Please use this identifier to cite or link to this item: http://hdl.handle.net/10668/3194
Title: VIGLA-M: visual gene expression data analytics
Authors: Navas-Delgado, Ismael
García-Nieto, José
López-Camacho, Esteban
Rybinski, Maciej
Lavado, Rocío
Berciano Guerrero, Miguel Ángel
Aldana-Montes, José F.
metadata.dc.contributor.authoraffiliation: [Navas-Delgado,I; García-Nieto,J; López-Camacho,E; Rybinski,M; Aldana-Montes,JF] Khaos Research, Universidad de Málaga, Málaga, Spain. [Lavado,R; Berciano Guerrero,MA] Unidad de Oncología Intercentros, Hospitales Univesitarios Regional y Virgen de la Victoria de Málaga, Instituto de Investigaciones Biomédicas (IBIMA), Málaga, Spain.
Keywords: Gene expression level analysis;Nanostring immune profiling panel;Metastatic melanoma;Gene Expression Profiling;Biomarkers;Perfilación de la expresión génica;Melanoma;Biomarcadores
metadata.dc.subject.mesh: Medical Subject Headings::Information Science::Information Science::Computing Methodologies::Algorithms
Medical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Epidemiologic Methods::Statistics as Topic::Cluster Analysis
Medical Subject Headings::Information Science::Information Science::Information Storage and Retrieval::Databases as Topic::Databases, Factual
Medical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Genetic Techniques::Gene Expression Profiling
Medical Subject Headings::Phenomena and Processes::Genetic Phenomena::Genetic Processes::Gene Expression Regulation
Medical Subject Headings::Phenomena and Processes::Genetic Phenomena::Genetic Structures::Base Sequence::Regulatory Sequences, Nucleic Acid::Gene Regulatory Networks
Medical Subject Headings::Organisms::Eukaryota::Animals::Chordata::Vertebrates::Mammals::Primates::Haplorhini::Catarrhini::Hominidae::Humans
Medical Subject Headings::Diseases::Neoplasms::Neoplasms by Histologic Type::Neoplasms, Germ Cell and Embryonal::Neuroectodermal Tumors::Neuroendocrine Tumors::Melanoma
Issue Date: 18-Apr-2019
Publisher: BioMed Central Ltd.
Citation: Navas-Delgado I, García-Nieto J, López-Camacho E, Rybinski M, Lavado R, Berciano Guerrero MÁ, et al. VIGLA-M: visual gene expression data analytics. BMC Bioinformatics. 2019 Apr 18;20(Suppl 4):150.
Abstract: Background: The analysis of gene expression levels is used in many clinical studies to know how patients evolve or to find new genetic biomarkers that could help in clinical decision making. However, the techniques and software available for these analyses are not intended for physicians, but for geneticists. However, enabling physicians to make initial discoveries on these data would benefit in the clinical assay development. Results: Melanoma is a highly immunogenic tumor. Therefore, in recent years physicians have incorporated immune system altering drugs into their therapeutic arsenal against this disease, revolutionizing the treatment of patients with an advanced stage of the cancer. This has led us to explore and deepen our knowledge of the immunology surrounding melanoma, in order to optimize the approach. Within this project we have developed a database for collecting relevant clinical information for melanoma patients, including the storage of patient gene expression levels obtained from the NanoString platform (several samples are taken from each patient). The Immune Profiling Panel is used in this case. This database is being exploited through the analysis of the different expression profiles of the patients. This analysis is being done with Python, and a parallel version of the algorithms is available with Apache Spark to provide scalability as needed. Conclusions: VIGLA-M, the visual analysis tool for gene expression levels in melanoma patients is available at http://khaos.uma.es/melanoma/ . The platform with real clinical data can be accessed with a demo user account, physician, using password physician_test_7634 (if you encounter any problems, contact us at this email address: mailto: khaos@lcc.uma.es). The initial results of the analysis of gene expression levels using these tools are providing first insights into the patients' evolution. These results are promising, but larger scale tests must be developed once new patients have been sequenced, to discover new genetic biomarkers.
URI: http://hdl.handle.net/10668/3194
metadata.dc.relation.publisherversion: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2695-7
metadata.dc.identifier.doi: 10.1186/s12859-019-2695-7
ISSN: 1471-2105 (Online)
Appears in Collections:01- Artículos - Hospital Regional de Málaga
01- Artículos - Hospital Virgen de la Victoria
01- Artículos - IBIMA. Instituto de Investigación Biomédica de Málaga

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