Artículo

Rodriguez, J.C.; González, G.A.; Fresno, C.; Llera, A.S.; Fernández, E.A. "Improving information retrieval in functional analysis" (2016) Computers in Biology and Medicine. 79:10-20
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Abstract:

Transcriptome analysis is essential to understand the mechanisms regulating key biological processes and functions. The first step usually consists of identifying candidate genes; to find out which pathways are affected by those genes, however, functional analysis (FA) is mandatory. The most frequently used strategies for this purpose are Gene Set and Singular Enrichment Analysis (GSEA and SEA) over Gene Ontology. Several statistical methods have been developed and compared in terms of computational efficiency and/or statistical appropriateness. However, whether their results are similar or complementary, the sensitivity to parameter settings, or possible bias in the analyzed terms has not been addressed so far. Here, two GSEA and four SEA methods and their parameter combinations were evaluated in six datasets by comparing two breast cancer subtypes with well-known differences in genetic background and patient outcomes. We show that GSEA and SEA lead to different results depending on the chosen statistic, model and/or parameters. Both approaches provide complementary results from a biological perspective. Hence, an Integrative Functional Analysis (IFA) tool is proposed to improve information retrieval in FA. It provides a common gene expression analytic framework that grants a comprehensive and coherent analysis. Only a minimal user parameter setting is required, since the best SEA/GSEA alternatives are integrated. IFA utility was demonstrated by evaluating four prostate cancer and the TCGA breast cancer microarray datasets, which showed its biological generalization capabilities. © 2016 Elsevier Ltd

Registro:

Documento: Artículo
Título:Improving information retrieval in functional analysis
Autor:Rodriguez, J.C.; González, G.A.; Fresno, C.; Llera, A.S.; Fernández, E.A.
Filiación:UA AREA CS. AGR. ING. BIO. Y S, Universidad Católica de Córdoba, CONICET, Córdoba, Argentina
Facultad de Matemática, Astronomía y Física, Universidad Nacional de Córdoba, Córdoba, Argentina
Instituto Nacional de Cáncer, MinSal, Córdoba, Argentina
IIBBA, Fund. Instituto Leloir, CONICET, Buenos Aires, Argentina
Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
Palabras clave:Big omics data; Biological insight; Breast cancer; Functional class scoring; Gene set enrichment analysis; Knowledge discovery; Over representation analysis; R framework; Singular enrichment analysis; Computational efficiency; Data mining; Diseases; Functional analysis; Genes; Information retrieval; Big omics data; Biological insight; Breast Cancer; Functional class; Gene set enrichment analysis; Over representation analysis; R framework; Singular enrichment analysis; Gene expression
Año:2016
Volumen:79
Página de inicio:10
Página de fin:20
DOI: http://dx.doi.org/10.1016/j.compbiomed.2016.09.017
Título revista:Computers in Biology and Medicine
Título revista abreviado:Comput. Biol. Med.
ISSN:00104825
CODEN:CBMDA
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00104825_v79_n_p10_Rodriguez

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Citas:

---------- APA ----------
Rodriguez, J.C., González, G.A., Fresno, C., Llera, A.S. & Fernández, E.A. (2016) . Improving information retrieval in functional analysis. Computers in Biology and Medicine, 79, 10-20.
http://dx.doi.org/10.1016/j.compbiomed.2016.09.017
---------- CHICAGO ----------
Rodriguez, J.C., González, G.A., Fresno, C., Llera, A.S., Fernández, E.A. "Improving information retrieval in functional analysis" . Computers in Biology and Medicine 79 (2016) : 10-20.
http://dx.doi.org/10.1016/j.compbiomed.2016.09.017
---------- MLA ----------
Rodriguez, J.C., González, G.A., Fresno, C., Llera, A.S., Fernández, E.A. "Improving information retrieval in functional analysis" . Computers in Biology and Medicine, vol. 79, 2016, pp. 10-20.
http://dx.doi.org/10.1016/j.compbiomed.2016.09.017
---------- VANCOUVER ----------
Rodriguez, J.C., González, G.A., Fresno, C., Llera, A.S., Fernández, E.A. Improving information retrieval in functional analysis. Comput. Biol. Med. 2016;79:10-20.
http://dx.doi.org/10.1016/j.compbiomed.2016.09.017