{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,9,14]],"date-time":"2023-09-14T00:18:25Z","timestamp":1694650705144},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"23","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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 fold-changes 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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Contact: \u00a0elmer.fernandez@ucc.edu.ar<\/jats:p>\n               <jats:p>Supplementary information: R and SAS codes to analyze DIGE data with the proposed approach are available at http:\/\/www.uccor.edu.ar\/modelo.php?param=3.8.5.15.2<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn508","type":"journal-article","created":{"date-parts":[[2008,9,26]],"date-time":"2008-09-26T00:13:43Z","timestamp":1222388023000},"page":"2706-2712","source":"Crossref","is-referenced-by-count":2,"title":["Improving 2D-DIGE protein expression analysis by two-stage linear mixed models: assessing experimental effects in a melanoma cell study"],"prefix":"10.1093","volume":"24","author":[{"given":"Elmer A.","family":"Fern\u00e1;ndez","sequence":"first","affiliation":[{"name":"1 School of Engineering, Intelligent Data Analysis Group, Catholic University of C\u00f3rdoba, 2CONICET, C\u00f3rdoba, 3Laboratory of Molecular and Cellular Therapy, Fundaci\u00f3n Instituto Leloir, Buenos Aires, Argentina, 4Unidad de Prote\u00f3mica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain, 5Facultad de Agronom\u00eda, UBA (University of Buenos Aires), Buenos Aires and 6Biometric Department, National University of C\u00f3rdoba, C\u00f3rdoba, Argentina"},{"name":"1 School of Engineering, Intelligent Data Analysis Group, Catholic University of C\u00f3rdoba, 2CONICET, C\u00f3rdoba, 3Laboratory of Molecular and Cellular Therapy, Fundaci\u00f3n Instituto Leloir, Buenos Aires, Argentina, 4Unidad de Prote\u00f3mica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain, 5Facultad de Agronom\u00eda, UBA (University of Buenos Aires), Buenos Aires and 6Biometric Department, National University of C\u00f3rdoba, C\u00f3rdoba, Argentina"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mar\u00eda R.","family":"Girotti","sequence":"additional","affiliation":[{"name":"1 School of Engineering, Intelligent Data Analysis Group, Catholic University of C\u00f3rdoba, 2CONICET, C\u00f3rdoba, 3Laboratory of Molecular and Cellular Therapy, Fundaci\u00f3n Instituto Leloir, Buenos Aires, Argentina, 4Unidad de Prote\u00f3mica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain, 5Facultad de Agronom\u00eda, UBA (University of Buenos Aires), Buenos Aires and 6Biometric Department, National University of C\u00f3rdoba, C\u00f3rdoba, Argentina"},{"name":"1 School of Engineering, Intelligent Data Analysis Group, Catholic University of C\u00f3rdoba, 2CONICET, C\u00f3rdoba, 3Laboratory of Molecular and Cellular Therapy, Fundaci\u00f3n Instituto Leloir, Buenos Aires, Argentina, 4Unidad de Prote\u00f3mica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain, 5Facultad de Agronom\u00eda, UBA (University of Buenos Aires), Buenos Aires and 6Biometric Department, National University of C\u00f3rdoba, C\u00f3rdoba, Argentina"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juan A. L\u00f3pez","family":"del Olmo","sequence":"additional","affiliation":[{"name":"1 School of Engineering, Intelligent Data Analysis Group, Catholic University of C\u00f3rdoba, 2CONICET, C\u00f3rdoba, 3Laboratory of Molecular and Cellular Therapy, Fundaci\u00f3n Instituto Leloir, Buenos Aires, Argentina, 4Unidad de Prote\u00f3mica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain, 5Facultad de Agronom\u00eda, UBA (University of Buenos Aires), Buenos Aires and 6Biometric Department, National University of C\u00f3rdoba, C\u00f3rdoba, Argentina"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrea S.","family":"Llera","sequence":"additional","affiliation":[{"name":"1 School of Engineering, Intelligent Data Analysis Group, Catholic University of C\u00f3rdoba, 2CONICET, C\u00f3rdoba, 3Laboratory of Molecular and Cellular Therapy, Fundaci\u00f3n Instituto Leloir, Buenos Aires, Argentina, 4Unidad de Prote\u00f3mica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain, 5Facultad de Agronom\u00eda, UBA (University of Buenos Aires), Buenos Aires and 6Biometric Department, National University of C\u00f3rdoba, C\u00f3rdoba, Argentina"},{"name":"1 School of Engineering, Intelligent Data Analysis Group, Catholic University of C\u00f3rdoba, 2CONICET, C\u00f3rdoba, 3Laboratory of Molecular and Cellular Therapy, Fundaci\u00f3n Instituto Leloir, Buenos Aires, Argentina, 4Unidad de Prote\u00f3mica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain, 5Facultad de Agronom\u00eda, UBA (University of Buenos Aires), Buenos Aires and 6Biometric Department, National University of C\u00f3rdoba, C\u00f3rdoba, Argentina"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Osvaldo L.","family":"Podhajcer","sequence":"additional","affiliation":[{"name":"1 School of Engineering, Intelligent Data Analysis Group, Catholic University of C\u00f3rdoba, 