Near-sigmoid Modeling to Simultaneously Profile Genome-wide DNA Replication Timing and Efficiency in Single DNA Replication Microarray Studies

DNA replication is a key process in cell division cycle. It is initiated in coordinated manner in several species. To understand the DNA replication in a species one needs to measure the half replication timing (or replication timing) and the efficiency of replication which vary across genome in higher eukaryotes. In the previous studies, no direct assessment of replication efficiency on a genomic scale was performed while the replication timing was indirectly assessed using average DNA. In this paper, we present a first-ever-method of directly measuring both half replication timing and efficiency simultaneously from a single DNA microarray time-course data. We achieve it by fitting the so called near-sigmoid model to each locus of the DNA. We use this model apply S. pombe DNA replication microarray data and show that it is effective for genome-scale replication timing and efficiency profiling studies.