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EvoPPI: A Web Application to Compare Protein-Protein Interactions (PPIs) from Different Databases and Species

  • Noé Vázquez
  • Sara Rocha
  • Hugo López-Fernández
  • André Torres
  • Rui Camacho
  • Florentino Fdez-Riverola
  • Jorge Vieira
  • Cristina P. Vieira
  • Miguel Reboiro-Jato
Conference paper
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 803)

Abstract

Biological processes are mediated by protein-protein interactions (PPI) that have been studied using different methodologies, and organized as centralized repositories - PPI databases. The data stored in the different PPI databases only overlaps partially. Moreover, some of the repositories are dedicated to a species or subset of species, not all have the same functionalities, or store data in the same format, making comparisons between different databases difficult to perform. Therefore, here we present EvoPPI (http://evoppi.i3s.up.pt), an open source web application tool that allows users to compare the protein interactions reported in two different interactomes. When interactomes belong to different species, a versatile BLAST search approach is used to identify orthologous/paralogous genes, which to our knowledge is a unique feature of EvoPPI.

Keywords

Protein-protein interactions databases Inter-specific comparisons Graphical view 

Notes

Acknowledgements

Sara Rocha and this work are supported by the project Norte-01-0145-FEDER-000008 - Porto Neurosciences and Neurologic Disease Research Initiative at I3S, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (FEDER). H. López-Fernández is supported by a post-doctoral fellowship from Xunta de Galicia (ED481B 2016/068-0). SING group thanks CITI (Centro de Investigación, Transferencia e Innovación) from University of Vigo for hosting its IT infrastructure. Financial support from the Xunta de Galicia (Centro singular de investigación de Galicia accreditation 2016-2019) and the European Union (European Regional Development Fund - ERDF), is gratefully acknowledged.

References

  1. 1.
    Alanis-Lobato, G., Andrade-Navarro, M.A., Schaefer, M.H.: HIPPIE v2.0: enhancing meaningfulness and reliability of protein–protein interaction networks. Nucleic Acids Res. 45, D408–D414 (2017)CrossRefGoogle Scholar
  2. 2.
    Chiti, F., Dobson, C.M.: Protein misfolding, amyloid formation, and human disease: a summary of progress over the last decade. Annu. Rev. Biochem. 86, 27–68 (2017)CrossRefGoogle Scholar
  3. 3.
    Cescatti, M., Saverioni, D., Capellari, S., Tagliavini, F., Kitamoto, T., Ironside, J., Giese, A., Parchi, P.: Analysis of conformational stability of abnormal prion protein aggregates across the spectrum of Creutzfeldt-Jakob disease prions. J. Virol. 90, 6244–6254 (2016)CrossRefGoogle Scholar
  4. 4.
    Peng, X., Wang, J., Peng, W., Wu, F.-X., Pan, Y.: Protein–protein interactions: detection, reliability assessment and applications. Brief. Bioinform. 18, 798–819 (2017)Google Scholar
  5. 5.
    Folador, E., de Oliveira Junior, A., Tiwari, S., Jamal, S., Ferreira, R., Barh, D., Ghosh, P., Silva, A., Azevedo, C.: In silico protein-protein interactions: avoiding data and method biases over sensitivity and specificity. Curr. Protein Pept. Sci. 16, 689–700 (2015)CrossRefGoogle Scholar
  6. 6.
    Bader, G.D., Cary, M.P., Sander, C.: Pathguide: a pathway resource list. Nucleic Acids Res. 34, D504–D506 (2006)CrossRefGoogle Scholar
  7. 7.
    Alonso-López, D., Gutiérrez, M.A., Lopes, K.P., Prieto, C., Santamaría, R., De Las Rivas, J.: APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. Nucleic Acids Res. 44, W529–W535 (2016)CrossRefGoogle Scholar
  8. 8.
    Mendivil Ramos, O., Ferrier, D.E.K.: Mechanisms of Gene Duplication and Translocation and Progress towards Understanding Their Relative Contributions to Animal Genome Evolution. https://www.hindawi.com/journals/ijeb/2012/846421/
  9. 9.
    Fielding, R.T.: Architectural Styles and the Design of Network-Based Software Architectures (2000)Google Scholar
  10. 10.
    Ng, H., Pulst, S.-M., Huynh, D.P.: Ataxin-2 mediated cell death is dependent on domains downstream of the polyQ repeat. Exp. Neurol. 208, 207–215 (2007)CrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Noé Vázquez
    • 1
    • 2
  • Sara Rocha
    • 3
    • 4
  • Hugo López-Fernández
    • 1
    • 2
    • 3
    • 4
    • 5
  • André Torres
    • 3
    • 4
  • Rui Camacho
    • 6
  • Florentino Fdez-Riverola
    • 1
    • 2
    • 5
  • Jorge Vieira
    • 3
    • 4
  • Cristina P. Vieira
    • 3
    • 4
  • Miguel Reboiro-Jato
    • 1
    • 2
    • 5
  1. 1.ESEI - Escuela Superior de Ingeniería InformáticaUniversidad de VigoOurenseSpain
  2. 2.Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia)VigoSpain
  3. 3.Instituto de Investigação e Inovação em Saúde (I3S)Universidade do PortoPortoPortugal
  4. 4.Instituto de Biologia Molecular e Celular (IBMC)PortoPortugal
  5. 5.SING Research GroupGalicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGOVigoSpain
  6. 6.LIAAD, DEI, Faculdade de EngenhariaUniversidade do PortoPortoPortugal

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