00527479,MA0074.1;0.8099,MA0076.1;0.134359,MA0077.1;0.581866,MA0078.1;0.37382,MA0081.1;0.177433,MA0083.1;0.68915,MA0084.1;1.24749,MA0087.1;0.648637,MA0088.1;0.251567,MA0089.1;0,MA0090.1;1.08371,MA0091.1;0.231874,MA0092.1;0.196497,MA0093.1;0.11723,MA0095.1;0,MA0098.1;0,MA0100.1;0.289731,MA0101.1;0.167439,MA0103.1;0.128989,MA0105.1;0.128193,MA0106.1;0.380511,MA0107.1;0.125067,MA0108.2;0.454274,MA0109.1;0,MA0111.1;0.206727,MA0113.1;0.356344,MA0114.1;0.263654,MA0115.1;0.692537,MA0116.1;0.344035,MA0117.1;0.662171,MA0119.1;0.502046,MA0122.1;0.680832,MA0124.1;0.875485,MA0125.1;0.804312,MA0130.1;0,MA0131.1;0.43,MA0132.1;0,MA0133.1;0,MA0135.1;1.72047,MA0136.1;0.315568,MA0139.1;0.0480655,MA0140.1;0.289637,MA0141.1;2.68809,MA0142.1;0.499475,MA0143.1;0.37032,MA0144.1;0.95924,MA0145.1;0.277688,MA0146.1;0.000633445,MA0147.1;0.286569,MA0148.1;8.58674,MA0149.1;0.171305,MA0062.2;0.0332891,MA0035.2;0.293466,MA0039.2;0.000979253,MA0138.2;0.423003,MA0002.2;0.728364,MA0137.2;0.432446,MA0104.2;0.0556953,MA0047.2;5.40956,MA0112.2;0.47728,MA0065.2;0.136177,MA0150.1;0.210447,MA0151.1;0,MA0152.1;0.337555,MA0153.1;1.75314,MA0154.1;0.0850581,MA0155.1;0.16166,MA0156.1;0.133796,MA0157.1;3.05876,MA0158.1;0,MA0159.1;0.0900717,MA0160.1;0.666246,MA0161.1;0,MA0162.1;0.00698895,MA0163.1;0.0215627,MA0164.1;0.315868,MA0080.2;0.396013,MA0018.2;0.323932,MA0099.2;0.417463,MA0079.2;4.69272e-05,MA0102.2;1.29919,MA0258.1;0.522754,MA0259.1;0.270549,MA0442.1;0}}
|coexpression_dpi_cluster_scores_mean=0.0115740986006597,0.0081252520238845,0.0101789228932298,0.0247003687405807,0.0110219076272184,0,0,0.00623536135712834,0,0,0,0,0,0,0,0,0,0,0,0,0.0372710753378099,0,0,0,0.00560603046105439,0.012316795394733,0.0168667898756469,0,0.00874336416530094,0.00610092376107201,0,0,0,0,0.00688768260454006,0.00779107554209925,0,0,0,0,0,0.0141309908194758,0,0,0,0,0.0156876915298209,0,0.00539050649512317,0.00482254163441899,0.0067000472166895,0.0241843245830836,0,0,0,0,0,0,0.00500117456590571,0.0115253076983119,0,0,0,0,0,0,0,0.00882528676151894,0,0,0.00518137438311073,0.00682019291818925,0.00541680644265801,0.00313642436770832,0,0,0,0.0097853820205215,0.00387860668349671,0.00904870487061325,0.0084646865692015,0.0113815298657951,0.00668329242374756,0,0.0115787451919086,0,0,0,0,0,0.00690900539658912,0.182285899980667,0.137295020023835,0.295962252377592,0.254295175729391,0.176108241147414,0.115496649301278,0,0,0,0,0,0,0,0,0,0,0.103492960524526,0,0.00375681996318749,0.00434235397251422,0,0.0271928759532352,0.0210883381232329,0.0229873796418868,0.0151095889171715,0.0494367800648696,0.0323759102616277,0,0,0,0.0107306230860421,0.0707264282650601,0,0.00516167102011915,0.0440227114026313,0,0,0,0,0,0.0032128159250339,0,0,0.0248065873354863,0.00408101813371937,0.00526478546708814,0.00954816174264315,0.0403939965227854,0,0.00332029568931945,0,0,0.0287066662735151,0.00178663090969042,0,0.00243118105718249,0.0062452122009643,0,0.00470128748518357,0.00439932947594467,0.00537958961434472,0,0,0.0