Bioinformatics Methods for Transcriptome Analysis on Teratogenesis Testing.

Autor:	Kowalski TW; Post-Graduation Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.; Laboratory Genetics Unit, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.; Teratogens Information System, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.; Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.; Bioinformatics Core, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.; Post-Graduation Program in Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil., Giudicelli GC; Post-Graduation Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.; Bioinformatics Core, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil., Gomes JDA; Post-Graduation Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.; Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil., Recamonde-Mendoza M; Bioinformatics Core, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.; Post-Graduation Program in Informatics, Informatics Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil., Vianna FSL; Post-Graduation Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.; Teratogens Information System, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.; Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.; Post-Graduation Program in Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
Jazyk:	angličtina
Zdroj:	Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2024; Vol. 2753, pp. 365-376.
DOI:	10.1007/978-1-0716-3625-1_20
Abstrakt:	Teratogenesis testing can be challenging due to the limitations of both in vitro and in vivo models. Test-systems, based especially on human embryonic cells, have been helping to overcome the difficulties when allied to omics strategies, such as transcriptomics. In these test-systems, cells exposed to different compounds are then analyzed in microarray or RNA-seq platforms regarding the impacts of the potential teratogens in the gene expression. Nevertheless, microarray and RNA-seq dataset processing requires computational resources and bioinformatics knowledge. Here, a pipeline for microarray and RNA-seq processing is presented, aiming to help researchers from any field to interpret the main transcriptome results, such as differential gene expression, enrichment analysis, and statistical interpretation. This chapter also discusses the main difficulties that can be encountered in a transcriptome analysis and the better alternatives to overcome these issues, describing both programming codes and user-friendly tools. Finally, specific issues in the teratogenesis field, such as time-course analysis, are also described, demonstrating how the pipeline can be applied in these studies. (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)
Databáze:	MEDLINE
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