IDEAS home Printed from https://ideas.repec.org/a/plo/pcbi00/1007403.html
   My bibliography  Save this article

Benchmarking network algorithms for contextualizing genes of interest

Author

Listed:
  • Abby Hill
  • Scott Gleim
  • Florian Kiefer
  • Frederic Sigoillot
  • Joseph Loureiro
  • Jeremy Jenkins
  • Melody K Morris

Abstract

Computational approaches have shown promise in contextualizing genes of interest with known molecular interactions. In this work, we evaluate seventeen previously published algorithms based on characteristics of their output and their performance in three tasks: cross validation, prediction of drug targets, and behavior with random input. Our work highlights strengths and weaknesses of each algorithm and results in a recommendation of algorithms best suited for performing different tasks.Author summary: In our labs, we aimed to use network algorithms to contextualize hits from functional genomics screens and gene expression studies. In order to understand how to apply these algorithms to our data, we characterized seventeen previously published algorithms based on characteristics of their output and their performance in three tasks: cross validation, prediction of drug targets, and behavior with random input.

Suggested Citation

  • Abby Hill & Scott Gleim & Florian Kiefer & Frederic Sigoillot & Joseph Loureiro & Jeremy Jenkins & Melody K Morris, 2019. "Benchmarking network algorithms for contextualizing genes of interest," PLOS Computational Biology, Public Library of Science, vol. 15(12), pages 1-14, December.
    • Handle: RePEc:plo:pcbi00:1007403
    DOI: 10.1371/journal.pcbi.1007403
    as

