The practical definition of a transcriptome is a entire population of mRNA in a defined source, i.e. a cell, cells, tissue, or an organism.c The composition , which gene and how abundant, is central to the transcriptome data. Since human genome project started in early 1990s, increasing amount of human transcriptome data have been generated. A large collection of fragmentary cDNA sequences and genome-wide gene expression pattern using parallel hybridization of thousands of cDNA probes are examples. In these data, every transcript has ID which enables compilation of different data set and makes characterization of individual gene, as well as mass mRNA, possible. After this cleansing step, entire data is analyzed for higher order structure using statistical technique and then local data structures are interpreted for domain specific knowledge.

Within such a context, ongoing projects in our group are as follows

• BodyMap and iAFLP : 　As an expansion of the world-first gene expression database BodyMap (http://bodymap.jp ) ,we are collecting gene expression data for human and mouse with newly developed technique iAFLP ( http://okubolab.genes.nig.ac.jp/bodymap_i ) .
• Machine interpretation of genome-wide measurement data (BOB): 　Construction of a system for automatic recruitment of biomedical knowledge and machine interpretation of genome-wide measurement data.

Sugawara, H., Ogasawara, O., Okubo, K., Gojobori, T. and Tateno, Y. (2008). DDBJ with new system and face. Nucleic Acids Res. 36, D22-D24.

Hoshino, H., Uchida, T., Otsuki, T., Kawamoto, S., Okubo, K., Takeichi, M. and Chisaka, O. Cornichon-like Protein Facilitates Secretion of HB-EGF and Regulates Proper Development of Cranial Nerves. Molecular Biology of the Cell 2007 Apr Vol.18, D1143-1152.

Ogasawara, O., Otsuji, M., Watanabe, K., Iizuka, T., Tamura, T., Hishiki, T., Kawamoto, S., Okubo, K. (2006). BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression. Nucleic Acids Res. 34, D628-D631.

Okubo, K., Sugawara, H., Gojobori, T., Tateno, Y. (2006). DDBJ in preparation for overview of research activities behind data submissions. Nucleic Acids Res. 34, D6-D9

Itoh, K., Kawasaki, S., Kawamoto, S., Seishima, M., Chiba, H., Michibata, H., Wakimoto, K., Imai, Y., Minesaki, Y., Otsuji, M., Okubo, K. (2005). Identification of differentially expressed genes in psoriasis using expression profiling approaches. Exp Dermatol. 14, 667-674

Kaimori, J.Y., Takenaka, M., Okubo, K. (2005). Quantification of gene expression in mouse and human renal proximal tubules. Methods Mol Biol. 293, 209-219.