New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources

被引:48
作者
Engel, Stacia R. [1 ]
Wong, Edith D. [1 ]
Nash, Robert S. [1 ]
Aleksander, Suzi [1 ]
Alexander, Micheal [1 ]
Douglass, Eric [1 ]
Karra, Kalpana [1 ]
Miyasato, Stuart R. [1 ]
Simison, Matt [1 ]
Skrzypek, Marek S. [1 ]
Weng, Shuai [1 ]
Cherry, J. Michael [1 ]
机构
[1] Stanford Univ, Dept Genet, Stanford, CA 94305 USA
基金
美国国家卫生研究院;
关键词
Saccharomyces cerevisiae; knowledgebase; reference genome; Saccharomyces Genome Database; Alliance of Genome Resources; PHYLOGENETIC TREES; GENE-EXPRESSION; PROVIDES TOOLS; ANTISENSE RNA; SGD; ANNOTATION; CEREVISIAE; PROTEIN; TRANSCRIPTION; INFORMATION;
D O I
10.1093/genetics/iyab224
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
Saccharomyces cerevisiae is used to provide fundamental understanding of eukaryotic genetics, gene product function, and cellular biological processes. Saccharomyces Genome Database (SGD) has been supporting the yeast research community since 1993, serving as its de facto hub. Over the years, SGD has maintained the genetic nomenclature, chromosome maps, and functional annotation, and developed various tools and methods for analysis and curation of a variety of emerging data types. More recently, SGD and six other model organism focused knowledgebases have come together to create the Alliance of Genome Resources to develop sustainable genome information resources that promote and support the use of various model organisms to understand the genetic and genomic bases of human biology and disease. Here we describe recent activities at SGD, including the latest reference genome annotation update, the development of a curation system for mutant alleles, and new pages addressing homology across model organisms as well as the use of yeast to study human disease.
引用
收藏
页数:11
相关论文
共 82 条
[1]   Alliance of Genome Resources Portal: unified model organism research platform [J].
Agapite, Julie ;
Albou, Laurent-Philippe ;
Aleksander, Suzi ;
Argasinska, Joanna ;
Arnaboldi, Valerio ;
Attrill, Helen ;
Bello, Susan M. ;
Blake, Judith A. ;
Blodgett, Olin ;
Bradford, Yvonne M. ;
Bult, Carol J. ;
Cain, Scott ;
Calvi, Brian R. ;
Carbon, Seth ;
Chan, Juancarlos ;
Chen, Wen J. ;
Cherry, J. Michael ;
Cho, Jaehyoung ;
Christie, Karen R. ;
Crosby, Madeline A. ;
De Pons, Jeff ;
Dolan, Mary E. ;
dos Santos, Gilberto ;
Dunn, Barbara Dunn Nathan ;
Eagle, Anne ;
Ebert, Dustin ;
Engel, Stacia R. ;
Fashena, David ;
Frazer, Ken ;
Gao, Sibyl ;
Gondwe, Felix ;
Goodman, Josh ;
Gramates, L. Sian ;
Grove, Christian A. ;
Harris, Todd ;
Harrison, Marie-Claire ;
Howe, Douglas G. ;
Howe, Kevin L. ;
Jha, Sagar ;
Kadin, James A. ;
Kaufman, Thomas C. ;
Kalita, Patrick ;
Karra, Kalpana ;
Kishore, Ranjana ;
Laulederkind, Stan ;
Lee, Raymond ;
MacPherson, Kevin A. ;
Marygold, Steven J. ;
Matthews, Beverley ;
Millburn, Gillian .
NUCLEIC ACIDS RESEARCH, 2020, 48 (D1) :D650-D658
[2]  
Alliance of Genome Resources, 2022, GENETICS SAME ISSUE
[3]   A regulatory circuit between lncRNA and TOR directs amino acid uptake in yeast [J].
Awasthi, Ankita ;
Nain, Vikrant ;
Srikanth, Chittur, V ;
Puria, Rekha .
