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International Journal of Genomics
Volume 2013, Article ID 670623, 11 pages
http://dx.doi.org/10.1155/2013/670623
Research Article

Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns

1School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China
2Department of Computer and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
3Computer Science Department, North Carolina State University, Raleigh, NC 27696, USA

Received 22 December 2012; Revised 5 February 2013; Accepted 23 February 2013

Academic Editor: G. Pesole

Copyright © 2013 Wenhong Tian and Nagiza F. Samatova. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Supplementary Material

1. Score[c]=1/3*S[c]+1/3*I[c]+1/3*F[c] where S[c] is the average similarity scores of all nodes in a cluster using BLAST scores or ortholog groups confidence scores, I[c] is the interaction conservation coefficient measured by the total number of interactions in a cluster divided by the |c|(|c|-1)/2, F[c] currently is the interaction over union of number of GO biological process terms covered in a cluster. These are explained the main paper too.

2. 26 clusters of Yeast-Fly pair (excel sheet “ScoreFor26ClustersYeastFly” ) are obtained using Hopmap with KO groups, also sheet “STM_ECO58ClustersScores”, “ECO_CCR42 ClustersScores”.

3. 79 clusters of Yeast-Fly (excel sheet “SoreFor79Clusters”) are obtained using Hopmap and data from NetworkBLAST.

4. GO termFinder results for each pair are provided, including excel sheet “YeastFlyIn26ClustersGO0.05”, “YeastFlyIn117ClustersGO”, and “YeastFly79ClusterGO0.05”, “Graemlin1.0Sce_Dme”, “Graemlin1.0ECO_STMGOResults”, “Graemlin1.0CCR_ECOGOresults”, as their sheet names suggest.

5. P-value for S[c]=(r+1)/(n+1) where r is the number of protein pairs which are in the same KO groups, n is the total number of possible pairs.

6. P-value for I[c]=(r+1)/(n+1) where r is the number of clusters which have values greater than or equal to the value of the actual cluster, n is the total number of random sample clusters

7. P-value for F[c]=(r+1)/(n+1) where r is the number of clusters which have values greater than or equal to the value of intersection over union of the number of GO terms in the cluster, n is the total number of random sample clusters

8. In all cases, n is large enough (3000-5000) so that the result will be statistically meaningful.

  1. Supplementary Tables