Prediction of human-Streptococcus pneumoniae protein-protein interactions using logistic regression.

Computational Biology and Chemistry
Vivitri Dewi PrasastyErnawati Sinaga

Abstract

Streptococcus pneumoniae is a major cause of mortality in children under five years old. In recent years, the emergence of antibiotic-resistant strains of S. pneumoniae increases the threat level of this pathogen. For that reason, the exploration of S. pneumoniae protein virulence factors should be considered in developing new drugs or vaccines, for instance by the analysis of host-pathogen protein-protein interactions (HP-PPIs). In this research, prediction of protein-protein interactions was performed with a logistic regression model with the number of protein domain occurrences as features. By utilizing HP-PPIs of three different pathogens as training data, the model achieved 57-77 % precision, 64-75 % recall, and 96-98 % specificity. Prediction of human-S. pneumoniae protein-protein interactions using the model yielded 5823 interactions involving thirty S. pneumoniae proteins and 324 human proteins. Pathway enrichment analysis showed that most of the pathways involved in the predicted interactions are immune system pathways. Network topology analysis revealed β-galactosidase (BgaA) as the most central among the S. pneumoniae proteins in the predicted HP-PPI networks, with a degree centrality of 1.0 and a betweenness central...Continue Reading

References

Jan 27, 1999·Bioinformatics·S R Eddy
May 31, 2001·Microbiology and Molecular Biology Reviews : MMBR·M J Jedrzejas
Feb 6, 2003·Proceedings of the National Academy of Sciences of the United States of America·Richard MalleyDouglas T Golenbock
Aug 14, 2003·Molecular Immunology·Hanna JarvaSeppo Meri
May 26, 2006·BMC Bioinformatics·Asa Ben-Hur, William Stafford Noble
Jun 6, 2006·PLoS Genetics·Xionglei He, Jianzhi Zhang
Mar 16, 2007·Proceedings of the National Academy of Sciences of the United States of America·Juwen ShenHualiang Jiang
Mar 15, 2008·Nature Reviews. Microbiology·Aras KadiogluPeter W Andrew
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Jan 31, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Jason E McDermottFred Heffron
Aug 31, 2010·Bioinformatics·Jiantao YuDavid R Westhead
Mar 9, 2011·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Matthew D DyerBruno W Sobral
Sep 11, 2012·Bioinformatics·Meghana KshirsagarJudith Klein-Seetharaman
Mar 22, 2013·Bioinformatics·Saliha Durmuş TekirKutlu Ö Ülgen
Apr 16, 2013·Lancet·Christa L Fischer WalkerRobert E Black
Jul 3, 2013·Bioinformatics·Meghana KshirsagarJudith Klein-Seetharaman
Jul 3, 2013·Cold Spring Harbor Perspectives in Medicine·Birgitta Henriques-Normark, Elaine I Tuomanen
Mar 5, 2015·PLoS Computational Biology·Vesna MemiševićAnders Wallqvist
Jun 19, 2015·Clinical Microbiology Reviews·K Aaron GenoMoon H Nahm
Oct 18, 2015·Nucleic Acids Research·Minoru KanehisaMao Tanabe
Dec 19, 2015·Bioinformatics·Fatma-Elzahraa EidLenwood S Heath
Jul 6, 2016·Methods : a Companion to Methods in Enzymology·Kai TianShuigeng Zhou
Dec 3, 2016·Nucleic Acids Research·UNKNOWN The UniProt Consortium
Mar 8, 2017·Frontiers in Microbiology·Greiciely O AndreMichelle Darrieux
Apr 22, 2017·American Journal of Therapeutics·Regine CherazardMiriam A Smith
May 5, 2017·Frontiers in Cellular and Infection Microbiology·Tungadri BoseSharmila S Mande
Mar 31, 2018·Nature Reviews. Microbiology·Jeffrey N WeiserJames C Paton
Aug 4, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Hang LiChang Zhou
Oct 26, 2018·Nucleic Acids Research·Sara El-GebaliRobert D Finn

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