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

Abstract

AbstractExpressAnalyst is a web‐based platform that enables intuitive, end‐to‐end transcriptomics and proteomics data analysis. Users can start from FASTQ files, gene/protein abundance tables, or gene/protein lists. ExpressAnalyst will perform read quantification, gene expression table processing and normalization, differential expression analysis, or meta‐analysis with complex study designs. The results are presented via various interactive visualizations such as volcano plots, heatmaps, networks, and ridgeline charts, with built‐in functional enrichment analysis to allow flexible data exploration and understanding. ExpressAnalyst currently contains built‐in support for 29 common organisms. For non‐model organisms without good reference genomes, it can perform comprehensive transcriptome profiling directly from RNA‐seq reads. These common tasks are covered in 11 Basic Protocols. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.Basic Protocol 1: RNA‐seq count table uploading, processing, and normalizationBasic Protocol 2: Differential expression analysis with linear modelsBasic Protocol 3: Functional analysis with volcano plot, enrichment network, and ridgeline visualizationBasic Protocol 4: Hierarchical clustering analysis of transcriptomics data using interactive heatmapsBasic Protocol 5: Cross‐species gene expression analysis based on ortholog mapping resultsBasic Protocol 6: Proteomics and microarray data processing and normalizationBasic Protocol 7: Preparing multiple gene expression tables for meta‐analysisBasic Protocol 8: Statistical and functional meta‐analysis of gene expression dataBasic Protocol 9: Functional analysis of transcriptomics signaturesBasic Protocol 10: Dose‐response and time‐series data analysisBasic Protocol 11: RNA‐seq reads processing and quantification with and without reference transcriptomes