Soybean Proteome Database 2012: Update on the comprehensive data repository for soybean proteomics

Frontiers in Plant Science

Volumn 3, Issue MAY, 2012, Pages

  Ohyanagi, Hajime ^a,b   Sakata, Katsumi ^c   Komatsu, Setsuko ^d  

^a MITSUBISHI SPACE SOFTWARE CO LTD   (Japan)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

^c MAEBASHI INSTITUTE OF TECHNOLOGY   (Japan)

^d NATIONAL INSTITUTE OF CROP SCIENCE   (Japan)

Author keywords

2 DE (two dimensional polyacrylamide gels electrophoresis); Database; Gel free proteomics technique; Glycine max cv. Enrei; Proteomics; Soybean

Indexed keywords

EID: 84896689156     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2012.00110     Document Type: Review

References (19)

1. Ahsan, N., Nanjo, Y., Sawada, H., Ko-hno, Y., and Komatsu, S. (2010). Ozone stress-induced proteomic cha-nges in leaf total soluble and chloroplast proteins of soybean reveal that carbon allocation is involved in adaptation in the early developmental stage. Proteomics 10, 2605-2619.
2. Boyer, J. S. (1982). Plant productivity and environment. Science 218, 443-448.
3. de Hoon, M. J. L., Imoto, S., Nolan, J., and Miyano, S. (2004). Open source clustering software. Bioinformatics 20, 1453-1454.
4. Groisman, P. Y., Knigh, R. W., Easterling, D. R., Karl, T. R., Heger, G. C., and Razuvaev, V. N. (2005). Trends in intense precipitation in the climate record. J. Clim. 18, 1326-1350.
5. Hajduch, M., Ganapathy, A., Stein, J. W., and Thelen, J. J. (2005). A systematic proteomic study of seed filling in soybean. Establishment of high-resolution two-dimensional reference maps, expression profiles, and an interactive proteome database. Plant Physiol. 137, 1397-1419.
6. Joshi, T., Patil, K., Fitzpatrick, M. R., Franklin, L. D., Yao, Q., Cook, J. R., Wang, Z., Libault, M., Brechenmacher, L., Valliyodan, B., Wu, X., Cheng, J., Stacey, G., Nguyen, H. T., and Xu, D. (2012). Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics. BMC Genomics 13(Suppl. 1), S15. doi:10.1186/1471-2164-13-S1-S15
7. Katayose, Y., Kanamori, H., Shimomura, M., Ohyanagi, H., Ikawa, H., Minami, H., Shibata, M., Ito, T., Kurita, K., Ito, K., Tsubokura, Y., Kaga, A., Wu, J., Matsumoto, T., Harada, K., and Sasaki, T. (2012). DaizuBase, an integrated soybean genome database including BAC-based physical maps. Breed. Sci. 61, 661-664.
8. Komatsu, S., Hiraga, S., and Yanagawa, Y. (2012). Proteomics techniques for the development of flood tolerant crops. J. Proteome Res. 11, 68-78.
9. Komatsu, S., Kobayashi, Y., Nishizawa, K., Nanjo, Y., and Furukawa, K. (2010). Comparative proteomics analysis of differentially expressed proteins in soybean cell wall during flooding stress. Amino Acids 39, 1435-1449.
10. Komatsu, S., Wada, T., Abaléa, Y., Nouri, M. Z., Nanjo, Y., Nakayama, N., Shimamura, S., Yamamoto, R., Nakamura, T., and Furukawa, K. (2009). Analysis of plasma membrane proteome in soybean and application to flooding stress response. J. Proteome Res. 8, 4487-4499.
11. Komatsu, S., Yamamoto, A., Nakamura, T., Nouri, M. Z., Nanjo, Y., Nishizawa, K., and Furukawa, K. (2011). Comprehensive analysis of mitochondria in roots and hypocotyls of soybean under flooding stress using proteomics and metabolomics techniques. J. Proteome Res. 10, 3993-4004.
12. Mohammadi, P. P., Moieni, A., Hiraga, S., and Komatsu, S. (2012). Organ-specific proteomic analysis of drought-stressed soybean seedlings. J. Proteomics 75, 1906-1923.
