OncoSplicing: an updated database for clinically relevant alternative splicing in 33 human cancers.
OncoSplicing: an updated database for clinically relevant alternative splicing in 33 human cancers.
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OncoSplicing：33 种人类癌症临床相关选择性剪接的更新数据库
DOI：
10.1093/nar/gkab851
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发表时间：
2022-01-07
影响因子：
14.9
通讯作者：
Xu H
中科院分区：
文献类型：
--
作者：
Zhang Y;Yao X;Zhou H;Wu X;Tian J;Zeng J;Yan L;Duan C;Liu H;Li H;Chen K;Hu Z;Ye Z;Xu H
选择性剪接（alternative splicing，AS）是在mRNA水平上调控基因表达的重要手段，并参与了蛋白质的复杂性。据报道，异常剪接在包括癌症在内的几种疾病中发挥作用。我们在2019年开发了OncoSplicing数据库，用于可视化生存相关和差异选择性剪接。在这里，我们提供了一个更新版本的OncoSplicing，用于基于TCGA SpliceSeq项目中33种癌症的122 423个AS事件和TCGA SplAdder项目中32种癌症的238 558个AS事件的临床相关可变剪接的综合视图。新版本的数据库包含几个有用的功能，如选择性剪接相关转录物的注释，基于中位数和最佳截止值的生存分析，TCGA肿瘤样本与相邻正常样本或GTEx正常样本之间的差异分析，选择性剪接的泛癌观点，剪接差异和考克斯PH回归的结果，临床指标相关和癌症特异性剪接事件的鉴定，和SplAdder项目中可下载的拼接数据。总体而言，OncoSplicing（www.oncosplicing.com）的大幅更新版本是一个用户友好且无需注册的数据库，用于浏览和搜索人类癌症中临床相关的替代剪接。
Alternative splicing (AS) represents a crucial method in mRNA level to regulate gene expression and contributes to the protein complexity. Abnormal splicing has been reported to play roles in several diseases, including cancers. We developed the OncoSplicing database for visualization of survival-associated and differential alternative splicing in 2019. Here, we provide an updated version of OncoSplicing for an integrative view of clinically relevant alternative splicing based on 122 423 AS events across 33 cancers in the TCGA SpliceSeq project and 238 558 AS events across 32 cancers in the TCGA SplAdder project. The new version of the database contains several useful features, such as annotation of alternative splicing-associated transcripts, survival analysis based on median and optimal cut-offs, differential analysis between TCGA tumour samples and adjacent normal samples or GTEx normal samples, pan-cancer views of alternative splicing, splicing differences and results of Cox’PH regression, identification of clinical indicator-relevant and cancer-specific splicing events, and downloadable splicing data in the SplAdder project. Overall, the substantially updated version of OncoSplicing (www.oncosplicing.com) is a user-friendly and registration-free database for browsing and searching clinically relevant alternative splicing in human cancers.
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影响因子：
14.9
作者：
Harrison PW;Ahamed A;Aslam R;Alako BTF;Burgin J;Buso N;Courtot M;Fan J;Gupta D;Haseeb M;Holt S;Ibrahim T;Ivanov E;Jayathilaka S;Balavenkataraman Kadhirvelu V;Kumar M;Lopez R;Kay S;Leinonen R;Liu X;O'Cathail C;Pakseresht A;Park Y;Pesant S;Rahman N;Rajan J;Sokolov A;Vijayaraja S;Waheed Z;Zyoud A;Burdett T;Cochrane G
通讯作者：
Cochrane G
影响因子：
14.9
作者：
Howe KL;Achuthan P;Allen J;Allen J;Alvarez-Jarreta J;Amode MR;Armean IM;Azov AG;Bennett R;Bhai J;Billis K;Boddu S;Charkhchi M;Cummins C;Da Rin Fioretto L;Davidson C;Dodiya K;El Houdaigui B;Fatima R;Gall A;Garcia Giron C;Grego T;Guijarro-Clarke C;Haggerty L;Hemrom A;Hourlier T;Izuogu OG;Juettemann T;Kaikala V;Kay M;Lavidas I;Le T;Lemos D;Gonzalez Martinez J;Marugán JC;Maurel T;McMahon AC;Mohanan S;Moore B;Muffato M;Oheh DN;Paraschas D;Parker A;Parton A;Prosovetskaia I;Sakthivel MP;Salam AIA;Schmitt BM;Schuilenburg H;Sheppard D;Steed E;Szpak M;Szuba M;Taylor K;Thormann A;Threadgold G;Walts B;Winterbottom A;Chakiachvili M;Chaubal A;De Silva N;Flint B;Frankish A;Hunt SE;IIsley GR;Langridge N;Loveland JE;Martin FJ;Mudge JM;Morales J;Perry E;Ruffier M;Tate J;Thybert D;Trevanion SJ;Cunningham F;Yates AD;Zerbino DR;Flicek P
通讯作者：
Flicek P
DOI：
10.1093/bioinformatics/bts452
发表时间：
2012-09-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Ryan MC;Cleland J;Kim R;Wong WC;Weinstein JN
通讯作者：
Weinstein JN
影响因子：
14.9
作者：
Ryan M;Wong WC;Brown R;Akbani R;Su X;Broom B;Melott J;Weinstein J
通讯作者：
Weinstein J
影响因子：
9.9
作者：
Hatje K;Rahman RU;Vidal RO;Simm D;Hammesfahr B;Bansal V;Rajput A;Mickael ME;Sun T;Bonn S;Kollmar M
通讯作者：
Kollmar M