GENCODE: reference annotation for the human and mouse genomes in 2023.
GENCODE: reference annotation for the human and mouse genomes in 2023.
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DOI：
10.1093/nar/gkac1071
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发表时间：
2023-01-06
影响因子：
14.9
通讯作者：
Flicek, Paul
中科院分区：
文献类型：
--
作者：
Frankish, Adam;Carbonell-Sala, Silvia;Diekhans, Mark;Jungreis, Irwin;Loveland, Jane E.;Mudge, Jonathan M.;Sisu, Cristina;Wright, James C.;Arnan, Carme;Barnes, If;Banerjee, Abhimanyu;Bennett, Ruth;Berry, Andrew;Bignell, Alexandra;Boix, Carles;Calvet, Ferriol;Cerdan-Velez, Daniel;Cunningham, Fiona;Davidson, Claire;Donaldson, Sarah;Dursun, Cagatay;Fatima, Reham;Giorgetti, Stefano;Giron, Carlos Garcia;Gonzalez, Jose Manuel;Hardy, Matthew;Harrison, Peter W.;Hourlier, Thibaut;Hollis, Zoe;Hunt, Toby;James, Benjamin;Jiang, Yunzhe;Johnson, Rory;Kay, Mike;Lagarde, Julien;Martin, Fergal J.;Gomez, Laura Martinez;Nair, Surag;Ni, Pengyu;Pozo, Fernando;Ramalingam, Vivek;Ruffier, Magali;Schmitt, Bianca M.;Schreiber, Jacob M.;Steed, Emily;Suner, Marie-Marthe;Sumathipala, Dulika;Sycheva, Irina;Uszczynska-Ratajczak, Barbara;Wass, Elizabeth;Yang, Yucheng T.;Yates, Andrew;Zafrulla, Zahoor;Choudhary, Jyoti S.;Gerstein, Mark;Guigo, Roderic;Hubbard, Tim J. P.;Kellis, Manolis;Kundaje, Anshul;Paten, Benedict;Tress, Michael L.;Flicek, Paul
GENCODE为人类和小鼠基因组提供高质量的基因和转录本注释。所有GENCODE注释都得到实验数据的支持，并可作为基因组生物学和临床基因组学的参考。GENCODE联合体生成有针对性的实验数据，开发生物信息学工具，并进行分析，沿着外部生成的数据和方法，支持转录本结构的鉴定和注释及其功能的确定。在这里，我们介绍了人类和小鼠基因注释的最新情况，包括支持这一进展的工具，数据，分析和主要合作的发展。例如，我们报告了在GENCODE转录物中鉴定的一组非规范ORF的创建，LRGASP合作评估使用长转录组数据构建转录物模型，与RefSeq和UniProt合作以增加人类和小鼠蛋白质编码基因注释的收敛性的进展，GENCODE在人类泛基因组中的传播以及开发新工具以支持GENCODE对调控特征的注释。我们的注释可通过Ensembl，UCSC基因组浏览器和https://www.gencodegenes.org访问。
GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported by experimental data and serves as a reference for genome biology and clinical genomics. The GENCODE consortium generates targeted experimental data, develops bioinformatic tools and carries out analyses that, along with externally produced data and methods, support the identification and annotation of transcript structures and the determination of their function. Here, we present an update on the annotation of human and mouse genes, including developments in the tools, data, analyses and major collaborations which underpin this progress. For example, we report the creation of a set of non-canonical ORFs identified in GENCODE transcripts, the LRGASP collaboration to assess the use of long transcriptomic data to build transcript models, the progress in collaborations with RefSeq and UniProt to increase convergence in the annotation of human and mouse protein-coding genes, the propagation of GENCODE across the human pan-genome and the development of new tools to support annotation of regulatory features by GENCODE. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.
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影响因子：
56.9
作者：
Nurk, Sergey;Koren, Sergey;Rhie, Arang;Rautiainen, Mikko;Bzikadze, Andrey V;Mikheenko, Alla;Vollger, Mitchell R;Altemose, Nicolas;Uralsky, Lev;Gershman, Ariel;Aganezov, Sergey;Hoyt, Savannah J;Diekhans, Mark;Logsdon, Glennis A;Alonge, Michael;Antonarakis, Stylianos E;Borchers, Matthew;Bouffard, Gerard G;Brooks, Shelise Y;Caldas, Gina V;Chen, Nae-Chyun;Cheng, Haoyu;Chin, Chen-Shan;Chow, William;de Lima, Leonardo G;Dishuck, Philip C;Durbin, Richard;Dvorkina, Tatiana;Fiddes, Ian T;Formenti, Giulio;Fulton, Robert S;Fungtammasan, Arkarachai;Garrison, Erik;Grady, Patrick G S;Graves-Lindsay, Tina A;Hall, Ira M;Hansen, Nancy F;Hartley, Gabrielle A;Haukness, Marina;Howe, Kerstin;Hunkapiller, Michael W;Jain, Chirag;Jain, Miten;Jarvis, Erich D;Kerpedjiev, Peter;Kirsche, Melanie;Kolmogorov, Mikhail;Korlach, Jonas;Kremitzki, Milinn;Li, Heng;Maduro, Valerie V;Marschall, Tobias;McCartney, Ann M;McDaniel, Jennifer;Miller, Danny E;Mullikin, James C;Myers, Eugene W;Olson, Nathan D;Paten, Benedict;Peluso, Paul;Pevzner, Pavel A;Porubsky, David;Potapova, Tamara;Rogaev, Evgeny I;Rosenfeld, Jeffrey A;Salzberg, Steven L;Schneider, Valerie A;Sedlazeck, Fritz J;Shafin, Kishwar;Shew, Colin J;Shumate, Alaina;Sims, Ying;Smit, Arian F A;Soto, Daniela C;Sovic, Ivan;Storer, Jessica M;Streets, Aaron;Sullivan, Beth A;Thibaud-Nissen, Francoise;Torrance, James;Wagner, Justin;Walenz, Brian P;Wenger, Aaron;Wood, Jonathan M D;Xiao, Chunlin;Yan, Stephanie M;Young, Alice C;Zarate, Samantha;Surti, Urvashi;McCoy, Rajiv C;Dennis, Megan Y;Alexandrov, Ivan A;Gerton, Jennifer L;O'Neill, Rachel J;Timp, Winston;Zook, Justin M;Schatz, Michael C;Eichler, Evan E;Miga, Karen H;Phillippy, Adam M
通讯作者：
Phillippy, Adam M
影响因子：
64.8
作者：
Boix CA;James BT;Park YP;Meuleman W;Kellis M
通讯作者：
Kellis M
来自1,092个人基因组的遗传变异的综合图。
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
64.8
作者：
Zoonomia Consortium
通讯作者：
Zoonomia Consortium
影响因子：
14.9
作者：
Rodriguez JM;Maietta P;Ezkurdia I;Pietrelli A;Wesselink JJ;Lopez G;Valencia A;Tress ML
通讯作者：
Tress ML