UNIGE document Professional Article
previous document  unige:112636  next document
add to browser collection

Scoring Targets of Transcription in Bacteria Rather than Focusing on Individual Binding Sites

Djordjevic, Marko
Djordjevic, Magdalena
Published in Frontiers in Microbiology. 2017, vol. 8, p. 2314
Abstract Reliable identification of targets of bacterial regulators is necessary to understand bacterial gene expression regulation. These targets are commonly predicted by searching for high-scoring binding sites in the upstream genomic regions, which typically leads to a large number of false positives. In contrast to the common approach, here we propose a novel concept, where overrepresentation of the scoring distribution that corresponds to the entire searched region is assessed, as opposed to predicting individual binding sites. We explore two implementations of this concept, based on Kolmogorov-Smirnov (KS) and Anderson-Darling (AD) tests, which both provide straightforward P-value estimates for predicted targets. This approach is implemented for pleiotropic bacterial regulators, including σ70 (bacterial housekeeping σ factor) target predictions, which is a classical bioinformatics problem characterized by low specificity. We show that KS based approach is both faster and more accurate, departing from the current paradigm of AD being slower, but more accurate. Moreover, KS approach leads to a significant increase in the search accuracy compared to the standard approach, while at the same time straightforwardly assigning well established P-values to each potential target. Consequently, the new KS based method proposed here, which assigns P-values to fixed length upstream regions, provides a fast and accurate approach for predicting bacterial transcription targets.
PMID: 29213263
Full text
Article (Published version) (1.7 MB) - public document Free access
Research group Génomique Evolutionnaire Computationnelle (830)
(ISO format)
DJORDJEVIC, Marko, DJORDJEVIC, Magdalena, ZDOBNOV, Evgeny. Scoring Targets of Transcription in Bacteria Rather than Focusing on Individual Binding Sites. In: Frontiers in Microbiology, 2017, vol. 8, p. 2314. doi: 10.3389/fmicb.2017.02314 https://archive-ouverte.unige.ch/unige:112636

160 hits



Deposited on : 2019-01-09

Export document
Format :
Citation style :