nach oben

Erschienen in:

2015 | OriginalPaper | Buchkapitel

1. Application of Machine-Learning Methods to Understand Gene Expression Regulation

verfasst von : Chao Cheng, William P. Worzel

Erschienen in: Genetic Programming Theory and Practice XII

Verlag: Springer International Publishing

Einloggen

Aktivieren Sie unsere intelligente Suche, um passende Fachinhalte oder Patente zu finden.

search-config

KI-gestützte Suche

Aus

Abstract

With the development and application of high-throughput technologies, an enormous amount of biological data has been produced in the past few years. These large-scale datasets make it possible and necessary to implement machine learning techniques for mining biological insights. In this chapter, we describe several examples to show how machine learning approaches are used to elucidate the mechanism of transcriptional regulation mediated by transcription factors and histone modifications. We demonstrate that machine learning provides powerful tools to quantitatively relate gene expression with transcription factor binding and histone modifications, to identify novel regulatory DNA elements in the genomes, and to predict gene functions. We also discuss the advantages and limitations of genetic programming in analyzing and processing biological data.

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

über 102.000 Bücher
über 537 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Finance + Banking
Management + Führung
Marketing + Vertrieb
Maschinenbau + Werkstoffe
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 390 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Maschinenbau + Werkstoffe

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 340 Zeitschriften

aus folgenden Fachgebieten:

Bauwesen + Immobilien
Business IT + Informatik
Finance + Banking
Management + Führung
Marketing + Vertrieb
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Nächstes Kapitel Identification of Novel Genetic Models of Glaucoma Using the “EMERGENT” Genetic Programming-Based Artificial Intelligence System

Andre D, Koza J (1996) A parallel implementation of genetic programming that achieves super-linear performance. Proceedings of the international conference on parallel and distributed processing techniques and applications, CSREA Press, Sunnyvale:A.H.R.

Berger S (2007) The complex language of chromatin regulation during transcription. Nature 447(7143):407–412CrossRef

Chadwick L (2012) The NIH roadmap epigenomics program data resource. Epigenomics 4(3):317–324MathSciNetCrossRef

Chen X, Xu H, Yuan P, Fang F, Huss M, Vega V, Wong E, Orlov Y, Zhang W, Jiang J (2008) Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133(6):1106–1117CrossRef

Cheng C, Gerstein M (2012) Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells. Nucleic Acids Res 40(2):553–568CrossRef

Cheng C, Li L (2008) Systematic identification of cell cycle regulated transcription factors from microarray time series data. BMC Genomics 9:116CrossRef

Cheng C, Shou C, Yip K, Gerstein M (2011a) Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors. Genome Biol 12(11):R111CrossRef

Cheng C, Yan K, Yip K, Rozowsky J, Alexander R, Shou C, Gerstein M (2011b) A statistical framework for modeling gene expression using chromatin features and application to modencode datasets. Genome Biol 12(2):R15CrossRef

Cheng C, Alexander R, Min R, Leng J, Yip K, Rozowsky J, Yan K, Dong X, Djebali S, Ruan Y (2012) Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res 22(9):1658–1667CrossRef

Cheng C, Ung M, Grant G, Whitfield M (2013) Transcription factor binding profiles reveal cyclic expression of human protein-coding genes and non-coding rnas. PLoS Computational Biol 9(7):e1003132CrossRef

Cloonan N, Forrest A, Kolle G, Gardiner B, Faulkner G, Brown M, Taylor D, Steptoe A, Wani S, Bethel G (2008) Stem cell transcriptome profiling via massive-scale mrna sequencing. Nat Methods 5(7):613–619CrossRef

Creyghton M, Cheng A, Welstead G, Kooistra T, Carey B, Steine E, Hanna J, Lodato M, Frampton G, Sharp P (2010) Histone h3k27ac separates active from poised enhancers and predicts developmental state. Proceedings of the National Academy of Sciences of the United States of America 107(50):21,931–21,936

Eggermont J, Kok J, Kosters W (2004) Genetic programming for data classification:partitioning the search space. Proceedings of the 2004 ACM symposium on Applied computing ACM Press, Nicosia, pp 1001–1005

ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57–74

Farnham P (2009)Insights from genomic profiling of transcription factors. Nat Rev Genet 10(9):605–616CrossRef

Gerstein M, Lu Z, Nostrand EV, Cheng C, Arshinoff B, Liu T, Yip K, Robilotto R, Rechtsteiner A, Ikegami K (2010) Integrative analysis of the caenorhabditis elegans genome by the modencode project. Science 330(6012):1775–1787CrossRef

Ghosh P, Bagchi M (2009) Qsar modeling for quinoxaline derivatives using genetic algorithm and simulated annealing based feature selection. Curr Med Chem 16(30):4032–4048CrossRef

Johnson D, Mortazavi A, Myers R, Wold B (2007) Genome-wide mapping of in vivo protein-dna interactions. Science 316(5830):1497–1502CrossRef

Kandoth C, McLellan M, Vandin F, Ye K, Niu B, Lu C, Xie M, Zhang Q, McMichael J, Wyczalkowski M (2013) Mutational landscape and significance across 12 major cancer types. Nature 502(7471):333–339CrossRef

Khan M, Alam M (2012) A survey of application: genomics and genetic programming, a new frontier. Genomics 100(2):65–71CrossRef

