A comparison between gene set and individual gene analyses using JProGO

Microarray, developed at the end of the last century, is one of the most significant achievements in biotechnology history. One of the most important applications of microarrays is to uncover the signature genes characterizing different samples or biological states. This application was initially used in individual gene analysis, but recently has been applied to gene set analysis. We compare these two approaches and compare the performance using JProGO (Java Tool for the Functional Analysis of Prokaryotic Microarray Data using the Gene Ontology). JProGO is able to examine microarray data from more than 20 different samples of prokaryotic and thus practical analysis of gene behavior data with regards to Gene Ontology (GO) is made possible. Two Escherichia coli datasets are used to compare the performance of the two analyses. The results show that the gene set analysis is more powerful because of its ability to detect the GO terms according to biological expectation. This research will provide a new platform and opportunities for further research or studies in microarray based gene sets.