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Genomic data integration tutorial, a plant case study.
- Source :
-
BMC genomics [BMC Genomics] 2024 Jan 17; Vol. 25 (1), pp. 66. Date of Electronic Publication: 2024 Jan 17. - Publication Year :
- 2024
-
Abstract
- Background: The ongoing evolution of the Next Generation Sequencing (NGS) technologies has led to the production of genomic data on a massive scale. While tools for genomic data integration and analysis are becoming increasingly available, the conceptual and analytical complexities still represent a great challenge in many biological contexts.<br />Results: To address this issue, we describe a six-steps tutorial for the best practices in genomic data integration, consisting of (1) designing a data matrix; (2) formulating a specific biological question toward data description, selection and prediction; (3) selecting a tool adapted to the targeted questions; (4) preprocessing of the data; (5) conducting preliminary analysis, and finally (6) executing genomic data integration.<br />Conclusion: The tutorial has been tested and demonstrated on publicly available genomic data generated from poplar (Populus L.), a woody plant model. We also developed a new graphical output for the unsupervised multi-block analysis, cimDiablo&#95;v2, available at https://forgemia.inra.fr/umr-gdec/omics-integration-on-poplar , and allowing the selection of master drivers in genomic data variation and interplay.<br /> (© 2024. The Author(s).)
Details
- Language :
- English
- ISSN :
- 1471-2164
- Volume :
- 25
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- BMC genomics
- Publication Type :
- Academic Journal
- Accession number :
- 38233804
- Full Text :
- https://doi.org/10.1186/s12864-023-09833-0