Abstract
Molecular interaction networks have emerged as a powerful data source for answering a plethora of biological questions ranging from how cells make decisions to how species evolve. The availability of such data from multiple organisms allows for their analysis from an evolutionary perspective. Indeed, work has emerged recently on network alignment, ancestral network reconstruction, and phylogenetic inference based on networks.
In this paper, we address two central issues in the area of evolutionary analysis of molecular interaction networks, namely (1) correcting genetic distances derived from observed differences between networks, and (2) reconstructing ancestral networks from extant ones. We address both issues computationally under the link dynamics and duplication-mutation with complementarity (DMC) evolutionary models. We demonstrate the utility and accuracy of our methods on biological and simulated data.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Atias, N., Sharan, R.: Comparative analysis of protein networks: hard problems, practical solutions. Commun. ACM 55(5), 88–97 (2012)
Bourlat, S., Nielsen, C., Economou, A.D., Telford, M.J.: Testing the new animal phylogeny: a phylum level molecular analysis of the animal kingdom. Molecular Phylogenetics and Evolution 49, 23–31 (2008)
Dunn, C.W., Hejnol, A., Matus, D.Q., Pang, K., Browne, W.E., Smith, S.A., Seaver, E., Rouse, G.W., Obst, M., Edgecombe, G.D., Sorensen, M.V., Haddock, S.H., Schmidt-Rhaesa, A., Okusu, A., Kristensen, R.M., Wheeler, W.C., Martindale, M.Q., Giribet, G.: Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452, 745–749 (2008)
Gibson, T.A., Goldberg, D.S.: Reverse engineering the evolution of protein interaction networks. In: Pacific Symposium on Biocomputing, pp. 190–202 (September 2008)
Jukes, T.H., Cantor, C.R.: Evolution of protein molecules. In: Mammalian Protein Metabolism, pp. 21–132 (1969)
Li, S., Choi, P., Wu, T., Zhang, L.: Reconstruction of network evolutionary history from extant network topology and duplication history. Quantitative Biology, arXiv:1203.2430 (March 2012)
Mithani, A., Preston, G.M., Hein, J.: A Bayesian approach to the evolution of metabolic networks on a phylogeny. PLoS Computational Biology 6(8), e1000868 (2010)
Navlakha, S., Kingsford, C.: Network archaeology: uncovering ancient networks from present-day interactions. PLoS Computational Biology 7(4), e1001119 (2011)
Pál, C., Papp, B., Lercher, M.: Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nature Genetics 37, 1372–1375 (2005)
Paps, J., Baguna, J., Riutort, M.: Bilaterian phylogeny: a broad sampling of 13 nuclear genes provides a new lophotrochozoa phylogeny and supports a paraphyletic basal a coelomorpha. Molecular Biology and Evolution 26, 2397–2406 (2009)
Patro, R., Sefer, E., Malin, J., Marçais, G., Navlakha, S., Kingsford, C.: Parsimonious Reconstruction of Network Evolution. In: Przytycka, T.M., Sagot, M.-F. (eds.) WABI 2011. LNCS (LNBI), vol. 6833, pp. 237–249. Springer, Heidelberg (2011)
Pinney, J.W., Amoutzias, G.D., Rattray, M., Robertson, D.L.: Reconstruction of ancestral protein interaction networks for the bZIP transcription factors. PNAS 104(51), 20449–20453 (2007)
Ratmann, O., Jørgensen, O., Hinkley, T., Stumpf, M.P.H., Richardson, S., Wiuf, C.: Using likelihood-free inference to compare evolutionary dynamics of the protein networks of H. pylori and P. falciparum. PLoS Computational Biology 3(11), e230 (2007)
Rogozin, I.B., Thomson, K., Carmel, L., Koonin, E.V.: Homoplasy in genome-wide analsis of rare amino acid replacemeents: the molecular-evolutionary basis for Vavilov’s law of homologous series. Biology Direct 3, 7 (2008)
Sharan, R., Ideker, T.: Modeling cellular machinery through biological network comparison. Nature Biotechnology 24(4), 427–433 (2006)
Stumpf, M.P.H., Ingram, P.J., Nouvel, I., Wiuf, C.: Statistical Model Selection Methods Applied to Biological Networks. In: Priami, C., Merelli, E., Gonzalez, P., Omicini, A. (eds.) Transactions on Computational Systems Biology III. LNCS (LNBI), vol. 3737, pp. 65–77. Springer, Heidelberg (2005)
Wiuf, C., Brameier, M., Hagberg, O., Stumpf, M.P.H.: A likelihood approach to analysis of network data. PNAS 103(20), 7566–7570 (2006)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Zhu, Y., Nakhleh, L. (2012). Reconstructing the Evolution of Molecular Interaction Networks under the DMC and Link Dynamics Models. In: Raphael, B., Tang, J. (eds) Algorithms in Bioinformatics. WABI 2012. Lecture Notes in Computer Science(), vol 7534. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-33122-0_5
Download citation
DOI: https://doi.org/10.1007/978-3-642-33122-0_5
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-33121-3
Online ISBN: 978-3-642-33122-0
eBook Packages: Computer ScienceComputer Science (R0)