101586056911953,0.0208231919017539,0.0144383719212608,0.0112703390793867,0,0,0,0,0,0.00487553754699696,0.0103240843190434,0.00567493055336004,0.00645080527485319,0.00299762047610559,0,0.0041259660964128,0.00802478654299069,0,0.00538747822455579,0.00341825629618836,0,0.0112672431746291,0.0325132783598014,0.0337466704242478,0,0.0313556257343931,0.030185197565756,0.018928376468211,0.0352831103293948,0.0439848832513401,0.0573097658692754,0.0436059229347696,0.0872889952993454,0.0753845886316103,0.0702541119943627,0.0174052288862936,0.0432062819173003,0.0622729132206112,0.00471410898868346,0.00880913681750981,0,0.0150938811146228,0.0137091735548101,0,0.038813991920549,0.0401382764133664,0.0753558110494994,0.0504011293181928,0.158034894424678,0.0161925863457788,0.0138701260315317,0.0759877099165137,0.0836646673403173,0.129599603726621,0.234315461977132,0.371885556293017,0.290572949155743,0.801046808338507,0.947744809284255,1.11517383399167,1.36318811801767,0.739417287142115,0.518294634072876,0.311782956253048,0.0235541767953294,0.00471008192133618,0.0226091738430399,0.012189422543107,0.00572237612848163,0.0126111031719554,0.0269350018980729,0.0173472241284104,0.0157756371141461,0.0202331999742781,0.0320346884519538,0.0324885344827072,0.0322006024265914,0.0258422856772345,0,0,0.0336830083089569,0.0316353655403374,0.00808300958689154,0.00601693374873821,0,0.0153046112930081,0.00744334787137725,0,0,0,0,0,0,0,0,0,0.0122049796269762,0.0232351344602085,0.00819218754451894,0.0118841822574593,0.04586007725706,0.011799309733175,0.0215097930612803,0.00937969774696677,0.00702318751122731,0.0348373821303768,0.0237875918460064,0.0770290800366508,0.0494910779085277,0.0223627536809717,0.0582500067434814,0,0.105128795012015,0.00898806151854494,0.00330199347217296,0,0.013294122293058,0.00445507759611179,0.00413486090472551,0.0201230960151591,0.00572196853749947,0.0237834016487351,0.0447637227976923,0,0,0.00955986034437394,0.00306091079498233,0.00412534672271503,0.0628649151683029,0,0.00856362567046751,0.00509291256689604,0.00461185234124171,0.00468444473488591,0,0,0,0,0,0.0289871664090176,0,0.0309074582795202,0.0369952471523168,0.0569330286692603,0.106973119995026,0.173609588219009,0.381761035409592,0.0731493763900727,0.080145980985152,0.0558765106190701,0.0121344671865587,0.0373439649197287,0.0444320412028374,0.0124736190154838,0.00953414967109671,0.0140142834925946,0.0155444037399381,0.0964978780061256,0.0114418447323334,0.0117470186954354,0.0192186706820119,0,0.0308020861186745,0.00530771124917056,0.00663100152518627,0,0.0147569531302271,0.00308086275854388,0,0.0071819292103795,0.00584400714946203,0.00498617796525572,0.0025242413422534,0.0123691457559943,0.0162266824494171,0.0101502070938866,0.0108832767195777,0.00233202958402155,0.00421249611574946,0.041227457278244,0,0.0361183968472787,0,0.0220682739294146,0,0,0,0,0,0,0.0140012903250161,0,0,0,0.0053606764446993,0,0.00427863030620287,0.0384943159250213,0.0330764347338358,0.116157643586