Intragenic differential expression in archaea transcriptomes revealed by computational analysis of tiling microarrays

Recent advances, in high-throughput technologies allows whole transcriptome analysis, providing a complete and panoramic view of intragenic differential expression in eukaryotes. However, intragenic differential expression in prokaryotes still mystery and incompletely understood. In this study, we investigated and collected the evidence for intragenic differential expression in several archaeal transcriptomes such as, Halobacterium salinarum NRC-1, Pyrococcus furiosus, Methanococcus maripaludis , and Sulfolobus solfataricus , based on computational methods; specifically, by well-known self-organizing map (SOM) for cluster analysis, which transforms high dimensional data into low dimensional. We found 104 (3.86%) of genes in Halobacterium salinarum NRC-1, 59 (2.56%) of genes in Pyrococcus furiosus, 43 (2.41%) of genes Methanococcus maripaludis and 13 (0.42%) of genes in Sulfolobus solfataricus have two or more clusters, i.e., showed the intragenic differential expression at different conditions.