qTeller: a tool for comparative multi-genomic gene expression analysis

Authors

Margaret R. Woodhouse, USDA ARS, Ames, IAFollow
Shatabdi Sen, Iowa State University
David Schott, Iowa State University
John L. Portwood II, USDA ARS, Ames, IA
Michael Freeling, University of California, Berkeley
Justin W. Walley, Iowa State University
Carson M. Andorf, USDA ARS, Ames, IA
James Schnable, University of Nebraska - LincolnFollow

Document Type

Article

Date of this Version

2022

Citation

Bioinformatics, 38(1), 2022, 236–242 doi: 10.1093/bioinformatics/btab604

Comments

Published by Oxford University Press 2021. This work is written by US Government employees and is in the public domain in the US.

Abstract

Motivation: Over the last decade, RNA-Seq whole-genome sequencing has become a widely used method for measuring and understanding transcriptome-level changes in gene expression. Since RNA-Seq is relatively inexpensive, it can be used on multiple genomes to evaluate gene expression across many different conditions, tissues and cell types. Although many tools exist to map and compare RNA-Seq at the genomics level, few web-based tools are dedicated to making data generated for individual genomic analysis accessible and reusable at a gene-level scale for comparative analysis between genes, across different genomes and meta-analyses. Results: To address this challenge, we revamped the comparative gene expression tool qTeller to take advantage of the growing number of public RNA-Seq datasets. qTeller allows users to evaluate gene expression data in a defined genomic interval and also perform two-gene comparisons across multiple user-chosen tissues. Though previously unpublished, qTeller has been cited extensively in the scientific literature, demonstrating its importance to researchers. Our new version of qTeller now supports multiple genomes for intergenomic comparisons, and includes capabilities for both mRNA and protein abundance datasets. Other new features include support for additional data formats, modernized interface and back-end database and an optimized framework for adoption by other organisms’ databases.

Availability and implementation: The source code for qTeller is open-source and available through GitHub (https:// github.com/Maize-Genetics-and-Genomics-Database/qTeller). A maize instance of qTeller is available at the Maize Genetics and Genomics database (MaizeGDB) (https://qteller.maizegdb.org/), where we have mapped over 200 unique datasets from GenBank across 27 maize genomes.