Abstract
Pathogen–host interactions (PHIs) underlie the process of infection. The systems biology view of the whole PHI system is superior to the investigation of the pathogen or host separately in understanding the infection mechanisms. Especially, the identification of host-oriented drug targets for the next-generation anti-infection therapeutics requires the properties of the host factors targeted by pathogens. Here, we provide an outline of computational analysis of PHI networks, focusing on the properties of the pathogen-targeted host proteins. We also provide information about the available PHI data and the related Web-based resources.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Durmuş Tekir S, Ülgen K (2013) Systems biology of pathogen-host interaction: networks of protein-protein interaction within pathogens and pathogen-human interactions in the post-genomic era. Biotechnol J 8:85–96
Bunnik EM, Le Roch KG (2013) An introduction to functional genomics and systems biology. Adv Wound Care 2:490–498
Dix A, Vlaic S, Guthke R, Linde J (2016) Use of systems biology to decipher host-pathogen interaction networks and predict biomarkers. Clin Microbiol Infect 22:600–606
Durmuş S, Çakır T, Özgür A, Guthke R (2015) A review on computational systems biology of pathogen-host interactions. Front Microbiol 6:1–19
de Chassey B, Meyniel-Schicklin L, Vonderscher J et al (2014) Virus-host interactomics: new insights and opportunities for antiviral drug discovery. Genome Med 6:115
CC W, Chen BS (2016) A systems biology approach to the coordination of defensive and offensive molecular mechanisms in the innate and adaptive host-pathogen interaction networks. PLoS One 11:e0149303
Forst CV (2006) Host – pathogen systems biology. Drug Discov Today 11:220–227
Sen R, Nayak L, De RK (2016) A review on host–pathogen interactions: classification and prediction. Eur J Clin Microbiol Infect Dis 35:1581–1599
Lengeling A, Pfeffer K, Balling R (2001) The battle of two genomes: genetics of bacterial host/pathogen interactions in mice. Mamm Genome 12:261–271
Stebbins CE (2005) Structural microbiology at the pathogen-host interface. Cell Microbiol 7:1227–1236
Korkin D, Thieu T, Joshi S, Warren S (2006) Mining host-pathogen interactions. In: Yang N-S (ed) Systems and computational biology – molecular and cellular experimental systems. InTech, Rijeka, pp 163–184
Davis FP, Barkan DT, Eswar N et al (2007) Host pathogen protein interactions predicted by comparative modeling. Protein Sci 16:2585–2596
Dyer MD, Murali TM, Sobral BW (2007) Computational prediction of host-pathogen protein-protein interactions. Bioinformatics 23:i159. https://doi.org/10.1093/bioinformatics/btm208
Krishnadev O, Srinivasan N (2008) A data integration approach to predict host-pathogen protein-protein interactions: application to recognize protein interactions between human and a malarial parasite. In Silico Biol 8:235–250
Lee S-A, Chan C, Tsai C-H et al (2008) Ortholog-based protein-protein interaction prediction and its application to inter-species interactions. BMC Bioinformatics 9(Suppl 12):S11
Tastan O, Qi Y, Carbonell JG, Klein-Seetharaman J (2009) Prediction of interactions between HIV-1 and human proteins by information integration. Pac Symp Biocomput 2009:516–527
Evans P, Dampier W, Ungar L, Tozeren A (2009) Prediction of HIV-1 virus-host protein interactions using virus and host sequence motifs. BMC Med Genomics 2:27
Doolittle JM, Gomez SM (2010) Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens. Virol J 7:82
Novkovic M, Onder L, Cupovic J et al (2016) Topological small-world organization of the fibroblastic reticular cell network determines lymph node functionality. PLoS Biol 14:1–20
Ramakrishnan G, Srinivasan N, Padmapriya P, Natarajan V (2015) Homology-based prediction of potential protein – protein interactions between human erythrocytes and plasmodium falciparum. Bioinform Biol Insight 9:195–206
