| Author | Ramos, Pablo Ivan Pereira | |
| Author | Arge, Luis Willian Pacheco | |
| Author | Lima, Nicholas Costa Barroso | |
| Author | Fukutani, Kiyoshi Ferreira | |
| Author | Queiroz, Artur Trancoso Lopo de | |
| Access date | 2019-12-16T12:16:34Z | |
| Available date | 2019-12-16T12:16:34Z | |
| Document date | 2019 | |
| Citation | RAMOS, Pablo Ivan Pereira et al. Leveraging user-friendly network approaches to extract knowledge from high-throughput omics datasets. Frontiers in Genetics, v. 10, p. 1-51, 2019. | |
| URI | https://www.arca.fiocruz.br/handle/icict/37958 | |
| Sponsorship | Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brazil [Universal 28/2018; grant protocol 427183/2018-9]. LA received a postdoctoral fellowship from the Coordenação de Aperfeiçoamento de Pessoal de 725 Nível Superior (CAPES). AQ acknowledges funding from Fundação Oswaldo Cruz (INOVA - Process VPPIS-001-FIO-18-45). Publication fees were defrayed by Fundação Oswaldo Cruz. The funders had no role in study design, analysis, decision to publish, or preparation of the manuscript. | |
| Language | eng | en_US |
| Publisher | Frontiers Media | |
| Rights | open access | |
| Subject in Portuguese | Redes de correlação | pt_BR |
| Subject in Portuguese | Gráfico | pt_BR |
| Subject in Portuguese | Network sequenciamento de alto rendimento | pt_BR |
| Subject in Portuguese | Análise de rede | pt_BR |
| Subject in Portuguese | Ômicas | pt_BR |
| Subject in Portuguese | Proteína- proteína interação | pt_BR |
| Subject in Portuguese | Redes reguladoras | pt_BR |
| Subject in Portuguese | Biologia de sistemas | pt_BR |
| Title | Leveraging User-Friendly Network Approaches to Extract Knowledge From High-Throughput Omics Datasets | en_US |
| Type | Preprint | |
| DOI | 10.3389/fgene.2019.01120 | |
| Abstract | Recent technological advances for the acquisition of multi-omics data have allowed an unprecedented understanding of the complex intricacies of biological systems. In parallel, a myriad of computational analysis techniques and bioinformatics tools have been developed, with many efforts directed towards the creation and interpretation of networks from this data. In this review, we begin by examining key network concepts and terminology. Then, computational tools that allow for their construction and analysis from high-throughput omics datasets are presented. We focus on the study of functional relationships such as co-expression, protein-protein interactions, and regulatory interactions that are particularly amenable to modeling using the framework of networks. We envisage that many potential users of these analytical strategies may not be completely literate in programming languages and code adaptation, and for this reason, emphasis is given to tools' user-friendliness, including plugins for the widely adopted Cytoscape software, an open-source, cross-platform tool for network analysis, visualization, and data integration. | en_US |
| Affilliation | Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Centro de Integração de Dados e Conhecimentos para Saúde. Salvador, BA, Brasil. | |
| Affilliation | Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, Brasil / Federal University of Rio de Janeiro. Centro de Ciências da Saúde. Laboratório de Genética Molecular e Biotecnologia Vegetal. Rio de Janeiro, RJ, Brasil. | |
| Affilliation | Universidade Federal do Ceará. Departamento de Bioquímica e Biologia Molecular. Fortaleza, CE, Brasil. | |
| Affilliation | Fundação José Silveira. Multinational Organization Network Sponsoring Translational and Epidemiological Research. Salvador, BA, Brazil. | |
| Affilliation | Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Centro de Integração de Dados e Conhecimentos para Saúde. Salvador, BA, Brasil. | |
| Subject | Correlation | en_US |
| Subject | Graph | en_US |
| Subject | High-throughput sequencing | en_US |
| Subject | Network analysis | en_US |
| Subject | Omics | en_US |
| Subject | Proteinprotein | en_US |
| Subject | Regulatory networks | en_US |
| Subject | Systems biology | en_US |
