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transcription start sites, gene regulation, 5'end mRNA, CAGE, gene expression profiling

Gene regulation is a significant problem in functional genomics. To understand gene regulation process, several tag-based sequencing methods such as Cap Analysis of Gene Expression (CAGE), 5’ end Serial Analysis of Gene Expression (5’ end SAGE) are developed. These novel methods pave the way to study gene regulation and expression profiling through Transcription Start Sites (TSSs). Several studies collected 5’end mRNA tag data from various species and showed that most of the promoters do not show a preference to a distinct TSS for a gene. Most of the promoters have several TSSs that are locally distributed in particular genomic regions. Analysis of these TSSs distributions may decipher the gene regulatory process. For that purpose, a numerical representation of TSS distribution is crucial for quantitative analysis of 5’end mRNA data. To characterize the TSSs distribution of a promoter as a single measurement score, we developed a novel scoring method that describes the distribution in a more meaningful way. Efficiency of this method to distinguish TSSs distribution is evaluated on both synthetic and real dataset. Finally, this numerical representation enables us to analyze 5’end mRNA data to understand gene regulation process more precisely.