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LOCATE


NAR Molecular Biology Database Collection entry number 836
Fink J.L.1,2, Aturaliya R.N.1,2, Davis M.J.2, Zhang F. 2, Hanson K.1,2, Teasdale M.S. 2, Kai C. 3, Kawai, J.3,4, Carninci P.3,4, Hayashizaki Y.3,4 and Teasdale R.D.1,2
1ARC Centre in Bioinformatics and 2Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia 4072
3Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
4Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan

Database Description

LOCATE is a curated, web-accessible database that houses data describing the membrane organization and subcellular localization of proteins from the FANTOM3 Isoform Protein Sequence set (1). Membrane organization is predicted by the high-throughput, computational pipeline MemO. The subcellular locations of selected proteins from this set were determined by a high-throughput, immunofluorescence-based assay and by manually reviewing over 1700 peer-reviewed publications. LOCATE represents the first effort to catalogue the experimentally-verified subcellular location and membrane organization of mammalian proteins using a high-throughput approach and provides localization data for nearly 40% of the mouse proteome.

Acknowledgements

The authors would like to acknowledge Nicholas Hamilton for implementing DomainDraw, the domain drawing program; Robert Luetterforst for assistance with the literature mining; and Emma Redhead for designing the LOCATE XML schema and XML document generator. The work was supported by funds from the Australian Research Council (ARC) and by the Research Grant for the RIKEN Genome Exploration Research Project from the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government to YH, and the Research Grant for the Genome Network Project from the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government. RDT is supported by a National Health and Medical Research Council of Australia R. Douglas Wright Career Development Award. RNA is supported by a Postgraduate Research Scholarship from the IMB, University of Queensland. MJD is supported by the National Institute for Diabetes, Digestion and Kidney Disease, National Institutes of Health (DK63400) as part of the Stem Cell Genome Anatomy Project (http://www.scgap.org/).

References

1. Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M.C. et al. (2005) The transcriptional landscape of the mammalian genome. Science, 309, 1559-1563.


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