Top

Published in:

2011 | OriginalPaper | Chapter

13. eQTL Mapping for Functional Classes of Saccharomyces cerevisiae Genes with Multivariate Sparse Partial Least Squares Regression

Authors : Dongjun Chung, Sündüz Keleş

Published in: Handbook of Statistical Bioinformatics

Publisher: Springer Berlin Heidelberg

Activate our intelligent search to find suitable subject content or patents.

search-config

AI-assisted search

Off

Abstract

The availability of high-throughput genotyping technologies and microarray assays has enabled investigation of genetic variations that influence levels of gene expression. Expression Quantitative Trait Loci (eQTL) mapping methods have been successfully used to identify the genetic basis of gene expression which in turn led to identification of candidate genes and construction of regulatory networks. One challenging statistical aspect of eQTL mapping is the existence of thousands of traits. We have recently proposed a multivariate sparse partial least squares framework for mapping multiple quantitative traits and identifying genetic variations that affect the expression of a group of genes. In this book chapter, we provide a comprehensive illustration of this methodology with a Saccharomyces cerevisiae linkage study. Data from this study involves segregants from a cross between two Saccharomyces cerevisiae strains. Our application focuses on elucidating genomic markers that affect expression of functional yeast gene classes. We illustrate identification of eQTL regions affecting whole functional classes of genes as well as eQTL regions influencing individual genes.

Dont have a licence yet? Then find out more about our products and how to get one now:

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!

inform now

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!

inform now

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!

inform now

previous chapter Computational Analysis of ChIP-chip Data

next chapter Statistical Analysis of Time Course Microarray Data

Alifano, P., Fani, R., Liò, P., Lazcano, A., Bazzicalupo, M., Carlomagno, M., & Bruni, C. (1996). Histidine biosynthetic pathway and genes: Structure, regulation, and evolution. Microbiological Reviews, 60, 44–69.

Allison, D. B., Thiel, B., Jean, P. S., Elston, R. C., Infante, M. C., & Schork, N. J. (1998). Multiple phenotype modeling in gene-mapping studies of quantitative traits: Power advantages. American Journal of Human Genetics, 63, 1190–1201.CrossRef

Andreadis, A., Hsu, Y., Hermodson, M., Kohlhaw, G., & Schimmel, P. (1984). Yeast LEU2. Repression of mRNA levels by leucine and primary structure of the gene product. The Journal of Biological Chemistry, 259, 8059–8062.

Bhat, P., & Murthy, T. (2001). Transcriptional control of the GAL/MEL regulon of yeast Saccharomyces cerevisiae: Mechanism of galactose-mediated signal transduction. Molecular Microbiology, 40, 1059–1066.CrossRef

Brem, R., & Kruglyak, L. (2005). The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proceedings of the National Academy of Sciences of the United States of America, 102, 1572–1577.CrossRef

Brem, R., Storey, J., Whittle, J., & Kruglyak, L. (2005). Genetic interactions between polymorphisms that affect gene expression in yeast. Nature, 436, 701–703.CrossRef

Brem, R., Yvert, G., Clinton, R., & Kryglyak, L. (2002). Genetic dissection of transcriptional regulation in budding yeast. Science, 296, 752–755.CrossRef

Broman, K. W., Wu, H., Sen, S., & Churchill, G. A. (2003). R/qtl: QTL mapping in experimental crosses. Bioinformatics, 19, 889–890.CrossRef

Chen, M., & Kendziorski, C. (2007). A statistical framework for expression quantitative trait loci (eQTL) mapping. Genetics, 177, 761–771.CrossRef

10.

Chen, W., Balzi, E., Capieaux, E., Choder, M., & Goffeau, A. (1991). The DNA sequencing of the 17 kb HindIII fragment spanning the LEU1 and ATE1 loci on chromosome VII from Saccharomyces cerevisiae reveals the PDR6 gene, a new member of the genetic network controlling pleiotropic drug resistance. Yeast, 7, 287–299.CrossRef

11.

Chesler, E. J., Lu, L., Shou, S., Qu, Y., Gu, J., Wang, J., Hsu, H. C., Mountz, J. D., Baldwin, N. E., Langston, M. A., Threadgill, D. W., Manly, K. F., & Williams, R. W. (2005). Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nature Genetics, 37(4), 233–242.CrossRef

12.

Chun, H., & Keleş, S. (2009). Expression quantitative trait loci mapping with multivariate sparse partial least squares regression. Genetics, 182, 79–90.CrossRef

13.

Chun, H., & Keleş, S. (2010). Sparse partial least squares for simultaneous dimension reduction and variable selection. Journal of the Royal Statistical Society: Series B, 72, 3–25.CrossRef

14.

Dwight, S. S., Balakrishnan, R., Christie, K. R., Costanzo, M. C., Dolinski, K., Engel, S. R., Feierbach, B., Fisk, D. G., Hirschman, J., Hong, E. L., Issel-Tarver, L., Nash, R. S., Sethuraman, A., Starr, B., Theesfeld, C. L., Andrada, R., Binkley, G., Dong, Q., Lane, C., Schroeder, M., Weng, S., Botstein, D., & Cherry, J. M. (2004). Saccharomyces genome database: Underlying principles and organisation. Briefings in Bioinformatics, 5(1), 922. http://dx.doi.org/10.1093/bib/5.1.9

15.

Felder, T., Bogengruber, E., Tenreiro, S., Ellinger, A., Sá-Correia, I., & Briza, P. (2002). Dtrlp, a multidrug resistance transporter of the major facilitator superfamily, plays an essential role in spore wall maturation in Saccharomyces cerevisiae. Eukaryotic cell, 1, 799–810.CrossRef

16.

