Ten quick tips for avoiding pitfalls in multi-omics data integration analyses

• Published in: PLoS computational biology Vol. 19; no. 7; p. e1011224
• Main Authors: Chicco, Davide, Cumbo, Fabio, Angione, Claudio
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.07.2023; Public Library of Science (PLoS)
• Subjects: Bioinformatics; Biology and Life Sciences; Biomarkers; Biophysics; Cancer; Computational biology; Computer and Information Sciences; Data analysis; Data integration; DNA methylation; Education; Electronic data processing; Engineering and Technology; Genomics; Heterogeneity; Integration; Machine learning; Metabolomics; Metadata; Metagenomics; Methods; Proteomics; Research and Analysis Methods; Science Policy; Software; Tips; Transcriptomics; Italy
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1011224

Data are the most important elements of bioinformatics: Computational analysis of bioinformatics data, in fact, can help researchers infer new knowledge about biology, chemistry, biophysics, and sometimes even medicine, influencing treatments and therapies for patients. Bioinformatics and high-throughput biological data coming from different sources can even be more helpful, because each of these different data chunks can provide alternative, complementary information about a specific biological phenomenon, similar to multiple photos of the same subject taken from different angles. In this context, the integration of bioinformatics and high-throughput biological data gets a pivotal role in running a successful bioinformatics study. In the last decades, data originating from proteomics, metabolomics, metagenomics, phenomics, transcriptomics, and epigenomics have been labelled -omics data, as a unique name to refer to them, and the integration of these omics data has gained importance in all biological areas. Even if this omics data integration is useful and relevant, due to its heterogeneity, it is not uncommon to make mistakes during the integration phases. We therefore decided to present these ten quick tips to perform an omics data integration correctly, avoiding common mistakes we experienced or noticed in published studies in the past. Even if we designed our ten guidelines for beginners, by using a simple language that (we hope) can be understood by anyone, we believe our ten recommendations should be taken into account by all the bioinformaticians performing omics data integration, including experts.