NDLI: Predicting transcriptional regulatory interactions with artificial neural networks applied to E. coli multidrug resistance efflux pumps

Content Provider	Springer Nature : BioMed Central
Author	Veiga, Diogo FT Vicente, Fábio FR Nicolás, Marisa F Vasconcelos, Ana Tereza R
Abstract	Background Little is known about bacterial transcriptional regulatory networks (TRNs). In Escherichia coli, which is the organism with the largest wet-lab validated TRN, its set of interactions involves only ~50% of the repertoire of transcription factors currently known, and ~25% of its genes. Of those, only a small proportion describes the regulation of processes that are clinically relevant, such as drug resistance mechanisms. Results We designed feed-forward (FF) and bi-fan (BF) motif predictors for E. coli using multi-layer perceptron artificial neural networks (ANNs). The motif predictors were trained using a large dataset of gene expression data; the collection of motifs was extracted from the E. coli TRN. Each network motif was mapped to a vector of correlations which were computed using the gene expression profile of the elements in the motif. Thus, by combining network structural information with transcriptome data, FF and BF predictors were able to classify with a high precision of 83% and 96%, respectively, and with a high recall of 86% and 97%, respectively. These results were found when motifs were represented using different types of correlations together, i.e., Pearson, Spearman, Kendall, and partial correlation. We then applied the best predictors to hypothesize new regulations for 16 operons involved with multidrug resistance (MDR) efflux pumps, which are considered as a major bacterial mechanism to fight antimicrobial agents. As a result, the motif predictors assigned new transcription factors for these MDR proteins, turning them into high-quality candidates to be experimentally tested. Conclusion The motif predictors presented herein can be used to identify novel regulatory interactions by using microarray data. The presentation of an example motif to predictors will make them categorize whether or not the example motif is a BF, or whether or not it is an FF. This approach is useful to find new \"pieces\" of the TRN, when inspecting the regulation of a small set of operons. Furthermore, it shows that correlations of expression data can be used to discriminate between elements that are arranged in structural motifs and those in random sets of transcripts.
Related Links	https://bmcmicrobiol.biomedcentral.com/counter/pdf/10.1186/1471-2180-8-101.pdf
Ending Page	14
Page Count	14
Starting Page	1
File Format	HTM / HTML
ISSN	14712180
DOI	10.1186/1471-2180-8-101
Journal	BMC Microbiology
Issue Number	1
Volume Number	8
Language	English
Publisher	BioMed Central
Publisher Date	2008-06-19
Access Restriction	Open
Subject Keyword	Microbiology Biological Microscopy Mycology Parasitology Virology Life Sciences Feature Vector Efflux Pump Network Motif True Motif Small Multidrug Resistance
Content Type	Text
Resource Type	Article
Subject	Microbiology Microbiology (medical)
Journal Impact Factor	4/2023
5-Year Journal Impact Factor	4.6/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Predicting transcriptional regulatory interactions with artificial neural networks applied to E. coli multidrug resistance efflux pumps

Characterization of genes related to the efflux pump and porin in multidrug-resistant Escherichia coli strains isolated from patients with COVID-19 after secondary infection

Efflux pump genes of the resistance-nodulation-division family in Burkholderia cenocepacia genome

Chlorpromazine inhibits the plasmid-mediated oqxAB multidrug efflux pump in Escherichia coli isolates of Egyptian patients with utis

Downregulation of Klebsiella pneumoniae RND efflux pump genes following indole signal produced by Escherichia coli

Investigating multidrug efflux pumps associated with fatty acid salt resistance in Escherichia coli

Clonality, outer-membrane proteins profile and efflux pump in KPC- producing Enterobacter sp. in Brazil

Thymol tolerance in Escherichia coli induces morphological, metabolic and genetic changes

Characterization of AcrD, a Resistance-Nodulation-Cell Division-type multidrug efflux pump from the fire blight pathogen Erwinia amylovora

Predicting transcriptional regulatory interactions with artificial neural networks applied to E. coli multidrug resistance efflux pumps

Similar Documents

Predicting transcriptional regulatory interactions with artificial neural networks applied to E. coli multidrug resistance efflux pumps

Characterization of genes related to the efflux pump and porin in multidrug-resistant Escherichia coli strains isolated from patients with COVID-19 after secondary infection

Efflux pump genes of the resistance-nodulation-division family in Burkholderia cenocepacia genome

Chlorpromazine inhibits the plasmid-mediated oqxAB multidrug efflux pump in Escherichia coli isolates of Egyptian patients with utis

Downregulation of Klebsiella pneumoniae RND efflux pump genes following indole signal produced by Escherichia coli

Investigating multidrug efflux pumps associated with fatty acid salt resistance in Escherichia coli

Clonality, outer-membrane proteins profile and efflux pump in KPC- producing Enterobacter sp. in Brazil

Thymol tolerance in Escherichia coli induces morphological, metabolic and genetic changes

Characterization of AcrD, a Resistance-Nodulation-Cell Division-type multidrug efflux pump from the fire blight pathogen Erwinia amylovora

Predicting transcriptional regulatory interactions with artificial neural networks applied to E. coli multidrug resistance efflux pumps