Gasch, A., & Eisen, M. (2002). Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biology, 3, research0059.1”0059.22.

17.

Gbelska, Y., Krijger, J., & Breunig, K. (2006). Evolution of gene families: The multidrug resistance transporter genes in five related yeast species. FEMS Yeast Research, 6, 345–355.CrossRef

18.

Gelfond, J. A. L., Ibrahim, J. G., & Zou, F. (2007). Proximity model for expression quantitative trait loci (eQTL) detection. Biometrics, 63(4), 1108–1116.MathSciNetMATHCrossRef

19.

Harbison, C., Gordon, D., Lee, T., Rinaldi, N., Macisaac, K., Danford, T., Hannett, N., Tagne, J. B., Reynolds, D., Yoo, J., Jennings, E., Zeitlinger, J., Pokholok, D., Kellis, M., Rolfe, P., Takusagawa, K., Lander, E., Gifford, D., Fraenkel, E., & Young, R. (2004). Transcriptional regulatory code of a eukaryotic genome. Nature, 431, 99–104.CrossRef

20.

Herskowitz, I. (1989). A regulatory hierarchy for cell specialization in yeast. Nature, 342, 749–757.CrossRef

21.

Jia, Z., & Xu, S. (2007). Mapping quantitative trait loci for expression abundance. Genetics, 176, 611–623.CrossRef

22.

Jiang, C., & Zeng, Z. (1995). Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics, 140, 1111–1127.

23.

Jiang, D., Tang, C., & Zhang, A. (2004). Cluster analysis for gene expression data: A survey. IEEE Transactions on Knowledge and Data Engineering, 16(11), 1370–1386.CrossRef

24.

Karpichev, I. V., & Small, G. M. (1998). Global regulatory functions of Oaf1p and Pip2p (Oaf2p), transcription factors that regulate genes encoding peroxisomal proteins in Saccharomyces cerevisiae. Molecular Cell Biology, 18, 6560–6570.

25.

Keesey, J. J., Bigelis, R., & Fink, G. (1979). The product of the his4 gene cluster in Saccharomyces cerevisiae. a trifunctional polypeptide. The Journal of Biological Chemistry, 254, 7427–7433.

26.

Kendziorski, C., & Wang, P. (2006). A review of statistical methods for expression quantitative trait loci mapping. Mammalian Genome, 17(6), 509–517.CrossRef

27.

Kendziorski, C. M., Chen, M., Yuan, M., Lan, H., & Attie, A. D. (2006). Statistical methods for expression quantitative trait loci (eQTL) mapping. Biometrics, 62, 19–27.MathSciNetMATHCrossRef

28.

Keng, T., Richard, C., & Larocque, R. (1992). Structure and regulation of yeast HEM3, the gene for porphobilinogen deaminase. Molecular and General Genetics, 234, 233–243.

29.

Kim, K. W., Kamerud, J. Q., Livingston, D. M., & Roon, R. (1988). Asparaginase II of Saccharomyces cerevisiae. Characterization of the ASP3 gene. Journal of Biological Chemistry, 263, 11948–11953.

30.

Kohlhaw, G. (2003). Leucine biosynthesis in fungi: Entering metabolism through the back door. Microbiology and Molecular Biology Reviews, 67, 1–15.CrossRef

31.

Lan, H., Chen, M., Flowers, J. B., Yandell, B. S., Stapleton, D. S., Mata, C. M., n Keen Mui, E. T., Flowers, M. T., Schueler, K. L., Manly, K. F., Williams, R. W., Kendziorski, C., & Attie, A. D. (2006). Combined expression trait correlations and expression quantitative trait locus mapping. PLoS Genetics, 2, e6.

32.

Lan, H., Stoehr, J. P., Nadler, S. T., Schueler, K. L., Yandell, B. S., & Attie, A. D. (2003). Dimension reduction for mapping mRNA abundance as quantitative traits. Genetics, 164, 1607–1614.

33.

Li, J., & Burmeister, M. (2005). Human molecular genetics review issue 2. BMC Genomics, 14(2), R163–R169.

34.

Morley, M., Molony, C. M., Weber, T. M., Devlin J. L. snd Ewens, K. G., Spielman, R. S., & Cheung, V. G. (2004). Genetic analysis of genome-wide variation in human gene expression. Nature, 430(7001), 743–747.

35.

Platt, A., & Reece, R. (1998). The yeast galactose genetic switch is mediated by the formation of a Gal4p-Gal80p-Gal3p complex. The EMBO Journal, 17, 4086–4091.CrossRef

36.

Rottensteiner, H., Kal, A. J., Hamilton, B., Ruis, H., & Tabak, H. F. (1997). A heterodimer of the Zn2Cys6 transcription factors Pip2p and Oaf1p controls induction of genes encoding peroxisomal proteins in Saccharomyces cerevisiae. European Journal of Biochemistry, 247, 776–783.CrossRef

37.

Saerens, S., Verstrepen, K., Van Laere, S., Voet, A., Van Dijck, P., Delvaux, F., & Thevelein, J. (2006). The Saccharomyces cerevisiae EHT1 and EEB1 genes encode novel enzymes with medium-chain fatty acid ethyl ester synthesis and hydrolysis capacity. The Journal of Biological Chemistry, 281, 4446–4456.CrossRef

38.

Schadt, E. E., Monks, S. A., Drake, T., Lusis, A. J., Che, N., Colinayo, V., