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Paper   IPM / Biological Sciences / 15806
School of Biological Sciences
  Title:   CDAP: An Online Package for Evaluation of Complex Detection Methods
1.  Changiz Eslahchi
2.  Ali Mohammad Ali Maddi
3.  Fatemeh Ahmadi Moughari
4.  Mohammad Mehdi Balouchi
  Status:   Published
  Journal: Scientific Reports
  No.:  1
  Vol.:  9 DOI https://doi.org/10.1038/s41598-019-49225-7
  Year:  2019
  Pages:   1-13
  Supported by:  IPM
Methods for detecting protein complexes from protein-protein interaction networks are of the most critical computational approaches. Numerous methods have been proposed in this area. Therefore, it is necessary to evaluate them. Various metrics have been proposed in order to compare these methods. Nevertheless, it is essential to define new metrics that evaluate methods both qualitatively and quantitatively. In addition, there is no tool for the comprehensive comparison of such methods. In this paper, a new criterion is introduced that can fully evaluate protein complex detection algorithms. We introduce CDAP (Complex Detection Analyzer Package); an online package for comparing protein complex detection methods. CDAP can quickly rank the performance of methods based on previously defined as well as newly introduced criteria in various settings (4 PPI datasets and 3 gold standards). It has the capability of integrating various methods and apply several filterings on the results. CDAP can be easily extended to include new datasets, gold standards, and methods. Furthermore, the user can compare the results of a custom method with the results of existing methods. Thus, the authors of future papers can use CDAP for comparing their method with the previous ones. A case study is done on YGR198W, a well-known protein, and the detected clusters are compared to the known complexes of this protein.

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