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

Briefings in Bioinformatics
Xin ShengJingfa Xiao

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...Continue Reading

References

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Citations

Dec 25, 2016·Briefings in Bioinformatics·Tyler WeirickShizuka Uchida
Dec 3, 2016·Nucleic Acids Research·UNKNOWN BIG Data Center Members
Apr 18, 2018·Scientific Data·Qingguo WangNikolaus Schultz
Oct 17, 2017·Nucleic Acids Research·UNKNOWN BIG Data Center Members
Jun 26, 2018·Briefings in Bioinformatics·Chunjie JiangXia Li
Nov 5, 2020·Proceedings of the National Academy of Sciences of the United States of America·Xin ShengKatalin Susztak

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Methods Mentioned

BETA
RNA-seq

Software Mentioned

AJAX
LAMP
Linux
jQuery
EMAGE
JPGraph
Apache
OrthoMCL
Perl scripts
Expression

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