2CONICET, C\u00f3rdoba, 3Laboratory of Molecular and Cellular Therapy, Fundaci\u00f3n Instituto Leloir, Buenos Aires, Argentina, 4Unidad de Prote\u00f3mica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain, 5Facultad de Agronom\u00eda, UBA (University of Buenos Aires), Buenos Aires and 6Biometric Department, National University of C\u00f3rdoba, C\u00f3rdoba, Argentina"},{"name":"1 School of Engineering, Intelligent Data Analysis Group, Catholic University of C\u00f3rdoba, 2CONICET, C\u00f3rdoba, 3Laboratory of Molecular and Cellular Therapy, Fundaci\u00f3n Instituto Leloir, Buenos Aires, Argentina, 4Unidad de Prote\u00f3mica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain, 5Facultad de Agronom\u00eda, UBA (University of Buenos Aires), Buenos Aires and 6Biometric Department, National University of C\u00f3rdoba, C\u00f3rdoba, Argentina"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rodolfo J. C.","family":"Cantet","sequence":"additional","affiliation":[{"name":"1 School of Engineering, Intelligent Data Analysis Group, Catholic University of C\u00f3rdoba, 2CONICET, C\u00f3rdoba, 3Laboratory of Molecular and Cellular Therapy, Fundaci\u00f3n Instituto Leloir, Buenos Aires, Argentina, 4Unidad de Prote\u00f3mica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain, 5Facultad de Agronom\u00eda, UBA (University of Buenos Aires), Buenos Aires and 6Biometric Department, National University of C\u00f3rdoba, C\u00f3rdoba, Argentina"},{"name":"1 School of Engineering, Intelligent Data Analysis Group, Catholic University of C\u00f3rdoba, 2CONICET, C\u00f3rdoba, 3Laboratory of Molecular and Cellular Therapy, Fundaci\u00f3n Instituto Leloir, Buenos Aires, Argentina, 4Unidad de Prote\u00f3mica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain, 5Facultad de Agronom\u00eda, UBA (University of Buenos Aires), Buenos Aires and 6Biometric Department, National University of C\u00f3rdoba, C\u00f3rdoba, Argentina"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M\u00f3nica","family":"Balzarini","sequence":"additional","affiliation":[{"name":"1 School of Engineering, Intelligent Data Analysis Group, Catholic University of C\u00f3rdoba, 2CONICET, C\u00f3rdoba, 3Laboratory of Molecular and Cellular Therapy, Fundaci\u00f3n Instituto Leloir, Buenos Aires, Argentina, 4Unidad de Prote\u00f3mica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain, 5Facultad de Agronom\u00eda, UBA (University of Buenos Aires), Buenos Aires and 6Biometric Department, National University of C\u00f3rdoba, C\u00f3rdoba, Argentina"},{"name":"1 School of Engineering, Intelligent Data Analysis Group, Catholic University of C\u00f3rdoba, 2CONICET, C\u00f3rdoba, 3Laboratory of Molecular and Cellular Therapy, Fundaci\u00f3n Instituto Leloir, Buenos Aires, Argentina, 4Unidad de Prote\u00f3mica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain, 5Facultad de Agronom\u00eda, UBA (University of Buenos Aires), Buenos Aires and 6Biometric Department, National University of C\u00f3rdoba, C\u00f3rdoba, Argentina"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,9,25]]},"reference":[{"key":"2023020212242076800_B1","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1002\/pmic.200390006","article-title":"A novel experimental design for comparative two-dimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard","volume":"3","author":"Alban","year":"2003","journal-title":"Proteomics"},{"key":"2023020212242076800_B2","volume-title":"DeCyder Differential Analysis Sotware User manual, version 5.0.","author":"Amersham","year":"2003"},{"key":"2023020212242076800_B3","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/j.matbio.2004.01.002","article-title":"International Hermelin brain tumor symposium on matricellular proteins in normal and cancer cell-matrix interactions","volume":"23","author":"Bos","year":"2004","journal-title":"Matrix Biol"},{"key":"2023020212242076800_B4","volume-title":"Experimental Designs","author":"Cochran","year":"1957","edition":"2nd edn"},{"key":"2023020212242076800_B5","volume-title":"Mixed Models: Theory and Applications","author":"Demidenko","year":"2005"},{"key":"2023020212242076800_B6","doi-asserted-by":"crossref","first-page":"1348","DOI":"10.1093\/bioinformatics\/btg165","article-title":"Noise sampling method: an ANOVA approach allowing robust selection of differentially regulated genes measured by DNA microarrays","volume":"19","author":"Draghici","year":"2003","journal-title":"Bioinformatics"},{"key":"2023020212242076800_B7","doi-asserted-by":"crossref","first-page":"3733","DOI":"10.1093\/bioinformatics\/bti612","article-title":"Statistical challenges in the analysis of two-dimensional difference gel electrophoresis experiments using DeCyder","volume":"21","author":"Fodor","year":"2005","journal-title":"Bioinformatics"},{"key":"2023020212242076800_B8","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1080\/01621459.1977.10480998","article-title":"Maximum likelihood approaches to variance component estimation and to related problems","volume":"72","author":"Harville","year":"1977","journal-title":"J. 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