Nourani E, Khunjush F, Durmuş S (2015) Computational approaches for prediction of pathogen-host protein-protein interactions. Front Microbiol 6:1–10
Calderwood MA, Venkatesan K, Xing L et al (2007) Epstein-Barr virus and virus human protein interaction maps. Proc Natl Acad Sci U S A 104:7606–7611
de Chassey B, Navratil V, Tafforeau L et al (2008) Hepatitis C virus infection protein network. Mol Syst Biol 4:230
Forsman A, Rüetschi U, Ekholm J, Rymo L (2008) Identification of intracellular proteins associated with the EBV-encoded nuclear antigen 5 using an efficient TAP procedure and FT-ICR mass spectrometry. J Proteome Res 7:2309–2319
Gautier VW, Gu L, O’Donoghue N et al (2009) In vitro nuclear interactome of the HIV-1 Tat protein. Retrovirology 6:47
Shapira SD, Gat-viks I, Shum BOV et al (2009) A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection. Cell 139:1255–1267
Dyer MD, Neff C, Dufford M et al (2010) The Human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis. PLoS One 5:e12089
Tripathi LP, Kataoka C, Taguwa S et al (2010) Network based analysis of hepatitis C virus core and NS4B protein interactions. Mol Biosyst 6:2539–2553
Khadka S, Vangeloff AD, Zhang C et al (2011) A physical interaction network of dengue virus and human proteins. Mol Cell Proteomics 10:1–16
Komarova AV, Combredet C, Meyniel-Schicklin L et al (2011) Proteomic analysis of virus-host interactions in an infectious context using recombinant viruses. Mol Cell Proteomics 10:M110.007443
Yang H, Ke Y, Wang J et al (2011) Insight into bacterial virulence mechanisms against host immune response via the yersinia pestis-human protein-protein interaction network. Infect Immun 79:4413–4424
Jäger S, Cimermancic P, Gulbahce N et al (2012) Global landscape of HIV-human protein complexes. Nature 481:365–370
Pichlmair A, Kandasamy K, Alvisi G et al (2012) Viral immune modulators perturb the human molecular network by common and unique strategies. Nature 487:486–490
Wu W, Tran KC, Teng MN et al (2012) The interactome of the human respiratory syncytial virus NS1 protein highlights multiple effects on host cell biology. J Virol 86:7777–7789
Dolan PT, Zhang C, Khadka S et al (2013) Identification and comparative analysis of hepatitis C virus-host cell protein interactions. Mol Biosyst 9:3199–3209
Ngo HTT, Pham LV, Kim J-W et al (2013) Modulation of mitogen-activated protein kinase-activated protein kinase 3 by hepatitis C virus core protein. J Virol 87:5718–5731
Kwofie SK, Schaefer U, Sundararajan VS et al (2011) HCVpro: Hepatitis C virus protein interaction database. Infect Genet Evol 11:1971–1977
Fu W, Sanders-Beer BE, Katz KS et al (2009) Human immunodeficiency virus type 1, human protein interaction database at NCBI. Nucleic Acids Res 37:417–422
Bleves S, Dunger I, Walter MC et al (2014) HoPaCI-DB: Host-Pseudomonas and Coxiella interaction database. Nucleic Acids Res 42:671–676
Kumar R, Nanduri B (2010) HPIDB - a unified resource for host-pathogen interactions. BMC Bioinformatics 11(Suppl. 6):S16
Wattam AR, Abraham D, Dalay O et al (2014) PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res 42:581–591
Urban M, Pant R, Raghunath A et al (2015) The Pathogen-Host Interactions database (PHI-base): additions and future developments. Nucleic Acids Res 43:D645–D655
Durmuş Tekir S, Çakır T, Ardıç E et al (2013) PHISTO: pathogen-host interaction search tool. Bioinformatics 29:1357–1358
Vialás V, Nogales-Cadenas R, Nombela C et al (2009) Proteopathogen, a protein database for studying Candida albicans - host interaction. Proteomics 9:4664–4668
Navratil V, De chassey B, Meyniel L et al (2009) VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks. Nucleic Acids Res 37:661–668
Calderone A, Licata L, Cesareni G (2015) VirusMentha: a new resource for virus-host protein interactions. Nucleic Acids Res 43:D588–D592
Dyer MD, Murali TM, Sobral BW (2008) The landscape of human proteins interacting with viruses and other pathogens. PLoS Pathog 4:e32
