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Current web-based tools enable functional characterization of transcriptome data, but most are restricted to applying gene-list-based methods to single datasets, inefficient in leveraging up-to-date and species-specific information, and limited in their visualization options. Additionally, there is no systematic way to explore data stored in the largest transcriptome repository, NCBI GEO. To fill these gaps, we have developed eVITTA (easy Visualization and Inference Toolbox for Transcriptome Analysis; https:\/\/tau.cmmt.ubc.ca\/eVITTA\/). eVITTA provides modules for analysis and exploration of studies published in NCBI GEO (easyGEO), detailed molecular- and systems-level functional profiling (easyGSEA), and customizable comparisons among experimental groups (easyVizR). We tested eVITTA on transcriptomes of SARS-CoV-2 infected human nasopharyngeal swab samples, and identified a downregulation of olfactory signal transducers, in line with the clinical presentation of anosmia in COVID-19 patients. We also analyzed transcriptomes of Caenorhabditis elegans worms with disrupted S-adenosylmethionine metabolism, confirming activation of innate immune responses and feedback induction of one-carbon cycle genes. Collectively, eVITTA streamlines complex computational workflows into an accessible interface, thus filling the gap of an end-to-end platform capable of capturing both broad and granular changes in human and model organism transcriptomes.<\/jats:p>","DOI":"10.1093\/nar\/gkab366","type":"journal-article","created":{"date-parts":[[2021,5,4]],"date-time":"2021-05-04T12:07:00Z","timestamp":1620130020000},"page":"W207-W215","source":"Crossref","is-referenced-by-count":91,"title":["eVITTA: a web-based visualization and inference toolbox for transcriptome analysis"],"prefix":"10.1093","volume":"49","author":[{"given":"Xuanjin","family":"Cheng","sequence":"first","affiliation":[{"name":"Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada"},{"name":"British Columbia Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada"},{"name":"Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junran","family":"Yan","sequence":"additional","affiliation":[{"name":"Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada"},{"name":"British Columbia Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada"},{"name":"Graduate Program for Cell and Developmental Biology, The University of British Columbia, Vancouver, British Columbia, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yongxing","family":"Liu","sequence":"additional","affiliation":[{"name":"Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada"},{"name":"British Columbia Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada"},{"name":"Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiahe","family":"Wang","sequence":"additional","affiliation":[{"name":"Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada"},{"name":"British Columbia Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada"},{"name":"Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2432-7257","authenticated-orcid":false,"given":"Stefan","family":"Taubert","sequence":"additional","affiliation":[{"name":"Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada"},{"name":"British Columbia Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada"},{"name":"Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada"},{"name":"Graduate Program for Cell and Developmental Biology, The University of British Columbia, Vancouver, British Columbia, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,5,21]]},"reference":[{"key":"2021070812084202500_B1","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nrg2484","article-title":"RNA-Seq: a revolutionary tool for transcriptomics","volume":"10","author":"Wang","year":"2009","journal-title":"Nat. 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