Kotanchek M, Smits G, Vladislavleva E (2006) Pursuing the pareto paradigm tournaments, algorithm variations & ordinal optimization. In: Riolo RL, Soule T, Worzel B (eds) Genetic programming theory and practice IV, genetic and evolutionary computation, vol 5. Springer, Ann Arbor, pp 167–185. doi:10.1007/978-0-387-49650-4–11

Kotanchek ME,Vladislavleva E, Smits G(2012) Symbolic regression is not enough: It takes a village to raise a model. In: Riolo R, Vladislavleva E, Ritchie MD, Moore JH (eds) Genetic programming theory and practice X, genetic and evolutionary computation. Springer, Ann Arbor, pp 187–203. doi:10.1007/978-1-4614-6846-2-13, http://dx.doi.org/10.1007/978-1-4614-6846-2-13

Koza JR, Mydlowec W, Lanza G, Yu J, Keane MA (2001) Automatic synthesis of both the topology and sizing of metabolic pathways using genetic programming. In: Spector L, Goodman ED, Wu A, Langdon WB, Voigt HM, Gen M, Sen S, Dorigo M, Pezeshk S, Garzon MH, Burke E (eds) Proceedings of the genetic and evolutionary computation conference (GECCO-2001). Morgan Kaufmann, San Francisco, pp 57–65. http://www.cs.bham.ac.uk/~wbl/biblio/gecco2001/koza-gecco2001.pdf

Kurdistani S, Tavazoie S, Grunstein M (2004) Mapping global histone acetylation patterns to gene expression. Cell 117(6):721–733CrossRef

Lander E, Linton L, Birren B, Nusbaum C, Zody M, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W (2001) Initial sequencing and analysis of the human genome. Nature 409(6822):860–921CrossRef

Li B, Carey M, Workman J (2007) The role of chromatin during transcription. Cell 128(4):707–719CrossRef

Maston G, Evans S, Green M (2006) Transcriptional regulatory elements in the human genome. Annu Rev Genomics Hum Genet 7:29–59

Mikkelsen T, Ku M, Jaffe D, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim T, Koche R (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448(7153):553–560CrossRef

Mitra A, Almal A, George B, Fry D, Lenehan P, Pagliarulo V, Cote R, Datar R, Worzel W (2006) The use of genetic programming in the analysis of quantitative gene expression profiles for identification of nodal status in bladder cancer. BMC Cancer 6:159CrossRef

Moore J, White B (2006) Genome-wide genetic analysis using genetic programming: the critical need for expert knowledge. In: Riolo RL, Soule T, Worzel B (eds) Genetic programming theory and practice IV, Springer, genetic and evolutionary computation, vol 5, pp 11–28

Orlando D, Lin C, Bernard A, Wang J, Socolar J, Iversen E, Hartemink A, Haase S (2008) Global control of cell-cycle transcription by coupled cdk and network oscillators. Nature 453(7197):944–947CrossRef

Pennacchio L, Ahituv N, Moses A, Prabhakar S, Nobrega M, Shoukry M, Minovisky S, Dubchak I, Holt A, Lewis K (2006) In vivo enhancer analysis of human conserved non-coding sequences. Nature 444(7118):499–502CrossRef

Pennacchio L, Bickmore W, Dean A, Nobrega M, Bejerano G (2013) Enhancers: five essential questions. Nat Rev Genet 14(4):288–295CrossRef

Ren B, Robert F, Wyrick J, Aparicio O, Jennings E, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E (2000) Genome-wide location and function of dna binding proteins. Science 290(5500):2306–2309CrossRef

Simon I, Barnett J, Hannett N, Harbison C, Rinaldi N, Volkert T, Wyrick J, Zeitlinger J, Gifford D, Jaakkola T (2001) Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106(6):697–708CrossRef

Stamatoyannopoulos J, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert D, Groudine M, Bender M, Kaul R, Canfield T (2012) An encyclopedia of mouse dna elements (mouse encode). Gen Biol 13(8):418

Stormo G (2000) Dna binding sites: representation and discovery. Bioinformatics 16(1):16–23CrossRef

Strahl B, Allis C (2000) The language of covalent histone modifications. Nature 403(6765):41–45CrossRef

Venter J, Adams M, Myers E, Li P, Mural R, Sutton G, Smith H, Yandell M, Evans C, Holt R (2001) The sequence of the human genome. Science 291(5507):1304–1351CrossRef

Whitfield M, Sherlock G, Saldanha A, Murray J, Ball C, Alexander K, Matese J, Perou C, Hurt M, Brown P (2002) Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell 13(6):1977–2000CrossRef

Worzel W, Yu J, Almal A, Chinnaiyan A (2009) Applications of genetic programming in cancer research. Int J Biochem Cell Biol 41(2):405–413CrossRef

Yip K, Cheng C, Bhardwaj N, Brown J, Leng J, Kundaje A, Rozowsky J, Birney E, Bickel P, Snyder M (2012) Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome biol 13(9):R48CrossRef

Titel: Application of Machine-Learning Methods to Understand Gene Expression Regulation
verfasst von: Chao Cheng
William P. Worzel
Verlag: Springer International Publishing
Buch: Genetic Programming Theory and Practice XII
Print ISBN: 978-3-319-16029-0

Electronic ISBN: 978-3-319-16030-6

Copyright-Jahr: 2015
DOI: https://doi.org/10.1007/978-3-319-16030-6_1

Springer Professional

Abstract

Bitte loggen Sie sich ein, um Zugang zu Ihrer Lizenz zu erhalten.

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Springer Professional "Technik"

Springer Professional "Wirtschaft"