Mutalisk: a web-based somatic MUTation AnaLyIS toolKit for genomic, transcriptional and epigenomic signatures.
Mutalisk: a web-based somatic MUTation AnaLyIS toolKit for genomic, transcriptional and epigenomic signatures.
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DOI：
10.1093/nar/gky406
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发表时间：
2018-07-02
影响因子：
14.9
通讯作者：
Hong D
中科院分区：
文献类型：
--
作者：
Lee J;Lee AJ;Lee JK;Park J;Kwon Y;Park S;Chun H;Ju YS;Hong D
体细胞基因组突变的发生是由于各种内在/外在突变过程和DNA修复机制的组合。不同的分子过程经常在其各自有利的环境中产生不同的体细胞突变特征。因此，区域性体细胞突变率取决于基因组中的局部DNA序列、DNA复制/RNA转录动力学和表观基因组染色质组织景观。在这里，我们提出了一个在线计算框架，称为Mutalisk，它与体细胞突变与各种基因组，转录和表观基因组特征，以了解突变过程，有助于产生的突变。这个用户友好的工具探索了局部超突变（kataegis）的存在，将突变谱分解为已知突变特征的最大似然组合，并将突变密度与基因组中的许多调控元件相关联。因此，可以有效地筛选任何查询样品中体细胞突变的全局模式，从而能够更深入地了解各种诱变因素。该工具将有助于更有效地对癌症基因组序列进行下游分析，以阐明癌细胞发展和克隆进化背后的突变过程的多样性。Mutalisk可在http://mutalisk.org上免费获得。
Somatic genome mutations occur due to combinations of various intrinsic/extrinsic mutational processes and DNA repair mechanisms. Different molecular processes frequently generate different signatures of somatic mutations in their own favored contexts. As a result, the regional somatic mutation rate is dependent on the local DNA sequence, the DNA replication/RNA transcription dynamics and epigenomic chromatin organization landscape in the genome. Here, we propose an online computational framework, termed Mutalisk, which correlates somatic mutations with various genomic, transcriptional and epigenomic features in order to understand mutational processes that contribute to the generation of the mutations. This user-friendly tool explores the presence of localized hypermutations (kataegis), dissects the spectrum of mutations into the maximum likelihood combination of known mutational signatures and associates the mutation density with numerous regulatory elements in the genome. As a result, global patterns of somatic mutations in any query sample can be efficiently screened, thus enabling a deeper understanding of various mutagenic factors. This tool will facilitate more effective downstream analyses of cancer genome sequences to elucidate the diversity of mutational processes underlying the development and clonal evolution of cancer cells. Mutalisk is freely available at http://mutalisk.org.
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影响因子：
64.8
作者：
Nik-Zainal S;Davies H;Staaf J;Ramakrishna M;Glodzik D;Zou X;Martincorena I;Alexandrov LB;Martin S;Wedge DC;Van Loo P;Ju YS;Smid M;Brinkman AB;Morganella S;Aure MR;Lingjærde OC;Langerød A;Ringnér M;Ahn SM;Boyault S;Brock JE;Broeks A;Butler A;Desmedt C;Dirix L;Dronov S;Fatima A;Foekens JA;Gerstung M;Hooijer GK;Jang SJ;Jones DR;Kim HY;King TA;Krishnamurthy S;Lee HJ;Lee JY;Li Y;McLaren S;Menzies A;Mustonen V;O'Meara S;Pauporté I;Pivot X;Purdie CA;Raine K;Ramakrishnan K;Rodríguez-González FG;Romieu G;Sieuwerts AM;Simpson PT;Shepherd R;Stebbings L;Stefansson OA;Teague J;Tommasi S;Treilleux I;Van den Eynden GG;Vermeulen P;Vincent-Salomon A;Yates L;Caldas C;van't Veer L;Tutt A;Knappskog S;Tan BK;Jonkers J;Borg Å;Ueno NT;Sotiriou C;Viari A;Futreal PA;Campbell PJ;Span PN;Van Laere S;Lakhani SR;Eyfjord JE;Thompson AM;Birney E;Stunnenberg HG;van de Vijver MJ;Martens JW;Børresen-Dale AL;Richardson AL;Kong G;Thomas G;Stratton MR
通讯作者：
Stratton MR
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
64.8
作者：
TABIN, CJ;BRADLEY, SM;CHANG, EH
通讯作者：
CHANG, EH
影响因子：
45.3
作者：
Lee, June-Koo;Lee, Junehawk;Ju, Young Seok
通讯作者：
Ju, Young Seok
DOI：
10.1126/science.1164382
发表时间：
2008-09-26
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Parsons DW;Jones S;Zhang X;Lin JC;Leary RJ;Angenendt P;Mankoo P;Carter H;Siu IM;Gallia GL;Olivi A;McLendon R;Rasheed BA;Keir S;Nikolskaya T;Nikolsky Y;Busam DA;Tekleab H;Diaz LA Jr;Hartigan J;Smith DR;Strausberg RL;Marie SK;Shinjo SM;Yan H;Riggins GJ;Bigner DD;Karchin R;Papadopoulos N;Parmigiani G;Vogelstein B;Velculescu VE;Kinzler KW
通讯作者：
Kinzler KW