DNA Chip Analysis Software

Specification

GenPlex is a comprehensively organized system addressing the key issues of DNA chip data analysis, modularized in four independent components: preprocessing, class comparison, class discovery, and class prediction. The four modules have their own unique analysis methods and are connected in a whole analysis pipeline. The preprocessing module translates various chip platforms raw data into the input files for the three subsequent analysis modules. It includes statistical methodologies like normalizations with useful plots to enhance data quality by reducing experimental errors. The connectivity between the preprocessing module and the other three modules is the basic gene expression matrix that is a baseline file format for further analysis. Given gene lists obtained from each analysis module, their biological meanings are further investigated by retrieving such biological information as GO annotations, pathway involvement. Moreover statistical data mining using GO is adopted to find meaningful biological themes on given gene lists.