Abstract
Functional constraints between genes display similar patterns of gain or loss during speciation. Similar phylogenetic profiles, therefore, can be an indication of a functional association between genes. The phylogenetic profiling method has been applied successfully to the reconstruction of gene pathways and the inference of unknown gene functions. This method requires only sequence data to generate phylogenetic profiles. This method therefore has the potential to take advantage of the recent explosion in available sequence data to reveal a significant number of functional associations between genes. Since the initial development of phylogenetic profiling, many modifications to improve this method have been proposed, including improvements in the measurement of profile similarity and the selection of reference species. Here, we describe the existing methods of phylogenetic profiling for the inference of functional associations and discuss their technical limitations and caveats.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Kensche PR, van Noort V, Dutilh BE, Huynen MA (2008) Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. J R Soc Interface 5(19):151–170
Huynen MA, Bork P (1998) Measuring genome evolution. Proc Natl Acad Sci U S A 95(11):5849–5856
Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D (1999) A combined algorithm for genome-wide prediction of protein function. Nature 402(6757):83–86
Lee I (2011) Probabilistic functional gene societies. Prog Biophys Mol Biol 106(2):435–442
Lee I (2013) Network approaches to the genetic dissection of phenotypes in animals and humans. Anim Cells Syst 17(2):75–79
Date SV, Marcotte EM (2003) Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat Biotechnol 21(9):1055–1062
Jothi R, Przytycka TM, Aravind L (2007) Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment. BMC Bioinformatics 8:173
Singh S, Wall DP (2008) Testing the accuracy of eukaryotic phylogenetic profiles for prediction of biological function. Evol Bioinform Online 4:217–223
Snitkin ES, Gustafson AM, Mellor J, Wu J, DeLisi C (2006) Comparative assessment of performance and genome dependence among phylogenetic profiling methods. BMC Bioinformatics 7:420
Sun J, Xu J, Liu Z, Liu Q, Zhao A, Shi T, Li Y (2005) Refined phylogenetic profiles method for predicting protein-protein interactions. Bioinformatics 21(16):3409–3415
Pagel P, Wong P, Frishman D (2004) A domain interaction map based on phylogenetic profiling. J Mol Biol 344(5):1331–1346
Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A 96(8):4285–4288
Glazko GV, Mushegian AR (2004) Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns. Genome Biol 5(5):R32
Yamada T, Goto S, Kanehisa M (2004) Extraction of phylogenetic network modules from prokaryote metabolic pathways. Genome Inform 15(1):249–258
Bowers PM, Cokus SJ, Eisenberg D, Yeates TO (2004) Use of logic relationships to decipher protein network organization. Science 306(5705):2246–2249
Huynen M, Snel B, Lathe W 3rd, Bork P (2000) Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res 10(8):1204–1210
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1):25–29
Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28(1):27–30
Genome KCS (2009) Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. J Hered 100(6):659–674
Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) Saccharomyces genome database provides new regulation data. Nucleic Acids Res 42(Database issue):D717–D725
Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2(10):2366–2382
Barabasi AL, Oltvai ZN (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5(2):101–113
Aravind L (2000) Guilt by association: contextual information in genome analysis. Genome Res 10(8):1074–1077
Acknowledgements
This work was supported by grants from the National Research Foundation of Korea (2015R1A2A1A15055859, 2012M3A9B4028641, 2012M3A9C7050151).
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer Science+Business Media New York
About this protocol
Cite this protocol
Shin, J., Lee, I. (2017). Construction of Functional Gene Networks Using Phylogenetic Profiles. In: Keith, J. (eds) Bioinformatics. Methods in Molecular Biology, vol 1526. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6613-4_5
Download citation
DOI: https://doi.org/10.1007/978-1-4939-6613-4_5
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-6611-0
Online ISBN: 978-1-4939-6613-4
eBook Packages: Springer Protocols