Abstract
One of the most important and challenging problems in functional genomics is how to select the disease genes. In this chapter, a computational method is reported to identify disease genes, judiciously integrating the information of gene expression profiles and shortest path analysis of protein-protein interaction networks. While the gene expression profiles have been used to select differentially expressed genes as disease genes using mutual information-based maximum relevance-maximum significance framework, the functional protein association network has been used to study the mechanism of diseases. Extensive experimental study on colorectal cancer establishes the fact that the genes identified by the integrated method have more colorectal cancer genes than the genes identified from the gene expression profiles alone. All these results indicate that the integrated method is quite promising and may become a useful tool for identifying disease genes.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Althaus IW, Gonzales AJ, Chou JJ, Romero DL, Deibel MR, Chou KC, Kezdy FJ, Resnick L, Busso ME, So AG (1993) The quinoline U-78036 is a potent inhibitor of HIV-1 reverse transcriptase. J Biol Chem 268(20):14,875–14,880
Altshuler D, Daly MJ, Lander ES (2008) Genetic mapping in human disease. Science 322(5903):881–888
Andraos J (2008) Kinetic plasticity and the determination of product ratios for kinetic schemes leading to multiple products without rate laws—new methods based on directed graphs. Can J Chem 86(4):342–357
Barrenas F, Chavali S, Holme P, Mobini R, Benson M (2009) Network properties of complex human disease genes identified through genome-wide association studies. PLoS One 4(11):e8090
Bogdanov P, Singh A (2010) Molecular function prediction using neighborhood features. IEEE/ACM Trans Comput Biol Bioinform 7(2):208–217
Cai YD, Huang T, Feng KY, Hu L, Xie L (2010) A unified 35-gene signature for both subtype classification and survival prediction in diffuse large b-cell lymphomas. PLoS One 5(9):e12,726
Chen J, Aronow B, Jegga A (2009) Disease candidate gene identification and prioritization using protein interaction networks. BMC Bioinform 10(1):73
Chen L, Cai YD, Shi XH, Huang T (2010) Analysis of metabolic pathway using hybrid properties. PLoS One 5(6):e10,972
Chou KC (1990) Applications of graph theory to enzyme kinetics and protein folding kinetics: steady and non-steady-state systems. Biophys Chem 35(1):1–24
Chou KC (1993) Graphic rule for non-steady-state enzyme kinetics and protein folding kinetics. J Math Chem 12(1):97–108
Chou KC (2010) Graphic rule for drug metabolism systems. Curr Drug Metab 11:369–378
Chou KC, Forsen S (1980) Graphical rules for enzyme-catalysed rate laws. Biochem J 187:829–835
Chou KC, Kezdy FJ, Reusser F (1994) Kinetics of processive nucleic acid polymerases and nucleases. Anal Biochem 221(2):217–230
Dermitzakis ET (2008) From gene expression to disease risk. Nat Genet 40:492–493
Dijkstra EW (1959) A note on two problems in connexion with graphs. Numer Math 1(1):269–271
Ding C, Peng H (2003) Minimum redundancy feature selection from microarray gene expression data. In: Proceedings of the international conference on computational systems, bioinformatics, pp. 523–528
Ding C, Peng H (2005) Minimum redundancy feature selection from microarray gene expression data. J Bioinform Comput Biol 3(2):185–205
Duda RO, Hart PE, Stork DG (1999) Pattern classification and scene analysis. Wiley, New York
Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabsi AL (2007) The human disease network. Proc Natl Acad Sci 104(21):8685–8690
Hinoue T, Weisenberger DJ, Lange CP, Shen H, Byun HM, Van Den Berg D, Malik S, Pan F, Noushmehr H, van Dijk CM, Tollenaar RAEM, Laird PW (2012) Genome-scale analysis of aberrant DNA methylation in colorectal cancer. Genome Res 22(2):271–282
Huang T, Cui W, Hu L, Feng K, Li YX, Cai YD (2009) Prediction of pharmacological and xenobiotic responses to drugs based on time course gene expression profiles. PLoS One 4(12):e8126
Huang T, Cai YD, Chen L, Hu LL, Kong XY, Li YX, Chou KC (2010) Selection of reprogramming factors of induced pluripotent stem cells based on the protein interaction network and functional profiles. PLoS One 5(9):e12,726
Huang T, Shi XH, Wang P, He Z, Feng KY, Hu L, Kong X, Li YX, Cai YD, Chou KC (2010) Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks. PLoS One 5(6):e10,972
Huang T, Chen L, Cai YD, Chou KC (2011) Classification and analysis of regulatory pathways using graph property, biochemical and physicochemical property, and functional property. PLoS One 6(9):e25,297
Huret JL, Dessen P, Bernheim A (2003) Atlas of genetics and cytogenetics in oncology and haematology, year 2003. Nucleic Acids Res 31(1):272–274
Jia P, Zheng S, Long J, Zheng W, Zhao Z (2011) dmGWAS: dense module searching for genome-wide association studies in protein–protein interaction networks. Bioinformatics 27(1):95–102