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH, 2020, 1867 (06)
[4]   Fungal BLAST and Model Organism BLASTP Best Hits:: new comparison resources at the Saccharomyces Genome Database (SGD) [J].
Balakrishnan, R ;
Christie, KR ;
Costanzo, MC ;
Dolinski, K ;
Dwight, SS ;
Engel, SR ;
Fisk, DG ;
Hirschman, JE ;
Hong, EL ;
Nash, R ;
Oughtred, R ;
Skrzypek, M ;
Theesfeld, CL ;
Binkley, G ;
Dong, Q ;
Lane, C ;
Sethuraman, A ;
Weng, S ;
Botstein, D ;
Cherry, JM .
NUCLEIC ACIDS RESEARCH, 2005, 33 :D374-D377
[5]   A guide to best practices for Gene Ontology (GO) manual annotation [J].
Balakrishnan, Rama ;
Harris, Midori A. ;
Huntley, Rachael ;
Van Auken, Kimberly ;
Cherry, J. Michael .
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2013,
[6]   Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data [J].
Ball, CA ;
Jin, H ;
Sherlock, G ;
Weng, S ;
Matese, JC ;
Andrada, R ;
Binkley, G ;
Dolinski, K ;
Dwight, SS ;
Harris, MA ;
Issel-Tarver, L ;
Schroeder, R ;
Botstein, D ;
Cherry, JM .
NUCLEIC ACIDS RESEARCH, 2001, 29 (01) :80-81
[7]   Integrating functional genomic information into the Saccharomyces genome database [J].
Ball, CA ;
Dolinski, K ;
Dwight, SS ;
Harris, MA ;
Issel-Tarver, L ;
Kasarskis, A ;
Scafe, CR ;
Sherlock, G ;
Binkley, G ;
Jin, H ;
Kaloper, M ;
Orr, SD ;
Schroeder, M ;
Weng, S ;
Zhu, Y ;
Botstein, D ;
Cherry, JM .
NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :77-80
[8]   The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases [J].
Bult, Carol J. ;
Blake, Judith A. ;
Calvi, Brian R. ;
Cherry, J. Michael ;
DiFrancesco, Valentina ;
Fullem, Robert ;
Howe, Kevin L. ;
Kaufman, Thom ;
Mungall, Chris ;
Perrimon, Norbert ;
Shimoyama, Mary ;
Sternberg, Paul W. ;
Thomas, Paul ;
Westerfield, Monte .
GENETICS, 2019, 213 (04) :1189-1196
[9]   Mouse Genome Database (MGD) 2019 [J].
Bult, Carol J. ;
Blake, Judith A. ;
Smith, Cynthia L. ;
Kadin, James A. ;
Richardson, Joel E. ;
Anagnostopoulos, A. ;
Asabor, R. ;
Baldarelli, R. M. ;
Beal, J. S. ;
Bello, S. M. ;
Blodgett, O. ;
Butler, N. E. ;
Christie, K. R. ;
Corbani, L. E. ;
Creelman, J. ;
Dolan, M. E. ;
Drabkin, H. J. ;
Giannatto, S. L. ;
Hale, P. ;
Hill, D. P. ;
Law, M. ;
Mendoza, A. ;
McAndrews, M. ;
Miers, D. ;
Motenko, H. ;
Ni, L. ;
Onda, H. ;
Perry, M. ;
Recla, J. M. ;
Richards-Smith, B. ;
Sitnikov, D. ;
Tomczuk, M. ;
Tonorio, G. ;
Wilming, L. ;
Zhu, Y. .
NUCLEIC ACIDS RESEARCH, 2019, 47 (D1) :D801-D806
[10]   Upregulation of SPS100 gene expression by an antisense RNA via a switch of mRNA isoforms with different stabilities [J].
Bunina, Daria ;
Stefl, Martin ;
Huber, Florian ;
Khmelinskii, Anton ;
Meurer, Matthias ;
Barry, Joseph D. ;
Kats, Ilia ;
Kirrmaier, Daniel ;
Huber, Wolfgang ;
Knop, Michael .
NUCLEIC ACIDS RESEARCH, 2017, 45 (19) :11144-11158