IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0110936.html
   My bibliography  Save this article

Relating Diseases by Integrating Gene Associations and Information Flow through Protein Interaction Network

Author

Listed:
  • Mehdi Bagheri Hamaneh
  • Yi-Kuo Yu

Abstract

Identifying similar diseases could potentially provide deeper understanding of their underlying causes, and may even hint at possible treatments. For this purpose, it is necessary to have a similarity measure that reflects the underpinning molecular interactions and biological pathways. We have thus devised a network-based measure that can partially fulfill this goal. Our method assigns weights to all proteins (and consequently their encoding genes) by using information flow from a disease to the protein interaction network and back. Similarity between two diseases is then defined as the cosine of the angle between their corresponding weight vectors. The proposed method also provides a way to suggest disease-pathway associations by using the weights assigned to the genes to perform enrichment analysis for each disease. By calculating pairwise similarities between 2534 diseases, we show that our disease similarity measure is strongly correlated with the probability of finding the diseases in the same disease family and, more importantly, sharing biological pathways. We have also compared our results to those of MimMiner, a text-mining method that assigns pairwise similarity scores to diseases. We find the results of the two methods to be complementary. It is also shown that clustering diseases based on their similarities and performing enrichment analysis for the cluster centers significantly increases the term association rate, suggesting that the cluster centers are better representatives for biological pathways than the diseases themselves. This lends support to the view that our similarity measure is a good indicator of relatedness of biological processes involved in causing the diseases. Although not needed for understanding this paper, the raw results are available for download for further study at ftp://ftp.ncbi.nlm.nih.gov/pub/qmbpmn/DiseaseRelations/.

Suggested Citation

  • Mehdi Bagheri Hamaneh & Yi-Kuo Yu, 2014. "Relating Diseases by Integrating Gene Associations and Information Flow through Protein Interaction Network," PLOS ONE, Public Library of Science, vol. 9(10), pages 1-14, October.
  • Handle: RePEc:plo:pone00:0110936
    DOI: 10.1371/journal.pone.0110936
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110936
    Download Restriction: no

    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0110936&type=printable
    Download Restriction: no

    File URL: https://libkey.io/10.1371/journal.pone.0110936?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. Gergely Palla & Imre Derényi & Illés Farkas & Tamás Vicsek, 2005. "Uncovering the overlapping community structure of complex networks in nature and society," Nature, Nature, vol. 435(7043), pages 814-818, June.
    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. Eustace, Justine & Wang, Xingyuan & Cui, Yaozu, 2015. "Community detection using local neighborhood in complex networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 436(C), pages 665-677.
    2. Xiao‐Bing Hu & Hang Li & XiaoMei Guo & Pieter H. A. J. M. van Gelder & Peijun Shi, 2019. "Spatial Vulnerability of Network Systems under Spatially Local Hazards," Risk Analysis, John Wiley & Sons, vol. 39(1), pages 162-179, January.
    3. Jorge Peña & Yannick Rochat, 2012. "Bipartite Graphs as Models of Population Structures in Evolutionary Multiplayer Games," PLOS ONE, Public Library of Science, vol. 7(9), pages 1-13, September.
    4. Pirvu Daniela & Barbuceanu Mircea, 2016. "Recent Contributions Of The Statistical Physics In The Research Of Banking, Stock Exchange And Foreign Exchange Markets," Annals - Economy Series, Constantin Brancusi University, Faculty of Economics, vol. 2, pages 85-92, April.
    5. Daniel M. Ringel & Bernd Skiera, 2016. "Visualizing Asymmetric Competition Among More Than 1,000 Products Using Big Search Data," Marketing Science, INFORMS, vol. 35(3), pages 511-534, May.
    6. Yu, Shuo & Alqahtani, Fayez & Tolba, Amr & Lee, Ivan & Jia, Tao & Xia, Feng, 2022. "Collaborative Team Recognition: A Core Plus Extension Structure," Journal of Informetrics, Elsevier, vol. 16(4).
    7. Shang, Jiaxing & Liu, Lianchen & Li, Xin & Xie, Feng & Wu, Cheng, 2016. "Targeted revision: A learning-based approach for incremental community detection in dynamic networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 443(C), pages 70-85.
    8. Roth, Camille, 2007. "Empiricism for descriptive social network models," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 378(1), pages 53-58.
    9. Ying Song & Zhiwen Zheng & Yunmei Shi & Bo Wang, 2023. "GLOD: The Local Greedy Expansion Method for Overlapping Community Detection in Dynamic Provenance Networks," Mathematics, MDPI, vol. 11(15), pages 1-16, July.
    10. Shiau, Wen-Lung & Dwivedi, Yogesh K. & Yang, Han Suan, 2017. "Co-citation and cluster analyses of extant literature on social networks," International Journal of Information Management, Elsevier, vol. 37(5), pages 390-399.
    11. Zhang, Zhiwei & Wang, Zhenyu, 2015. "Mining overlapping and hierarchical communities in complex networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 421(C), pages 25-33.
    12. J. Sylvan Katz & Guillermo Armando Ronda-Pupo, 2019. "Cooperation, scale-invariance and complex innovation systems: a generalization," Scientometrics, Springer;Akadémiai Kiadó, vol. 121(2), pages 1045-1065, November.
    13. Masa Tsuchiya & Vincent Piras & Alessandro Giuliani & Masaru Tomita & Kumar Selvarajoo, 2010. "Collective Dynamics of Specific Gene Ensembles Crucial for Neutrophil Differentiation: The Existence of Genome Vehicles Revealed," PLOS ONE, Public Library of Science, vol. 5(8), pages 1-10, August.
    14. Wu, Zhihao & Lin, Youfang & Wan, Huaiyu & Tian, Shengfeng & Hu, Keyun, 2012. "Efficient overlapping community detection in huge real-world networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 391(7), pages 2475-2490.
    15. Atieh Mirshahvalad & Johan Lindholm & Mattias Derlén & Martin Rosvall, 2012. "Significant Communities in Large Sparse Networks," PLOS ONE, Public Library of Science, vol. 7(3), pages 1-7, March.
    16. Nie, Yanyi & Li, Wenyao & Pan, Liming & Lin, Tao & Wang, Wei, 2022. "Markovian approach to tackle competing pathogens in simplicial complex," Applied Mathematics and Computation, Elsevier, vol. 417(C).
    17. Cerqueti, Roy & Ciciretti, Rocco & Dalò, Ambrogio & Nicolosi, Marco, 2022. "A new measure of the resilience for networks of funds with applications to socially responsible investments," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 593(C).
    18. Rizman Žalik, Krista & Žalik, Borut, 2014. "A local multiresolution algorithm for detecting communities of unbalanced structures," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 407(C), pages 380-393.
    19. Shi, Xiaolin & Adamic, Lada A. & Strauss, Martin J., 2007. "Networks of strong ties," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 378(1), pages 33-47.
    20. Zhang, Shihua & Wang, Rui-Sheng & Zhang, Xiang-Sun, 2007. "Identification of overlapping community structure in complex networks using fuzzy c-means clustering," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 374(1), pages 483-490.

    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:pone00:0110936. 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: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    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.