%0 Journal Article
%T Genomic data integration tutorial, a plant case study.
%A Mardoc E
%A Sow MD
%A Déjean S
%A Salse J
%J BMC Genomics
%V 25
%N 1
%D 2024 Jan 17
%M 38233804
%F 4.547
%R 10.1186/s12864-023-09833-0
%X <B>BACKGROUND: </B>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><B>RESULTS: </B>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><B>CONCLUSIONS: </B>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.