094,0.133763384529262,0.140451652296565,0.138400102115558,0.164071400961013,0.145690207995137,0.135328058064685,0.144864177076938,0.134399843228519,0.151939228599517,0.136980452898469,0.129457456171155,0.145266362440524,0.143511901486574,0.145707007704539,0.139937385539654,0.155242471112894,0.142512851441204,0.150440376887568,0.116765669748733,0.139800945170266,0.132504076971865,0.147318756937544,0.13878608525988,0.136075695246267,0.128428896548759,0.12198337404791,0.127843070419852,0.144014650016826,0.11979761701144,0.0109988474120983,0.116291410348522,0.127314044481597,0.00950211101987381,0.0862547716564259,0.0169807717184789
|gostat_on_MCL_coexpression=GO:0045160;myosin I complex;0.009203966471265;17913!GO:0016461;unconventional myosin complex;0.0138051932993965;17913!GO:0032420;stereocilium;0.0230042431219055;17913!GO:0032421;stereocilium bundle;0.0230042431219055;17913!GO:0008022;protein C-terminus binding;0.0239224461872794;17913!GO:0005902;microvillus;0.0260664748441257;17913!GO:0005903;brush border;0.0275967712637765;17913!GO:0007623;circadian rhythm;0.0306555151069646;246691!GO:0045765;regulation of angiogenesis;0.0306555151069646;246691!GO:0000187;activation of MAPK activity;0.0331025101815151;246691!GO:0043406;positive regulation of MAP kinase activity;0.0342681020504265;246691!GO:0016459;myosin complex;0.0424111867249851;17913!GO:0043405;regulation of MAP kinase activity;0.0424111867249851;246691!
}}

Latest revision as of 15:20, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:4922184..4922209,+p@chr10:4922184..4922209
+
Mm9::chr11:110006928..110006939,+p@chr11:110006928..110006939
+
Mm9::chr11:75475116..75475125,+p19@Myo1c
Mm9::chr13:60581723..60581732,-p@chr13:60581723..60581732
-
Mm9::chr16:33124135..33124150,-p@chr16:33124135..33124150
-
Mm9::chr2:153426878..153426919,+p@chr2:153426878..153426919
+
Mm9::chr2:158037521..158037530,-p@chr2:158037521..158037530
-
Mm9::chr3:107041575..107041625,-p1@Prok1
Mm9::chr4:11542152..11542159,-p1@ENSMUST00000148576
p1@uc008rzu.1
Mm9::chr4:138015834..138015847,-p@chr4:138015834..138015847
-
Mm9::chr4:41577595..41577612,+p@chr4:41577595..41577612
+
Mm9::chr4:41577627..41577640,+p@chr4:41577627..41577640
+
Mm9::chr5:22095470..22095488,-p@chr5:22095470..22095488
-
Mm9::chr7:14840233..14840239,-p1@Sult2a6
Mm9::chr7:85980668..85980685,-p@chr7:85980668..85980685
-
Mm9::chrX:136369277..136369283,-p@chrX:136369277..136369283
-


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:0045160myosin I complex0.009203966471265
GO:0016461unconventional myosin complex0.0138051932993965
GO:0032420stereocilium0.0230042431219055
GO:0032421stereocilium bundle0.0230042431219055
GO:0008022protein C-terminus binding0.0239224461872794
GO:0005902microvillus0.0260664748441257
GO:0005903brush border0.0275967712637765
GO:0007623circadian rhythm0.0306555151069646
GO:0045765regulation of angiogenesis0.0306555151069646
GO:0000187activation of MAPK activity0.0331025101815151
