MTD: a mammalian transcriptomic database to explore gene expression and regulation

Abstract

A systematic transcriptome survey is essential for the characterization and comprehension of the molecular basis underlying phenotypic variations. Recently developed RNA-seq methodology has facilitated efficient data acquisition and information mining of transcriptomes in multiple tissues/cell lines. Current mammalian transcriptomic databases are either tissue-specific or species-specific, and they lack in-depth comparative features across tissues and species. Here, we present a mammalian transcriptomic database (MTD) that is focused on mammalian transcriptomes, and the current version contains data from humans, mice, rats and pigs. Regarding the core features, the MTD browses genes based on their neighboring genomic coordinates or joint KEGG pathway and provides expression information on exons, transcripts and genes by integrating them into a genome browser. We developed a novel nomenclature for each transcript that considers its genomic position and transcriptional features. The MTD allows a flexible search of genes or isoforms with user-defined transcriptional characteristics and provides both table-based descriptions and associated visualizations. To elucidate the dynamics of gene expression regulation, the MTD also enables comparative transcriptomic analysis in both intraspecies and interspecies manner. The MTD thus constitutes a valuable resource for transcriptomic and evolutionary studies. The MTD is freely accessible at http://mtd.cbi.ac.cn.

Keywords: RNA-seq; gene expression and regulation; mammalian transcriptomic database.

Figure 1

The pipeline of data processing and database construction.

Figure 2

Representative screen shots of the Browse functionalities. (A) Browse by chromosome. (B) Browse by region. (C) Browse by pathway.

Figure 3

Representative screen shots of the Search functionalities. For genes, (A) view overviews of the expression levels across tissues/cell lines. (B) Search genes with specific transcriptional features in a specific tissue/cell line. For isoforms, (C) view overviews of the expression levels across tissues/cell lines. (D) Search isoform with specific transcriptional features in a specific tissue/cell line.

Figure 4

Representative screen shots of the Analysis functionalities. (A) An intraspecies interface allows the comparison of transcriptomes across tissues or cell lines on gene, transcript and exon levels. (B) An interspecies interface allows comparison of the transcriptomic details of homologous genes in physiologically equivalent tissues/cell lines across species.