The Drosophila Gene Expression Tool (DGET) for expression analyses. Issue 1 (December 2017)

• Record Type: Journal Article
• Authors: Hu, Yanhui; Comjean, Aram; Perrimon, Norbert; Mohr, Stephanie E.
• Is Part Of: BMC bioinformatics. Volume 18:Issue 1(2017)
• Page Start: 1
• Page End: 9
• Publication Date: 2017-12
• Subjects: Drosophila -- RNA-Seq -- Expression profile -- Synexpression; Bioinformatics -- Periodicals; Computational biology -- Periodicals; 570.285
• DOI: 10.1186/s12859-017-1509-z
• Languages: English
• ISSNs: 1471-2105

Abstract

Abstract Background Next-generation sequencing technologies have greatly increased our ability to identify gene expression levels, including at specific developmental stages and in specific tissues. Gene expression data can help researchers understand the diverse functions of genes and gene networks, as well as help in the design of specific and efficient functional studies, such as by helping researchers choose the most appropriate tissue for a study of a group of genes, or conversely, by limiting a long list of gene candidates to the subset that are normally expressed at a given stage or in a given tissue. Results We report DGET, aDrosophila Gene Expression Tool (www.flyrnai.org/tools/dget/web/ ), which stores and facilitates search of RNA-Seq based expression profiles available from the modENCODE consortium and other public data sets. Using DGET, researchers are able to look up gene expression profiles, filter results based on threshold expression values, and compare expression data across different developmental stages, tissues and treatments. In addition, at DGET a researcher can analyze tissue or stage-specific enrichment for an inputted list of genes (e.g., 'hits' from a screen) and search for additional genes with similar expression patterns. We performed a number of analyses to demonstrate the quality and robustness of the resource. In particular, we show that evolutionary conserved genes expressed at high or moderate levels in both fly and human tend to be expressed in similar tissues. Using DGET, we compared whole tissue profile and sub-region/cell-type specific datasets and estimated a potential source of false positives in one dataset. We also demonstrated the usefulness of DGET for synexpression studies by querying genes with expression profile similar to the mesodermal master regulator Twist. Conclusion Altogether, DGET provides a flexible tool for expression data retrieval and analysis with short or long lists ofDrosophila genes, which can help scientists to design stage- or tissue-specific in vivo studies and do other subsequent analyses.