Genomic data integration tutorial, a plant case study
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 rep...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2024-01-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-023-09833-0 |
| _version_ | 1827377441380761600 |
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| author | Emile Mardoc Mamadou Dia Sow Sébastien Déjean Jérôme Salse |
| author_facet | Emile Mardoc Mamadou Dia Sow Sébastien Déjean Jérôme Salse |
| author_sort | Emile Mardoc |
| collection | DOAJ |
| description | 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. 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_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. |
| first_indexed | 2024-03-08T12:40:14Z |
| format | Article |
| id | doaj.art-4436600db7f7408e976679a3951ed4e6 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-08T12:40:14Z |
| publishDate | 2024-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-4436600db7f7408e976679a3951ed4e62024-01-21T12:11:43ZengBMCBMC Genomics1471-21642024-01-0125111510.1186/s12864-023-09833-0Genomic data integration tutorial, a plant case studyEmile Mardoc0Mamadou Dia Sow1Sébastien Déjean2Jérôme Salse3UCA-INRAE UMR 1095 Genetics, Diversity and Ecophysiology of Cereals (GDEC)UCA-INRAE UMR 1095 Genetics, Diversity and Ecophysiology of Cereals (GDEC)Institut de Mathématiques de Toulouse, UMR 5219, Université de Toulouse, CNRS, Université Paul SabatierUCA-INRAE UMR 1095 Genetics, Diversity and Ecophysiology of Cereals (GDEC)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. 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_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.https://doi.org/10.1186/s12864-023-09833-0OmicsIntegrationSystemBiology |
| spellingShingle | Emile Mardoc Mamadou Dia Sow Sébastien Déjean Jérôme Salse Genomic data integration tutorial, a plant case study BMC Genomics Omics Integration System Biology |
| title | Genomic data integration tutorial, a plant case study |
| title_full | Genomic data integration tutorial, a plant case study |
| title_fullStr | Genomic data integration tutorial, a plant case study |
| title_full_unstemmed | Genomic data integration tutorial, a plant case study |
| title_short | Genomic data integration tutorial, a plant case study |
| title_sort | genomic data integration tutorial a plant case study |
| topic | Omics Integration System Biology |
| url | https://doi.org/10.1186/s12864-023-09833-0 |
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