A unified platform for RNA-seq analysis in non-model species

Abstract

The increasing application of RNA-seq to study non-model organisms demands easy-to-use and efficient bioinformatics tools to help researchers quickly uncover biological and functional insights from large datasets. Here, we present a unified software suite for processing, analyzing, and interpreting RNA-seq data from any eukaryotic species. This suite consists of a) EcoOmicsDB (www.ecoomicsdb.ca), a database for ortholog mapping and cross-species comparison; b) EcoOmicsAnalyst (www.ecoomicsanalyst.ca), a platform for raw data processing and annotation; and c) ExpressAnalyst (www.expressanalyst.ca), a platform for statistical and functional analysis. The utilities of this suite are demonstrated through case studies of RNA-seq data from multiple non-model species with or without reference transcriptomes. By coupling ultra-fast read mapping algorithms with high-resolution ortholog databases through a user-friendly web interface, the tool suite enables researchers to obtain global expression profiles and gene-level insights from raw RNA-seq reads within 24 hours.

Extracellular vesicle biogenesis of three‐dimensional human pluripotent stem cells in a novel Vertical‐Wheel bioreactor

“…Differential expressed miRs were analysed by both OASIS and miRNet using default settings. RNA‐seq data were analysed by ExpressAnalyst (Liu, 2023). Genes with counts less than 10, variance less than 10% and unannotated were filtered and normalized by Log2‐counts per million.…”

Hepatic Transcriptomic Responses to Ethinylestradiol in Embryonic Japanese Quail and Double‐Crested Cormorant

“…The Seq2Fun method allows functional profiling of RNAseq data for organisms without a reference genome or transcriptome by mapping RNA reads to an ortholog database, EcoOmicsDB (2023). This common database makes Seq2Fun particularly useful for nonmodel species as well as for cross‐species comparative studies (Liu et al, 2023). The RNA sequencing data of JQ and DCCO were processed into a count table using the Seq2Fun module embedded in EcoOmicsAnalyst (now ExpressAnalyst, 2022).…”

“…The need to incorporate experimental information into risk assessments led to the development of the species sensitivity distribution method. More recently, the efforts to tackle interspecies variability was extended to comparative toxicogenomic tools such as Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS; U.S. Environmental Protection Agency, 2023) and Seq2Fun (Liu et al, 2023), taking advantage of the unprecedented wealth of sequence data and prior knowledge about toxicological pathways (LaLone et al, 2021).…”

Using ExpressAnalyst for Comprehensive Gene Expression Analysis in Model and Non‐Model Organisms

“…There is an urgent demand for user‐friendly software to relieve the omics data analysis bottleneck. Here we provide detailed protocols on using ExpressAnalyst, a web‐based platform that provides end‐to‐end support for common tasks involved in transcriptomics data analysis (Liu et al., 2023). While many of the modules were originally designed for RNA‐seq or microarray data (Zhou et al., 2019), we have added proteomics‐specific annotation libraries and normalization methods so that the differential expression and functional analysis methods can be used to analyze abundance tables from proteomics.…”

“…The general statistical and functional analysis modules were split from the network analysis module to form the basis of ExpressAnalyst. ExpressAnalyst was expanded to include bulk RNA‐seq processing, annotation and functional libraries for ecological species (common reference transcriptomes and Seq2Fun ortholog IDs), as described in our recent publication (Liu et al., 2023). All modules were further modified to support complex metadata, including continuous variables and the ability to consider multiple factors during differential expression analysis, and to support proteomics intensity/abundance tables.…”