Singh I, Tastan O, Klein-Seetharaman J (2010) Comparison of virus interactions with human signal transduction pathways. In: Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, Niagara Falls, NY, 17–24
Durmuş S, Ülgen K (2016) Comparative interactomics for virus-human protein-protein interactions: DNA viruses versus RNA viruses. FEBS Open Bio 7:96–107
Tekir SD, Çakır T, Ülgen KÖ (2012) Infection strategies of bacterial and viral pathogens through pathogen-human protein-protein interactions. Front Microbiol 3:1–11
Gene Ontology Consortium (2010) The Gene Ontology in 2010 : extensions and refinements. Nucleic Acids Res 38:331–335
Ashburner M, Ball CA, Blake JA et al (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25–29
Du Z, Zhou X, Ling Y et al (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38:64–70
Reimand J, Arak T, Adler P et al (2016) g:Profiler—a web server for functional interpretation of gene lists (2016 update). Nucleic Acids Res 44:W83–W89
Carbon S, Ireland A, Mungall CJ et al (2009) AmiGO: online access to ontology and annotation data. Bioinformatics 25:288–289
Maere S, Heymans K, Kuiper M (2005) BiNGO : a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks. Bioinformatics 21:3448–3449
Zheng Q, Wang X (2008) GOEAST : a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res 36:358–363
Huang DW, Sherman BT, Lempicki RA (2008) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44–57
Eden E, Navon R, Steinfeld I et al (2009) GOrilla : a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 7:1–7
Falcon SÃ, Gentleman R (2007) Using GOstats to test gene lists for GO term association. Bioinformatics 23:257–258
Beißbarth T, Speed TP (2004) GOstat : find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 20:1464–1465
Bauer S, Grossmann S, Vingron M, Robinson PN (2008) Ontologizer 2.0 - a multifunctional tool for GO term enrichment analysis and data exploration. Bioinformatics 24:1650–1651
Xu Q, Shi Y, Lu Q et al (2008) GORouter: an RDF model for providing semantic query and inference services for Gene Ontology and its associations. BMC Bioinformatics 9(Suppl 1):S6
Na D, Son H, Gsponer J (2014) Categorizer: a tool to categorize genes into user-defined biological groups based on semantic similarity. BMC Genomics 15:1091
Gene Ontology Consortium. GO slim and subset guide. http://geneontology.org/page/go-slim-and-subset-guide.
Biswas M, O’Rourke JF, Camon E et al (2002) Applications of InterPro in protein annotation and genome analysis. Brief Bioinform 3:285–295
Camon E, Magrane M, Barrell D et al (2003) The Gene Ontology Annotation (GOA) Project:implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res 13:662–672
Khatri P, Sirota M, Butte AJ (2012) Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol 8:e1002375
Robinson MD, Grigull J, Mohammad N, Hughes TR (2002) FunSpec: a web-based cluster interpreter for yeast. BMC Bioinformatics 3:35
Xie C, Mao X, Huang J et al (2011) KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res 39:316–322
Mi H, Muruganujan A, Thomas PD (2013) PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res 41:377–386
Tian L, Greenberg SA, Kong SW et al (2005) Discovering statistically significant pathways in expression profiling studies. Proc Natl Acad Sci U S A 102:13544–13549
Wang J, Duncan D, Shi Z, Zhang B (2013) WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. Nucleic Acids Res 41:77–83
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Cesur, M.F., Durmuş, S. (2018). Systems Biology Modeling to Study Pathogen–Host Interactions. In: Medina, C., López-Baena, F. (eds) Host-Pathogen Interactions. Methods in Molecular Biology, vol 1734. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7604-1_10
Download citation
DOI: https://doi.org/10.1007/978-1-4939-7604-1_10
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-7603-4
Online ISBN: 978-1-4939-7604-1
eBook Packages: Springer Protocols