algebraic comparison of partial lists in bioinformatics在生物信息学中代数比较部分列表.pdfVIP

Algebraic Comparison of Partial Lists in Bioinformatics 1 1 1,2 1 Giuseppe Jurman *, Samantha Riccadonna , Roberto Visintainer , Cesare Furlanello 1 Fondazione Bruno Kessler, Trento, Italy, 2 DISI, University of Trento, Trento, Italy Abstract The outcome of a functional genomics pipeline is usually a partial list of genomic features, ranked by their relevance in modelling biological phenotype in terms of a classification or regression model. Due to resampling protocols or to a meta- analysis comparison, it is often the case that sets of alternative feature lists (possibly of different lengths) are obtained, instead of just one list. Here we introduce a method, based on permutations, for studying the variability between lists (‘‘list stability’’) in the case of lists of unequal length. We provide algorithms evaluating stability for lists embedded in the full feature set or just limited to the features occurring in the partial lists. The method is demonstrated by finding and comparing gene profiles on a large prostate cancer dataset, consisting of two cohorts of patients from different countries, for a total of 455 samples. Citation: Jurman G, Riccadonna S, Visintainer R, Furlanello C (2012) Algebraic Comparison of Partial Lists in Bioinformatics. PLoS ONE 7(5): e36540. doi:10.1371/ journal.pone.0036540 Editor: Arkady B. Khodursky, University of Minnesota, United States of America Received June 10, 2011; Accepted April 6, 2012; Published May 17, 2012 Copyright: 2012 Jurman et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any