Project title: Detecting functional orthology with global alignment of multiple protein interaction networks using IsoRank algorithm
Team members' names: Tae Seung Kang
A brief (5-10 sentences) abstract of the project which describes what you aim to
do in your project.
It is important to understand interactions among proteins in biological
networks. These protein-protein interactions (PPIs) can
be viewed as an eigenvalue problem. I am going to use IsoRank algorithm for global network alignment
and make some variations using various parameters.
The resulting PPI data can be used to detect orthology. I am going to show how the
algorithm works and how it handles node similarity and PPI network similarity
in various environments.
A brief itemized plan of action. This plan will discuss what specifc steps you are planning to take to achieve the aim you stated in the abstract, such as as
What will you implement?
I will implement the IsoRank algorithm and PPI networks.
What methods are you going to compare and how will you get them?
sequence-only approaches in ortholog prediction and local alignments of the yeast
and fly networks from the Internet or by myself
Which datasets are you going to use and where will you get them from (links if
possible)?
the Saccthe Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans,
Mus musculus, Homo sapiens, and more PPI networks from GenBank, Protein Data
Bank, SCOP and others.
What kind of experiment will you run and what will you measure (e.g., time,
score, p-value etc).
I will construct a score matrix using BLAST similarity scores and functional
similarity between two proteins of the networks and run the alorithm with the
matrix. I will measure the final scores after the experiment.
List of papers I have (will) read for this project.
Rohit Singh, Jinbo Xu, and Bonnie Berger, "Global alignment of multiple protein interaction networks with application to functional orthology detection", Proc Natl Acad Sci U S A. 2008 September 2; 105(35): 12763–12768.
Eric Franzosa, Bolan Linghu and Yu Xia, "Computational Reconstruction of Protein–Protein Interaction Networks: Algorithms and Issues", Computational Systems Biology, Humana Press, Volume 541, 2008, pp. 1-12.
Stephen A. Chervitz, L. Aravind, Gavin Sherlock, Catherine A. Ball, Eugene V. Koonin, Selina S. Dwight, Midori A. Harris, Kara Dolinski, Scott Mohr, Temple Smith, Shuai Weng, J. Michael Cherry, David Botstein, "Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence", Science 11 December 1998: Vol. 282. no. 5396, pp. 2022 - 2028.
Mikhail Zaslavskiy, Francis Bach and Jean-Philippe Vert et al., "Global alignment of protein-protein interaction networks by graph matching methods", Vol. 25 ISMB 2009, pages i259–i267.
Simon P. Kanaan, Chengbang Huang, Stefan Wuchty, Danny Z. Chen, and Jesu´ s A. Izaguirre, "Inferring Protein–Protein Interactions from Multiple Protein Domain Combinations", Computational Systems Biology, Humana Press, Vol. 541, 2009, pp. 1-17.
Rohit Singh, Jinbu Xu , Bonnie Berger, "GLOBAL ALIGNMENT OF MULTIPLE PROTEIN INTERACTION NETWORKS", Pac Symp Biocomput. 2008;:303-314.
Chung-Shou Liao, Kanghao Lu, Michael Baym, Rohit Singh and Bonnie Berger, "IsoRankN: spectral methods for global alignment of multiple protein networks", Computational Systems Biology, Humana Press, Vol. 541, 2009, pp. 1-17.