ArrayQue: The comprehensive transcriptome data analysis tool

We have developed microarray analysis pipeline software for covering the entire process of transcriptome data analysis. This software, part of the Korea Toxicogenomics Integrated System (KOTIS), is freely distributed to users who upload their microarray data to the KOTIS database, which is operated under the server system of the National Institute of Toxicological Research (NITR). The uploaded microarray data can be downloaded by users through a web search interface within KOTIS and are used as input data of the analysis software. The software, which consists of four major analysis modules and one meta-analysis module, is connected to a gene-related annotation database through the web. Major analysis modules consist of (1) data import and preprocessing, (2) differentially expressed gene finding, (3) clustering analysis, and (4) classification analysis. A gene-related annotation database provides the biological meanings of the analysis results. A highly standardized analysis flow, from data import to differentially expressed gene finding, can be easily implemented using the interface series of a run wizard. The KOTIS system and analysis software are accessible at http://kotis.nitr.go.kr.