13. Mostaguir, K., Hoogland, C., Binz, P.-A., and Appel, R. D. (2003). The Make 2D-DB II package: conversion of federated two-dimensional gel electrophoresis databases into a relational format and interconnection of distributed databases. Proteomics 3, 1441-1444.
14. Sakata, K., Ohyanagi, H., Nobori, H., Nakamura, T., Hashiguchi, A., Nanjo, Y., Mikami, Y., Yunokawa, H., and Komatsu, S. (2009). Soybean proteome database: a data resource for plant differential omics. J. Proteome Res. 8, 3539-3548.
15. Saldanha, A. J. (2004). Java Treeview-extensible visualization of microarray data. Bioinformatics 20, 3246-3248.
16. Sato, S., Nakamura, Y., Kaneko, T., Asamizu, E., Kato, T., Nakao, M., Sasamoto, S., Watanabe, A., Ono, A., Kawashima, K., Fujishiro, T., Katoh, M., Kohara, M., Kishida, Y., Minami, C., Nakayama, S., Nakazaki, N., Shimizu, Y., Shinpo, S., Takahashi, C., Wada, T., Yamada, M., Ohmido, N., Hayashi, M., Fukui, K., Baba, T., Nakamichi, T., Mori, H., and Tabata, S. (2008). Genome structure of the legume, Lotus japonicus. DNA Res. 15, 227-239.
17. Schmutz, J., Cannon, S. B., Schlueter, J., Ma, J., Mitros, T., Nelson, W., Hyten, D. L., Song, Q., Thelen, J. J., Cheng, J., Xu, D., Hellsten, U., May, G. D., Yu, Y., Sakurai, T., Umezawa, T., Bhattacharyya, M. K., Sandhu, D., Valliyodan, B., Lindquist, E., Peto, M., Grant, D., Shu, S., Goodstein, D., Barry, K., Futrell-Griggs, M., Abernathy, B., Du, J., Tian, Z., Zhu, L., Gill, N., Joshi, T., Libault, M., Sethuraman, A., Zhang, X. C., Shinozaki, K., Nguyen, H. T., Wing, R. A., Cregan, P., Specht, J., Grimwood, J., Rokhsar, D., Stacey, G., Shoemaker, R. C., and Jackson, S. A. (2010). Genome sequence of the palaeopolyploid soybean. Nature 463, 178-183.
18. Sobhanian, H., Razavizadeh, R., Nanjo, Y., Ehsanpour, A. A., Jazii, F. R., Motamed, N., and Komatsu, S. (2010). Proteome analysis of soybean leaves, hypocotyls and roots under salt stress. Proteome Sci. 8, 19.
19. Young, N. D., Debellé, F., Oldroyd, G. E., Geurts, R., Cannon, S. B., Udvardi, M. K., Benedito, V. A., Mayer, K. F., Gouzy, J., Schoof, H., Van de Peer, Y., Proost, S., Cook, D. R., Meyers, B. C., Spannagl, M., Cheung, F., De Mita, S., Krishnakumar, V., Gundlach, H., Zhou, S., Mudge, J., Bharti, A. K., Murray, J. D., Naoumkina, M. A., Rosen, B., Silverstein, K. A., Tang, H., Rombauts, S., Zhao, P. X., Zhou, P., Barbe, V., Bardou, P., Bechner, M., Bellec, A., Berger, A., Bergès, H., Bidwell, S., Bisseling, T., Choisne, N., Couloux, A., Denny, R., Deshpande, S., Dai, X., Doyle, J. J., Dudez, A. M., Farmer, A. D., Fouteau, S., Franken, C., Gibelin, C., Gish, J., Goldstein, S., González, A. J., Green, P. J., Hallab, A., Hartog, M., Hua, A., Humphray, S. J., Jeong, D. H., Jing, Y., Jöcker, A., Kenton, S. M., Kim, D. J., Klee, K., Lai, H., Lang, C., Lin, S., Macmil, S. L., Magdelenat, G., Matthews, L., McCorrison, J., Monaghan, E. L., Mun, J. H., Najar, F. Z., Nicholson, C., Noirot, C., O'Bleness, M., Paule, C. R., Poulain, J., Prion, F., Qin, B., Qu, C., Retzel, E. F., Riddle, C., Sallet, E., Samain, S., Samson, N., Sanders, I., Saurat, O., Scarpelli, C., Schiex, T., Segurens, B., Severin, A. J., Sherrier, D. J., Shi, R., Sims, S., Singer, S. R., Sinharoy, S., Sterck, L., Viollet, A., Wang, B. B., Wang, K., Wang, M., Wang, X., Warfsmann, J., Weissenbach, J., White, D. D., White, J. D., Wiley, G. B., Wincker, P., Xing, Y., Yang, L., Yao, Z., Ying, F., Zhai, J., Zhou, L., Zuber, A., Dénarié, J., Dixon, R. A., May, G. D., Schwartz, D. C., Rogers, J., Quétier, F., Town, C. D., and Roe, B. A. (2011). The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480, 520-524.