    Download full text from publisher

    File URL: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007403
    Download Restriction: no
    File URL: https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007403&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pcbi.1007403?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Tune H. Pers & Juha M. Karjalainen & Yingleong Chan & Harm-Jan Westra & Andrew R. Wood & Jian Yang & Julian C. Lui & Sailaja Vedantam & Stefan Gustafsson & Tonu Esko & Tim Frayling & Elizabeth K. Spel, 2015. "Biological interpretation of genome-wide association studies using predicted gene functions," Nature Communications, Nature, vol. 6(1), pages 1-9, May.
    2. Susan Dina Ghiassian & Jörg Menche & Albert-László Barabási, 2015. "A DIseAse MOdule Detection (DIAMOnD) Algorithm Derived from a Systematic Analysis of Connectivity Patterns of Disease Proteins in the Human Interactome," PLOS Computational Biology, Public Library of Science, vol. 11(4), pages 1-21, April.
    3. Oron Vanunu & Oded Magger & Eytan Ruppin & Tomer Shlomi & Roded Sharan, 2010. "Associating Genes and Protein Complexes with Disease via Network Propagation," PLOS Computational Biology, Public Library of Science, vol. 6(1), pages 1-9, January.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Ke Hu & Ju Xiang & Yun-Xia Yu & Liang Tang & Qin Xiang & Jian-Ming Li & Yong-Hong Tang & Yong-Jun Chen & Yan Zhang, 2020. "Significance-based multi-scale method for network community detection and its application in disease-gene prediction," PLOS ONE, Public Library of Science, vol. 15(3), pages 1-24, March.
    2. Juan J Cáceres & Alberto Paccanaro, 2019. "Disease gene prediction for molecularly uncharacterized diseases," PLOS Computational Biology, Public Library of Science, vol. 15(7), pages 1-14, July.
    3. Jacob Joseph & Chang Liu & Qin Hui & Krishna Aragam & Zeyuan Wang & Brian Charest & Jennifer E. Huffman & Jacob M. Keaton & Todd L. Edwards & Serkalem Demissie & Luc Djousse & Juan P. Casas & J. Micha, 2022. "Genetic architecture of heart failure with preserved versus reduced ejection fraction," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    4. T M Murali & Matthew D Dyer & David Badger & Brett M Tyler & Michael G Katze, 2011. "Network-Based Prediction and Analysis of HIV Dependency Factors," PLOS Computational Biology, Public Library of Science, vol. 7(9), pages 1-15, September.
    5. Lili Liu & Atlas Khan & Elena Sanchez-Rodriguez & Francesca Zanoni & Yifu Li & Nicholas Steers & Olivia Balderes & Junying Zhang & Priya Krithivasan & Robert A. LeDesma & Clara Fischman & Scott J. Heb, 2022. "Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    6. Brittany L. Mitchell & Jake R. Saklatvala & Nick Dand & Fiona A. Hagenbeek & Xin Li & Josine L. Min & Laurent Thomas & Meike Bartels & Jouke Hottenga & Michelle K. Lupton & Dorret I. Boomsma & Xianjun, 2022. "Genome-wide association meta-analysis identifies 29 new acne susceptibility loci," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    7. Deborah Chasman & Brandi Gancarz & Linhui Hao & Michael Ferris & Paul Ahlquist & Mark Craven, 2014. "Inferring Host Gene Subnetworks Involved in Viral Replication," PLOS Computational Biology, Public Library of Science, vol. 10(5), pages 1-22, May.
    8. Xing Chen & Jun Yin & Jia Qu & Li Huang, 2018. "MDHGI: Matrix Decomposition and Heterogeneous Graph Inference for miRNA-disease association prediction," PLOS Computational Biology, Public Library of Science, vol. 14(8), pages 1-24, August.
    9. David Lamparter & Daniel Marbach & Rico Rueedi & Zoltán Kutalik & Sven Bergmann, 2016. "Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics," PLOS Computational Biology, Public Library of Science, vol. 12(1), pages 1-20, January.
    10. Aysu Okbay & Jonathan P. Beauchamp & Mark Alan Fontana & James J. Lee & Tune H. Pers & Cornelius A. Rietveld & Patrick Turley & Guo-Bo Chen & Valur Emilsson & S. Fleur W. Meddens & Sven Oskarsson & Jo, 2016. "Genome-wide association study identifies 74 loci associated with educational attainment," Nature, Nature, vol. 533(7604), pages 539-542, May.
    11. Li-Chen Hung & Pei-Tseng Kung & Chi-Hsuan Lung & Ming-Hsui Tsai & Shih-An Liu & Li-Ting Chiu & Kuang-Hua Huang & Wen-Chen Tsai, 2020. "Assessment of the Risk of Oral Cancer Incidence in A High-Risk Population and Establishment of A Predictive Model for Oral Cancer Incidence Using A Population-Based Cohort in Taiwan," IJERPH, MDPI, vol. 17(2), pages 1-15, January.
    12. Michael G. Levin & Noah L. Tsao & Pankhuri Singhal & Chang Liu & Ha My T. Vy & Ishan Paranjpe & Joshua D. Backman & Tiffany R. Bellomo & William P. Bone & Kiran J. Biddinger & Qin Hui & Ozan Dikilitas, 2022. "Genome-wide association and multi-trait analyses characterize the common genetic architecture of heart failure," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    13. Peter Marx & Peter Antal & Bence Bolgar & Gyorgy Bagdy & Bill Deakin & Gabriella Juhasz, 2017. "Comorbidities in the diseasome are more apparent than real: What Bayesian filtering reveals about the comorbidities of depression," PLOS Computational Biology, Public Library of Science, vol. 13(6), pages 1-23, June.
    14. Jianhua Li & Xiaoyan Lin & Yueyang Teng & Shouliang Qi & Dayu Xiao & Jianying Zhang & Yan Kang, 2016. "A Comprehensive Evaluation of Disease Phenotype Networks for Gene Prioritization," PLOS ONE, Public Library of Science, vol. 11(7), pages 1-18, July.
    15. Zhao Wang & Qian Liang & Xinyi Qian & Bolang Hu & Zhanye Zheng & Jianhua Wang & Yuelin Hu & Zhengkai Bao & Ke Zhao & Yao Zhou & Xiangling Feng & Xianfu Yi & Jin Li & Jiandang Shi & Zhe Liu & Jihui Hao, 2023. "An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping," Nature Communications, Nature, vol. 14(1), pages 1-23, December.
    16. Sepideh Sadegh & James Skelton & Elisa Anastasi & Andreas Maier & Klaudia Adamowicz & Anna Möller & Nils M. Kriege & Jaanika Kronberg & Toomas Haller & Tim Kacprowski & Anil Wipat & Jan Baumbach & Dav, 2023. "Lacking mechanistic disease definitions and corresponding association data hamper progress in network medicine and beyond," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    17. Le Ou-Yang & Dao-Qing Dai & Xiao-Fei Zhang, 2013. "Protein Complex Detection via Weighted Ensemble Clustering Based on Bayesian Nonnegative Matrix Factorization," PLOS ONE, Public Library of Science, vol. 8(5), pages 1-18, May.
    18. Xiaofeng Zhu & Yihe Yang & Noah Lorincz-Comi & Gen Li & Amy R. Bentley & Paul S. de Vries & Michael Brown & Alanna C. Morrison & Charles N. Rotimi & W. James Gauderman & Dabeeru C. Rao & Hugues Aschar, 2024. "An approach to identify gene-environment interactions and reveal new biological insight in complex traits," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    19. Anurag Sethi & J. Graham Ruby & Matthew A. Veras & Natalie Telis & Eugene Melamud, 2023. "Genetics implicates overactive osteogenesis in the development of diffuse idiopathic skeletal hyperostosis," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    20. Gianmarco Mignogna & Caitlin E. Carey & Robbee Wedow & Nikolas Baya & Mattia Cordioli & Nicola Pirastu & Rino Bellocco & Kathryn Fiuza Malerbi & Michel G. Nivard & Benjamin M. Neale & Raymond K. Walte, 2023. "Patterns of item nonresponse behaviour to survey questionnaires are systematic and associated with genetic loci," Nature Human Behaviour, Nature, vol. 7(8), pages 1371-1387, August.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pcbi00:1007403. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: ploscompbiol (email available below). General contact details of provider: https://journals.plos.org/ploscompbiol/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.