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

2023; Wiley; Volume: 3; Issue: 11 Linguagem: Inglês

10.1002/cpz1.922

2691-1299

Jessica Ewald, Guangyan Zhou, Yao Lü, Jianguo Xia,

Molecular Biology Techniques and Applications

Abstract ExpressAnalyst 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 normalization Basic Protocol 2 : Differential expression analysis with linear models Basic Protocol 3 : Functional analysis with volcano plot, enrichment network, and ridgeline visualization Basic Protocol 4 : Hierarchical clustering analysis of transcriptomics data using interactive heatmaps Basic Protocol 5 : Cross‐species gene expression analysis based on ortholog mapping results Basic Protocol 6 : Proteomics and microarray data processing and normalization Basic Protocol 7 : Preparing multiple gene expression tables for meta‐analysis Basic Protocol 8 : Statistical and functional meta‐analysis of gene expression data Basic Protocol 9 : Functional analysis of transcriptomics signatures Basic Protocol 10 : Dose‐response and time‐series data analysis Basic Protocol 11 : RNA‐seq reads processing and quantification with and without reference transcriptomes