{Reference Type}: Journal Article
{Title}: Genomic data integration tutorial, a plant case study.
{Author}: Mardoc E;Sow MD;Déjean S;Salse J;
{Journal}: BMC Genomics
{Volume}: 25
{Issue}: 1
{Year}: 2024 Jan 17
{Factor}: 4.547
{DOI}: 10.1186/s12864-023-09833-0
{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.
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.
CONCLUSIONS: 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_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.