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

Abstract

BodyMap-Xs () 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.

In Silico Screening for Palmitoyl Substrates Reveals a Role for DHHC1/3/10 (zDHHC1/3/11)-mediated Neurochondrin Palmitoylation in Its Targeting to Rab5-positive Endosomes

“…To find palmitoyl candidate proteins that are expressed predominantly in the brain, the listed protein sequences were further analyzed by a gene expression database, BodyMap-Xs (27). The entire dataset for mouse genes (38,632 gene data) was automatically downloaded from BodyMap-Xs, and data files were saved as CSV files.…”

Prediction of human miRNAs using tissue-selective motifs in 3′ UTRs

“…198) data of 40 tissues from the BodyMap-Xs database (16) and map these UniGene entries to Ensembl gene identification numbers. These entries belong to 18,021 human Ensembl genes.…”

“…We downloaded the human UniGene (Homo sapiens: Build no. 198) data and the tissue expression information from the BodyMap-Xs database (16). Then, we mapped the UniGene data to the Ensembl gene identification number and downloaded the transcript data from Ensembl.…”

Evolutionary origin of sex-related genes in the mouse brain

“…As shown in Table 1, 4 genes of Ddx3y, Ddx3x, Eif2s3x and Jarid1d were classified into "nucleic acid binding" category by GO. At the gene expression level, all of these 6 genes were expressed in most of organs or organ systems (9 or 10 organs or organ systems) in mice according to BodyMap-Xs database (Ogasawara et al, 2005; http://bodymap.jp/). Thus, 6 sexrelated genes that emerged in period (A) would have basic functions in a cell of vertebrate brains.…”