Mapping Transcription Factors from a Model to a Non-model Organism

Abstract

Identification of regulatory elements, such as transcription factors, is useful in construction of regulatory networks and to understand gene regulation. These transcription factors have already been recognized for model organisms based on extensive experiments but have not been as heavily investigated for non-model organisms. This paper proposes to use Basic Local Alignment Search Tool (BLAST) to map the transcription factors from a model to a non-model organism. Experiments are performed on bacterial organisms based on evolutionary distance to compare the results. Analysis of the results suggest that transcription factors can be mapped from one bacterial organism to another as transcription factor motifs are well preserved among these organisms. Results are also analyzed to determine the best suitable threshold for the e-value parameter of BLAST that can be used to map transcription factors, determine to be the e-value thresholds of 0.01 and 0.1. Both the BLAST e-value threshold and evolutionary distance from the model organism used for mapping have significant impact on the quality of results.