eVITTA: a web-based visualization and inference toolbox for transcriptome analysis

被引:46
作者
Cheng, Xuanjin [1 ,2 ,3 ]
Yan, Junran [1 ,2 ,4 ]
Liu, Yongxing [1 ,2 ,3 ]
Wang, Jiahe [1 ,2 ,3 ]
Taubert, Stefan [1 ,2 ,3 ,4 ]
机构
[1] Univ British Columbia, Ctr Mol Med & Therapeut, Vancouver, BC, Canada
[2] Univ British Columbia, British Columbia Childrens Hosp, Res Inst, Vancouver, BC, Canada
[3] Univ British Columbia, Dept Med Genet, Vancouver, BC, Canada
[4] Univ British Columbia, Grad Program Cell & Dev Biol, Vancouver, BC, Canada
基金
加拿大健康研究院; 加拿大自然科学与工程研究理事会;
关键词
GENE-EXPRESSION OMNIBUS; TOLL-LIKE RECEPTOR; ENRICHMENT ANALYSIS; PATHWAY; PACKAGE; ANNOTATION; SERVER;
D O I
10.1093/nar/gkab366
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Transcriptome profiling is essential for gene regulation studies in development and disease. 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.
引用
收藏
页码:W207 / W215
页数:9
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