metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research

被引：12

作者：

Lyne, Mike ^{[1
,2
]}

Smith, Richard N. ^{[1
,2
]}

Lyne, Rachel ^{[1
,2
]}

Aleksic, Jelena ^{[1
,2
]}

Hu, Fengyuan ^{[1
,2
]}

Kalderimis, Alex ^{[1
,2
]}

Stepan, Radek ^{[1
,2
]}

Micklem, Gos ^{[1
,2
]}

机构：

[1] Univ Cambridge, Cambridge Syst Biol Ctr, Cambridge CB2 1QR, England

[2] Univ Cambridge, Dept Genet, Cambridge CB2 3EH, England

来源：

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION | 2013年

基金：

英国惠康基金;

关键词：

WIDE ASSOCIATION; TOOLS; RESOURCE;

D O I：

10.1093/database/bat060

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Common metabolic and endocrine diseases such as diabetes affect millions of people worldwide and have a major health impact, frequently leading to complications and mortality. In a search for better prevention and treatment, there is ongoing research into the underlying molecular and genetic bases of these complex human diseases, as well as into the links with risk factors such as obesity. Although an increasing number of relevant genomic and proteomic data sets have become available, the quantity and diversity of the data make their efficient exploitation challenging. Here, we present metabolicMine, a data warehouse with a specific focus on the genomics, genetics and proteomics of common metabolic diseases. Developed in collaboration with leading UK metabolic disease groups, metabolicMine integrates data sets from a range of experiments and model organisms alongside tools for exploring them. The current version brings together information covering genes, proteins, orthologues, interactions, gene expression, pathways, ontologies, diseases, genome-wide association studies and single nucleotide polymorphisms. Although the emphasis is on human data, key data sets from mouse and rat are included. These are complemented by interoperation with the RatMine rat genomics database, with a corresponding mouse version under development by the Mouse Genome Informatics (MGI) group. The web interface contains a number of features including keyword search, a library of Search Forms, the QueryBuilder and list analysis tools. This provides researchers with many different ways to analyse, view and flexibly export data. Programming interfaces and automatic code generation in several languages are supported, and many of the features of the web interface are available through web services. The combination of diverse data sets integrated with analysis tools and a powerful query system makes metabolicMine a valuable research resource. The web interface makes it accessible to first-time users, whereas the Application Programming Interface (API) and web services provide convenient data access and tools for bioinformaticians. metabolicMine is freely available online at http://www.metabolicmine.org

引用

页数：12

共 46 条

[1] T2D-Db: An integrated platform to study the molecular basis of Type 2 diabetes [J].

Agrawal, Shipra ;

Dimitrova, Nevenka ;

Nathan, Prasanthi ;

Udayakumar, K. ;

Lakshmi, S. Sai ;

Sriram, S. ;

Manjusha, N. ;

Sengupta, Urmi .

BMC GENOMICS, 2008, 9 (1)

[2] A New Face and New Challenges for Online Mendelian Inheritance in Man (OMIM®) [J].

Amberger, Joanna ;

Bocchini, Carol ;

Hamosh, Ada .

HUMAN MUTATION, 2011, 32 (05) :564-567

[3]

[Anonymous], DATABASE OXFORD

[4] Gene Ontology Annotations and Resources [J].

Blake, J. A. ;

Dolan, M. ;

Drabkin, H. ;

Hill, D. P. ;

Ni, Li ;

Sitnikov, D. ;

Bridges, S. ;

Burgess, S. ;

Buza, T. ;

McCarthy, F. ;

Peddinti, D. ;

Pillai, L. ;

Carbon, S. ;

Dietze, H. ;

Ireland, A. ;

Lewis, S. E. ;

Mungall, C. J. ;

Gaudet, P. ;

Chisholm, R. L. ;

Fey, P. ;

Kibbe, W. A. ;

Basu, S. ;

Siegele, D. A. ;

McIntosh, B. K. ;

Renfro, D. P. ;

Zweifel, A. E. ;

Hu, J. C. ;

Brown, N. H. ;

Tweedie, S. ;

Alam-Faruque, Y. ;

Apweiler, R. ;

Auchinchloss, A. ;

Axelsen, K. ;

Bely, B. ;

Blatter, M-C. ;

Bonilla, C. ;

Bougueleret, L. ;

Boutet, E. ;

Breuza, L. ;

Bridge, A. ;

Chan, W. M. ;

Chavali, G. ;

Coudert, E. ;

Dimmer, E. ;

Estreicher, A. ;

Famiglietti, L. ;

Feuermann, M. ;

Gos, A. ;

Gruaz-Gumowski, N. ;

Hieta, R. .

NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D530-D535

[5] ZFIN: enhancements and updates to the zebrafish model organism database [J].

Bradford, Yvonne ;

Conlin, Tom ;

Dunn, Nathan ;

Fashena, David ;

Frazer, Ken ;

Howe, Douglas G. ;

Knight, Jonathan ;

Mani, Prita ;

Martin, Ryan ;

Moxon, Sierra A. T. ;

Paddock, Holly ;

Pich, Christian ;

Ramachandran, Sridhar ;

Ruef, Barbara J. ;

Ruzicka, Leyla ;

Schaper, Holle Bauer ;

Schaper, Kevin ;

Shao, Xiang ;

Singer, Amy ;

Sprague, Judy ;

Sprunger, Brock ;

Van Slyke, Ceri ;

Westerfield, Monte .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D822-D829

[6] The Mouse Genome Database: Genotypes, Phenotypes, and Models of Human Disease [J].

Bult, Carol J. ;

Eppig, Janan T. ;

Blake, Judith A. ;

Kadin, James A. ;

Richardson, Joel E. .

NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D885-D891

[7] Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls [J].

Burton, Paul R. ;

Clayton, David G. ;

Cardon, Lon R. ;

Craddock, Nick ;

Deloukas, Panos ;

Duncanson, Audrey ;

Kwiatkowski, Dominic P. ;

McCarthy, Mark I. ;

Ouwehand, Willem H. ;

Samani, Nilesh J. ;

Todd, John A. ;

Donnelly, Peter ;

Barrett, Jeffrey C. ;

Davison, Dan ;

Easton, Doug ;

Evans, David ;

Leung, Hin-Tak ;

Marchini, Jonathan L. ;

Morris, Andrew P. ;

Spencer, Chris C. A. ;

Tobin, Martin D. ;

Attwood, Antony P. ;

Boorman, James P. ;

Cant, Barbara ;

Everson, Ursula ;

Hussey, Judith M. ;

Jolley, Jennifer D. ;

Knight, Alexandra S. ;

Koch, Kerstin ;

Meech, Elizabeth ;

Nutland, Sarah ;

Prowse, Christopher V. ;

Stevens, Helen E. ;

Taylor, Niall C. ;

Walters, Graham R. ;

Walker, Neil M. ;

Watkins, Nicholas A. ;

Winzer, Thilo ;

Jones, Richard W. ;

McArdle, Wendy L. ;

Ring, Susan M. ;

Strachan, David P. ;

Pembrey, Marcus ;

Breen, Gerome ;

St Clair, David ;

Caesar, Sian ;

Gordon-Smith, Katherine ;

Jones, Lisa ;

Fraser, Christine ;

Green, Elain K. .

NATURE, 2007, 447 (7145) :661-678

[8] The BioGRID interaction database: 2013 update [J].

Chatr-aryamontri, Andrew ;

Breitkreutz, Bobby-Joe ;

Heinicke, Sven ;

Boucher, Lorrie ;

Winter, Andrew ;

Stark, Chris ;

Nixon, Julie ;

Ramage, Lindsay ;

Kolas, Nadine ;

O'Donnell, Lara ;

Reguly, Teresa ;

Breitkreutz, Ashton ;

Sellam, Adnane ;

Chen, Daici ;

Chang, Christie ;

Rust, Jennifer ;

Livstone, Michael ;

Oughtred, Rose ;

Dolinski, Kara ;

Tyers, Mike .

NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D816-D823

[9] Saccharomyces Genome Database: the genomics resource of budding yeast [J].

Cherry, J. Michael ;

Hong, Eurie L. ;

Amundsen, Craig ;

Balakrishnan, Rama ;

Binkley, Gail ;

Chan, Esther T. ;

Christie, Karen R. ;

Costanzo, Maria C. ;

Dwight, Selina S. ;

Engel, Stacia R. ;

Fisk, Dianna G. ;

Hirschman, Jodi E. ;

Hitz, Benjamin C. ;

Karra, Kalpana ;

Krieger, Cynthia J. ;

Miyasato, Stuart R. ;

Nash, Rob S. ;

Park, Julie ;

Skrzypek, Marek S. ;

Simison, Matt ;

Weng, Shuai ;

Wong, Edith D. .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D700-D705

[10] Developments in Obesity Genetics in the Era of Genome-Wide Association Studies [J].

Day, Felix R. ;

Loos, Ruth J. F. .

JOURNAL OF NUTRIGENETICS AND NUTRIGENOMICS, 2011, 4 (04) :222-238

← 1 2 3 4 5 →