BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression

Abstract

BodyMap-Xs (http://bodymap.jp) is a database for cross-species gene expression comparison. It was created by the anatomical breakdown of 17 million animal expressed sequence tag (EST) records in DDBJ using a sorting program tailored for this purpose. In BodyMap-Xs, users are allowed to compare the expression patterns of orthologous and paralogous genes in a coherent manner. This will provide valuable insights for the evolutionary study of gene expression and identification of a responsive motif for a particular expression pattern. In addition, starting from a concise overview of the taxonomical and anatomical breakdown of all animal ESTs, users can navigate to obtain gene expression ranking of a particular tissue in a particular animal. This method may lead to the understanding of the similarities and differences between the homologous tissues across animal species. BodyMap-Xs will be automatically updated in synchronization with the major update in DDBJ, which occurs periodically.

Figure 1

Outline of BodyMap-Xs construction with some relevant figures for the data. Starting from three public resources, construction of database is structured as a pipe-line.

Figure 2

Browsing data in BodyMap-Xs. Starting from the index page, the expression ranking of relevant organs is shown (a). For genes with expression patterns of interest, the expression of orthologous partners can be shown (b). Similarity search allows users to compare expression patterns of genes structurally similar to the query (c). For validation of expression patterns, every figure in the table can be broken down to the library level. The library list shows why these libraries were categorized in a particular manner with KWIC format (d).