Improved method for protein complex detection using bottleneck proteins

Jaegyoon Ahn, Dae Hyun Lee, Youngmi Yoon, Yunku Yeu, Sanghyun Park

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)


Background: Detecting protein complexes is one of essential and fundamental tasks in understanding various biological functions or processes. Therefore accurate identification of protein complexes is indispensable. Methods. For more accurate detection of protein complexes, we propose an algorithm which detects dense protein sub-networks of which proteins share closely located bottleneck proteins. The proposed algorithm is capable of finding protein complexes which allow overlapping with each other. Results: We applied our algorithm to several PPI (Protein-Protein Interaction) networks of Saccharomyces cerevisiae and Homo sapiens, and validated our results using public databases of protein complexes. The prediction accuracy was even more improved over our previous work which used also bottleneck information of the PPI network, but showed limitation when predicting small-sized protein complex detection. Conclusions: Our algorithm resulted in overlapping protein complexes with significantly improved F1 score over existing algorithms. This result comes from high recall due to effective network search, as well as high precision due to proper use of bottleneck information during the network search.

Original languageEnglish
Article numberS5
JournalBMC Medical Informatics and Decision Making
Issue numberSUPPL1
Publication statusPublished - 2013

Bibliographical note

Funding Information:
This work was supported by National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST) (No. 2012010775). This work is based on an earlier work: “Protein complex prediction via bottleneck-based graph partitioning”, in Proceedings of the ACM Sixth International Workshop on Data and Text Mining in Biomedical Informatics, 2012 © ACM, 2012.

All Science Journal Classification (ASJC) codes

  • Health Policy
  • Health Informatics


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