Karaoz U, Murali TM, Letovsky S, Zheng Y, Ding C, Cantor CR, Kasif S (2004) Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci 101(9):2888–2893
Karni S, Soreq H, Sharan R (2009) A network-based method for predicting disease-causing genes. J Comput Biol 16(2):181–189
Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A (2009) Human protein reference database-2009 update. Nucleic Acids Res 37(suppl 1):D767–D772
Kohler S, Bauer S, Horn D, Robinson PN (2008) Walking the interactome for prioritization of candidate disease genes. Am J Hum Genet 82(4):949–958
Kourmpetis YAI, van Dijk ADJ, Bink MCAM, van Ham RCHJ, ter Braak CJF (2010) Bayesian Markov random field analysis for protein function prediction based on network data. PLoS One 5(2):e9293
Letovsky S, Kasif S (2003) Predicting protein function from protein/protein interaction data: a probabilistic approach. Bioinformatics 19(suppl 1):i197–i204
Li BQ, Huang T, Liu L, Cai YD, Chou KC (2012) Identification of colorectal cancer related genes with mRMR and shortest path in protein–protein interaction network. PLoS one 7(4):e33,393
Li Y, Li J (2012) Disease gene identification by random walk on multigraphs merging heterogeneous genomic and phenotype data. BMC Genomics 13(Suppl 7):S27
Maji P, Paul S (2011) Rough set based maximum relevance-maximum significance criterion and gene selection from microarray data. Int J Approximate Reasoning 52(3):408–426
Meltzer PS (2001) Spotting the target: microarrays for disease gene discovery. Curr Opin Genet Dev. 11(3):258–263
Mohammadi A, Saraee M, Salehi M (2011) Identification of disease-causing genes using microarray data mining and gene ontology. BMC Med Genomics 4(1):12
Nagaraj S, Reverter A (2011) A boolean-based systems biology approach to predict novel genes associated with cancer: application to colorectal cancer. BMC Syst Biol 5(1):35
Navlakha S, Kingsford C (2010) The power of protein interaction networks for associating genes with diseases. Bioinformatics 26(8):1057–1063
Ng KL, Ciou JS, Huang CH (2010) Prediction of protein functions based on function–function correlation relations. Comput Biol Med 40(3):300–305
Nitsch D, Tranchevent LC, Thienpont B, Thorrez L, Van Esch H, Devriendt K, Moreau Y (2009) Network analysis of differential expression for the identification of disease-causing genes. PLoS One 4(5):e5526
Novershtern N, Itzhaki Z, Manor O, Friedman N, Kaminski N (2008) A functional and regulatory map of asthma. Am J Resp Cell Mol Biol 38(3):324–336
Oti M, Snel B, Huynen MA, Brunner HG (2006) Predicting disease genes using protein–protein interactions. J Med Genet 43(8):691–698
Paul S, Maji P (2013) Gene ontology based quantitative index to select functionally diverse genes. Int J Mach Learn Cybern. doi:10.1007/s13042-012-0133-5.
Quenouille MH (1949) Approximate tests of correlation in time-series. J Roy Stat Soc Ser B (Methodol) 11(1):68–84
Ruan X, Wang J, Li H, Perozzi RE, Perozzi EF (2008) The use of logic relationships to model colon cancer gene expression networks with mRNA microarray data. J Biomed Inform 41(4):530–543
Sabates-Bellver J, Van der Flier LG, de Palo M, Cattaneo E, Maake C, Rehrauer H, Laczko E, Kurowski MA, Bujnicki JM, Menigatti M, Luz J, Ranalli TV, Gomes V, Pastorelli A, Faggiani R, Anti M, Jiricny J, Clevers H, Marra G (2007) Transcriptome profile of human colorectal adenomas. Mol Cancer Res 5(12):1263–1275
Sharan R, Ulitsky I, Shamir R (2007) Network-based prediction of protein function. Mol Syst Biol 3(88):1–13
Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering C (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 39(suppl 1):D561–D568
Vajda I (1989) Theory of statistical inference and information. Kluwer Academic, Dordrecht
Wu C, Zhu J, Zhang X (2012) Integrating gene expression and protein–protein interaction network to prioritize cancer-associated genes. BMC Bioinform 13(1):182
Zhao J, Jiang P, Zhang W (2010) Molecular networks for the study of TCM pharmacology. Briefings Bioinform 11(4):417–430
Zhao J, Yang TH, Huang Y, Holme P (2011) Ranking candidate disease Genes from gene expression and protein interaction: a Katz-centrality based approach. PLoS One 6(9):e24,306
Zhou GP (2011) The disposition of the LZCC protein residues in Wenxiang diagram provides new insights into the protein–protein interaction mechanism. J Theor Biol 284(1):142–148
Zhou GP, Deng MH (1984) An extension of Chou’s graphic rules for deriving enzyme kinetic equations to systems involving parallel reaction pathways. Biochem J 222:169–176
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
Copyright information
© 2014 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Maji, P., Paul, S. (2014). Identification of Disease Genes Using Gene Expression and Protein–Protein Interaction Data. In: Scalable Pattern Recognition Algorithms. Springer, Cham. https://doi.org/10.1007/978-3-319-05630-2_6
Download citation
DOI: https://doi.org/10.1007/978-3-319-05630-2_6
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-05629-6
Online ISBN: 978-3-319-05630-2
eBook Packages: Computer ScienceComputer Science (R0)