Most promoters are derived from an arbitrary truncation of sequences upstream from the transcription start site of a gene, which is typically around 1,000 base pairs. Since the truncation is arbitrary, regulatory elements might be missing for transcription. Unfortunately, there exists no reasonable rationale for selecting a truncation threshold. Therefore, providing a reasonable rationale for truncation is crucial for obtaining the expected expression profiles of genes. In this work, we arrive at a reasonable rationale by first identifying putative shared promoters based on the similarity of expression profile between neighboring genes and second discovering that shorter shared promoters correspond to genes that have more similar expression profiles. Using this novel insight, we subsequently defined aggressive, standard, and conservative thresholds of human promoter sequences. We further refined human promoter sequences using known cis-regulatory elements and transcription factor binding regions, resulting in slightly reduced thresholds. Our study provides a reasonable rationale for truncating human promoter sequences that forms the starting point for future experimental verification by the biological community
Open the excel file. The data for each figure are recorded.