The expressions of proteins in the cell are carefully regulated by transcription factors that interact with their downstream targets in specific signal transduction cascades. Our understanding of the regulation of functional genes responsive to stress signals is still nascent. Plants like Arabidopsis thaliana, are convenient model systems to study fundamental questions related to regulation of the stress transcriptome in response to stress challenges. Microarray results of the Arabidopsis transcriptome indicate that several genes could be upregulated during multiple stresses, such as cold, salinity, drought etc. Experimental biochemical validations have proved the involvement of several transcription factors could be involved in the upregulation of these stress responsive genes. In order to follow the intricate and complicated networks of transcription factors and genes that respond to stress situations in plants, we have developed a computer algorithm that can identify key transcription factor binding sites upstream of a gene of interest. Hidden Markov models of the transcription factor binding sites enable the identification of predicted sites upstream of plant stress genes. The search algorithm, STIF, performs very well, with more than 90% sensitivity, when tested on experimentally validated positions of transcription factor binding sites on a dataset of 60 stress upregulated genes. AVAILABILITY: Supplementary data is available at http://caps.ncbs.res.in/download/stif.
Sundar, A. S., Varghese, S. M., Shameer, K., Karaba, N., Udayakumar, M., & Sowdhamini, R. (2012). STIF: Identification of stress-upregulated transcription factor binding sites in Arabidopsis thaliana. Bioinformation, 2(10), 431–437. https://doi.org/10.6026/97320630002431