Improving 2D-DIGE protein expression analysis by two-stage linear mixed models: assessing experimental effects in a melanoma cell study

Fernández, Elmer A. ORCID: https://orcid.org/0000-0002-4711-8634, Girotti, María R., López del Olmo, Juan A., Llera, Andrea S., Podhajcer, Osvaldo ORCID: https://orcid.org/0000-0002-6512-8553, Cantet, Rodolfo J. C. and Balzarini, Mónica (2008) Improving 2D-DIGE protein expression analysis by two-stage linear mixed models: assessing experimental effects in a melanoma cell study. Bioinformatics, 24 (23). pp. 2706-2712. ISSN 1460-2059

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Resumen

Motivation: Difference in-gel electrophoresis (DIGE)-based protein expression analysis allows assessing the relative expression of proteins in two biological samples differently labeled (Cy5, Cy3 CyDyes). In the same gel, a reference sample is also used (Cy2 CyDye) for spot matching during image analysis and volume normalization. The standard statistical techniques to identify differentially expressed (DE) proteins are the calculation of foldchanges and the comparison of treatment means by the t-test. The analyses rarely accounts for other experimental effects, such as CyDye and gel effects, which could be important sources of noise while detecting treatment effects. Results: We propose to identify DIGE DE proteins using a two-stage linear mixed model. The proposal consists of splitting the overall model for the measured intensity into two interconnected models. First, we fit a normalization model that accounts for the general experimental effects, such as gel and CyDye effects as well as for the features of the associated random term distributions. Second, we fit a model that uses the residuals from the first step to account for differences between treatments in protein-by-protein basis. The modeling strategy was evaluated using data from a melanoma cell study. We found that a heteroskedastic model in the first stage, which also account for CyDye and gel effects, best normalized the data, while allowing for an efficient estimation of the treatment effects. The Cy2 reference channel was used as a covariate in the normalization model to avoid skewness of the residual distribution. Its inclusion improved the detection of DE proteins in the second stage.

Tipo de documento:	Artículo
DOI:	https://doi.org/10.1093/bioinformatics/btn508
Palabras clave:	Carbocyanines. Cell Line, Tumor. Computational Biology. Electrophoresis. Gel, Two-Dimensional. Fluorescent Dyes. Humans. Image Processing, Computer-Assisted. Linear Model. Melanoma. Proteome. Proteomics.
Temas:	T Tecnología > TA Ingeniería de asistencia técnica (General). Ingeniería Civil (General)
Unidad académica:	Universidad Católica de Córdoba > Facultad de Ingeniería
Google Académico:	Ver citaciones
URI:	http://pa.bibdigital.ucc.edu.ar/id/eprint/4179

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