https://scholars.lib.ntu.edu.tw/handle/123456789/385322
標題: | MAVTgsa: An R package for gene set (enrichment) analysis | 作者: | Chien, C.-Y. Chang, C.-W. CHEN-AN TSAI Chen, J.J. |
公開日期: | 2014 | 卷: | 2014 | 來源出版物: | BioMed Research International | 摘要: | Gene set analysis methods aim to determine whether an a priori defined set of genes shows statistically significant difference in expression on either categorical or continuous outcomes. Although many methods for gene set analysis have been proposed, a systematic analysis tool for identification of different types of gene set significance modules has not been developed previously. This work presents an R package, called MAVTgsa, which includes three different methods for integrated gene set enrichment analysis. (1) The one-sided OLS (ordinary least squares) test detects coordinated changes of genes in gene set in one direction, either up- or downregulation. (2) The two-sided MANOVA (multivariate analysis variance) detects changes both up- and downregulation for studying two or more experimental conditions. (3) A random forests-based procedure is to identify gene sets that can accurately predict samples from different experimental conditions or are associated with the continuous phenotypes. MAVTgsa computes the P values and FDR (false discovery rate) q -value for all gene sets in the study. Furthermore, MAVTgsa provides several visualization outputs to support and interpret the enrichment results. This package is available online. ? 2014 Chih-Yi Chien,et al. |
URI: | http://www.scopus.com/inward/record.url?eid=2-s2.0-84904807864&partnerID=MN8TOARS http://scholars.lib.ntu.edu.tw/handle/123456789/385322 |
DOI: | 10.1155/2014/346074 | SDG/關鍵字: | algorithm; analysis of covariance; article; breast cancer; cancer cell line; cell cycle regulation; computer program; down regulation; gene expression; gene mutation; gene set analysis; genetic analysis; mavtgsa package; multivariate analysis of variance; phenotype; random forest; upregulation; DNA microarray; gene expression profiling; gene expression regulation; genetic database; genetics; procedures; statistical model; Algorithms; Databases, Genetic; Gene Expression Profiling; Gene Expression Regulation; Models, Statistical; Oligonucleotide Array Sequence Analysis |
顯示於: | 農藝學系 |
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