@inproceedings{f7dcc01dacca4a1196d640e02f743e73,
title = "Principle Angle Enrichment Analysis (PAEA): Dimensionally reduced multivariate gene set enrichment analysis tool",
abstract = "Gene set analysis of differential expression, which identifies collectively differentially expressed gene sets, has become an important tool for biology. The power of this approach lies in its reduction of the dimensionality of the statistical problem and its incorporation of biological interpretation by construction. Many approaches to gene set analysis have been proposed, but benchmarking their performance in the setting of real biological data is difficult due to the lack of a gold standard. In a previously published work we proposed a geometrical approach to differential expression which performed highly in benchmarking tests and compared well to the most popular methods of differential gene expression. As reported, this approach has a natural extension to gene set analysis which we call Principal Angle Enrichment Analysis (PAEA). PAEA employs dimensionality reduction and a multivariate approach for gene set enrichment analysis. However, the performance of this method has not been assessed nor its implementation as a web-based tool. Here we describe new benchmarking protocols for gene set analysis methods and find that PAEA performs highly. The PAEA method is implemented as a user-friendly web-based tool, which contains 70 gene set libraries and is freely available to the community.",
keywords = "dimensionality reduction, gene set analysis, multivariate, online enrichment analysis tool",
author = "Clark, {Neil R.} and Maciej Szymkiewicz and Zichen Wang and Monteiro, {Caroline D.} and Jones, {Matthew R.} and Avi Ma'ayan",
note = "Publisher Copyright: {\textcopyright} 2015 IEEE.; IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 ; Conference date: 09-11-2015 Through 12-11-2015",
year = "2015",
month = dec,
day = "16",
doi = "10.1109/BIBM.2015.7359689",
language = "English",
series = "Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015",
publisher = "Institute of Electrical and Electronics Engineers Inc.",
pages = "256--262",
editor = "Schapranow, {lng. Matthieu} and Jiayu Zhou and Hu, {Xiaohua Tony} and Bin Ma and Sanguthevar Rajasekaran and Satoru Miyano and Illhoi Yoo and Brian Pierce and Amarda Shehu and Gombar, {Vijay K.} and Brian Chen and Vinay Pai and Jun Huan",
booktitle = "Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015",
address = "United States",
}