FlyBase: establishing a Gene Group resource for Drosophila melanogaster

被引:231
作者
Attrill, Helen [1 ]
Falls, Kathleen [2 ]
Goodman, Joshua L. [3 ]
Millburn, Gillian H. [1 ]
Antonazzo, Giulia [1 ]
Rey, Alix J. [1 ]
Marygold, Steven J. [1 ]
机构
[1] Univ Cambridge, Dept Genet, Downing St, Cambridge CB2 3EH, England
[2] Harvard Univ, Biol Labs, 16 Divin Ave, Cambridge, MA 02138 USA
[3] Indiana Univ, Dept Biol, Bloomington, IN 47405 USA
基金
英国医学研究理事会; 美国国家卫生研究院;
关键词
BIOLOGY; TOOL;
D O I
10.1093/nar/gkv1046
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
070307 [化学生物学]; 071010 [生物化学与分子生物学];
摘要
Many publications describe sets of genes or gene products that share a common biology. For example, genome-wide studies and phylogenetic analyses identify genes related in sequence; high-throughput genetic and molecular screens reveal functionally related gene products; and advanced proteomic methods can determine the subunit composition of multiprotein complexes. It is useful for such gene collections to be presented as discrete lists within the appropriate Model Organism Database (MOD) so that researchers can readily access these data alongside other relevant information. To this end, FlyBase (flybase.org), the MOD for Drosophila melanogaster, has established a 'Gene Group' resource: high-quality sets of genes derived from the published literature and organized into individual report pages. To facilitate further analyses, Gene Group Reports also include convenient download and analysis options, together with links to equivalent gene groups at other databases. This new resource will enable researchers with diverse backgrounds and interests to easily view and analyse acknowledged D. melanogaster gene sets and compare them with those of other species.
引用
收藏
页码:D786 / D792
页数:7
相关论文
共 17 条
[1]
BASIC LOCAL ALIGNMENT SEARCH TOOL [J].
ALTSCHUL, SF ;
GISH, W ;
MILLER, W ;
MYERS, EW ;
LIPMAN, DJ .
JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410
[2]
Gene Ontology: tool for the unification of biology [J].
Ashburner, M ;
Ball, CA ;
Blake, JA ;
Botstein, D ;
Butler, H ;
Cherry, JM ;
Davis, AP ;
Dolinski, K ;
Dwight, SS ;
Eppig, JT ;
Harris, MA ;
Hill, DP ;
Issel-Tarver, L ;
Kasarskis, A ;
Lewis, S ;
Matese, JC ;
Richardson, JE ;
Ringwald, M ;
Rubin, GM ;
Sherlock, G .
NATURE GENETICS, 2000, 25 (01) :25-29
[3]
Network organization of the human autophagy system [J].
Behrends, Christian ;
Sowa, Mathew E. ;
Gygi, Steven P. ;
Harper, J. Wade .
NATURE, 2010, 466 (7302) :68-U84
[4]
Ten Quick Tips for Using the Gene Ontology [J].
Blake, Judith A. .
PLOS COMPUTATIONAL BIOLOGY, 2013, 9 (11)
[5]
Directly e-mailing authors of newly published papers encourages community curation [J].
Bunt, Stephanie M. ;
Grumbling, Gary B. ;
Field, Helen I. ;
Marygold, Steven J. ;
Brown, Nicholas H. ;
Millburn, Gillian H. .
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2012,
[6]
Gene family matters: expanding the HGNC resource [J].
Daugherty, Louise C. ;
Seal, Ruth L. ;
Wright, Mathew W. ;
Bruford, Elspeth A. .
HUMAN GENOMICS, 2012, 6
[7]
FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations [J].
dos Santos, Gilberto ;
Schroeder, Andrew J. ;
Goodman, Joshua L. ;
Strelets, Victor B. ;
Crosby, Madeline A. ;
Thurmond, Jim ;
Emmert, David B. ;
Gelbart, William M. .
NUCLEIC ACIDS RESEARCH, 2015, 43 (D1) :D690-D697
[8]
Loss of the starvation-induced gene Rack1 leads to glycogen deficiency and impaired autophagic responses in Drosophila [J].
Erdi, Balazs ;
Nagy, Peter ;
Zvara, Agnes ;
Varga, Agnes ;
Pircs, Karolina ;
Menesi, Dalma ;
Puskas, Laszlo G. ;
Juhasz, Gabor .
AUTOPHAGY, 2012, 8 (07) :1124-1135
[9]
WormBase 2014: new views of curated biology [J].
Harris, Todd W. ;
Baran, Joachim ;
Bieri, Tamberlyn ;
Cabunoc, Abigail ;
Chan, Juancarlos ;
Chen, Wen J. ;
Davis, Paul ;
Done, James ;
Grove, Christian ;
Howe, Kevin ;
Kishore, Ranjana ;
Lee, Raymond ;
Li, Yuling ;
Muller, Hans-Michael ;
Nakamura, Cecilia ;
Ozersky, Philip ;
Paulini, Michael ;
Raciti, Daniela ;
Schindelman, Gary ;
Tuli, Mary Ann ;
Van Auken, Kimberly ;
Wang, Daniel ;
Wang, Xiaodong ;
Williams, Gary ;
Wong, J. D. ;
Yook, Karen ;
Schedl, Tim ;
Hodgkin, Jonathan ;
Berriman, Matthew ;
Kersey, Paul ;
Spieth, John ;
Stein, Lincoln ;
Sternberg, Paul W. .
NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) :D789-D793
[10]
Hu Yanhui, 2015, J Genomics, V3, P75, DOI 10.7150/jgen.12863