Anking based on the HIV-1/SIVcpz alignment.Interaction binning testThe interactions
Anking based on the HIV-1/SIVcpz alignment.Interaction binning testThe interactions were grouped into bins defined by viral gene ranking. The ranks of host genes within bins were averaged. Bins of different sizes were slid along the viral gene ranking scale, advancing from one gene to adjacently ranked gene in each step. For each bin size we calculated the correlation between PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/27597769 viral gene ranks and the averaged host gene ranks. Because of the small number of viral genes (18) a symmetrical approach of averaging over viral gene ranks was not performed. We tested all 18 possible bin sizes. We then used the Crotaline web Permutation procedures described below to test for the significance of the correlation obtained for the averaged binned ranks of each bin size.Permutation proceduresIn order to assess the statistical significance of previous analyses we developed permutation tests of the HIVhuman interactions. The HIV-human interaction data can be represented by a bipartite graph with nodes representing host and viral proteins and edges connecting interacting host and viral proteins. We PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26080418 designed two procedures of permuting the host-virus interaction network. The host-oriented test consists of retaining the degree of each of the host gene nodes in the network and randomly sampling a corresponding number of interacting viral genes from the set of all viral genes. The virus-oriented test consists of retaining the degree of each viral gene node and randomly sampling a corresponding number of interacting host genes. Performing two different permutation tests allowed us to test if certain results were due to the differing numbers of interactions reported for different host and viral proteins. We developed additional permutation tests allowing for random node degrees in the network and found the permutation tests conserving aspects of the network topology to be more stringent in assessing the statistical significance of our observations. We therefore used the host- and virus-oriented tests to assess statistical significance of the results of our analyses.Additional materialAdditional file 1 list of all analyzed genes, scores and annotations. Additional file 2 detailed results of the GO term enrichment tests. Additional file 3 information on the alignment quality.Bo k and Lengauer BMC Evolutionary Biology 2010, 10:186 http://www.biomedcentral.com/1471-2148/10/Page 14 ofAuthors’ contributions KB and TL conceived this project and wrote the manuscript. KB designed the study, and collected and analyzed the data. All authors read and approved the final manuscript. Acknowledgements We would like to thank Christoph Bock and David Robertson for helpful comments on the manuscript. Author Details Max Planck Institute for Informatics Computational Biology and Applied Algorithmics Campus E1 4 66123 Saarbr cken, Germany Received: 23 March 2010 Accepted: 18 June 2010 Published: 18 JuneThis is an Open Access from: http://www.biomedcentral.com/1471-2148/10/186 ?2010 Boekavailable article licensee BioMed Central Ltd. of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. BMC article is and Lengauer; distributed under the terms Evolutionary Biology 2010, 10:References 1. Gao F, Bailes E, Robertson DL, Chen Y, Rodenburg CM, Michael SF, Cummins LB, Arthur LO, Peeters M, Shaw GM, et al.: Origin of HIV-1 in the chimpanzee Pan tro.