GO:0043406positive regulation of MAP kinase activity0.0342681020504265
GO:0016459myosin complex0.0424111867249851
GO:0043405regulation of MAP kinase activity0.0424111867249851



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
liver6.21e-2222
epithelial sac6.21e-2222
digestive gland6.21e-2222
epithelium of foregut-midgut junction6.21e-2222
anatomical boundary6.21e-2222
hepatobiliary system6.21e-2222
foregut-midgut junction6.21e-2222
hepatic diverticulum6.21e-2222
liver primordium6.21e-2222
septum transversum6.21e-2222
liver bud6.21e-2222
digestive tract diverticulum7.81e-2123
sac7.81e-2123
exocrine gland6.71e-1925
exocrine system6.71e-1925
trunk mesenchyme4.76e-0945
epithelial tube1.57e-0847
abdomen element4.71e-0849
abdominal segment element4.71e-0849
abdominal segment of trunk4.71e-0849
abdomen4.71e-0849
gut epithelium7.74e-0755


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)
MA0003.10.0116141
MA0004.10.221835
MA0006.10.105852
MA0007.10.210531
MA0009.10.599391
MA0014.10.0122179
MA0017.10.774877
MA0019.10.434009
MA0024.10.558971
MA0025.10.819843
MA0027.12.21717
MA0028.10.112137
MA0029.10.53905
MA0030.14.57127
MA0031.13.24836
MA0038.10.33811
MA0040.10.611015
MA0041.10.964068
MA0042.10.926457
MA0043.10.689898
MA0046.12.59352
MA0048.10.0196258
MA0050.11.29684
MA0051.10.345658
MA0052.10.618515
MA0055.10.0964477
MA0056.10
MA0057.10.195768
MA0058.10.152805
MA0059.10.48573
MA0060.10.485984
MA0061.10.0774738
MA0063.10
MA0066.10.328887
MA0067.10.92691
MA0068.12.22212
MA0069.10.618831
MA0070.10.609808
MA0071.12.79721
MA0072.11.46522
MA0073.10.00527479
MA0074.10.8099
MA0076.10.134359
MA0077.10.581866
MA0078.10.37382
MA0081.10.177433
MA0083.10.68915
MA0084.11.24749
MA0087.10.648637
MA0088.10.251567
MA0089.10
MA0090.11.08371
MA0091.10.231874
MA0092.10.196497
MA0093.10.11723
MA0095.10
MA0098.10
MA0100.10.289731
MA0101.10.167439
MA0103.10.128989
MA0105.10.128193
MA0106.10.380511
MA0107.10.125067
MA0108.20.454274
MA0109.10
MA0111.10.206727
MA0113.10.356344
MA0114.10.263654
MA0115.10.692537
MA0116.10.344035
MA0117.10.662171
MA0119.10.502046
MA0122.10.680832
MA0124.10.875485
MA0125.10.804312
MA0130.10
MA0131.10.43
MA0132.10
MA0133.10
MA0135.11.72047
MA0136.10.315568
MA0139.10.0480655
MA0140.10.289637
MA0141.12.68809
MA0142.10.499475
MA0143.10.37032
MA0144.10.95924
MA0145.10.277688
MA0146.10.000633445
MA0147.10.286569
MA0148.18.58674
MA0149.10.171305
MA0062.20.0332891
MA0035.20.293466
MA0039.20.000979253
MA0138.20.423003
MA0002.20.728364
MA0137.20.432446
MA0104.20.0556953
MA0047.25.40956
MA0112.20.47728
MA0065.20.136177
MA0150.10.210447
MA0151.10
MA0152.10.337555
MA0153.11.75314
MA0154.10.0850581
MA0155.10.16166
MA0156.10.133796
MA0157.13.05876
MA0158.10
MA0159.10.0900717
MA0160.10.666246
MA0161.10
MA0162.10.00698895
MA0163.10.0215627
MA0164.10.315868
MA0080.20.396013
MA0018.20.323932
MA0099.20.417463
MA0079.24.69272e-05
MA0102.21.29919
MA0258.10.522754
MA0259.10.270549
MA0442.10
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