PMID- 29213263
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20231112
IS  - 1664-302X (Print)
IS  - 1664-302X (Electronic)
IS  - 1664-302X (Linking)
VI  - 8
DP  - 2017
TI  - Scoring Targets of Transcription in Bacteria Rather than Focusing on Individual 
      Binding Sites.
PG  - 2314
LID - 10.3389/fmicb.2017.02314 [doi]
LID - 2314
AB  - 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 sigma(70) (bacterial housekeeping sigma 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.
FAU - Djordjevic, Marko
AU  - Djordjevic M
AD  - Institute of Physiology and Biochemistry, Faculty of Biology, University of 
      Belgrade, Belgrade, Serbia.
FAU - Djordjevic, Magdalena
AU  - Djordjevic M
AD  - Institute of Physics Belgrade, University of Belgrade, Belgrade, Serbia.
FAU - Zdobnov, Evgeny
AU  - Zdobnov E
AD  - Swiss Institute of Bioinformatics and Department of Genetic Medicine and 
      Development, University of Geneva, Geneva, Switzerland.
LA  - eng
PT  - Journal Article
DEP - 20171122
PL  - Switzerland
TA  - Front Microbiol
JT  - Frontiers in microbiology
JID - 101548977
PMC - PMC5702782
OTO - NOTNLM
OT  - bacterial gene expression regulation
OT  - direct target gene predictions
OT  - position specific weight matrices
OT  - sigma70
OT  - transcription factor binding site predictions
OT  - transcription regulation
OT  - transcription start starts
OT  - transcription targets
EDAT- 2017/12/08 06:00
MHDA- 2017/12/08 06:01
PMCR- 2017/11/22
CRDT- 2017/12/08 06:00
PHST- 2017/07/31 00:00 [received]
PHST- 2017/11/09 00:00 [accepted]
PHST- 2017/12/08 06:00 [entrez]
PHST- 2017/12/08 06:00 [pubmed]
PHST- 2017/12/08 06:01 [medline]
PHST- 2017/11/22 00:00 [pmc-release]
AID - 10.3389/fmicb.2017.02314 [doi]
PST - epublish
SO  - Front Microbiol. 2017 Nov 22;8:2314. doi: 10.3389/fmicb.2017.02314. eCollection 
      2017.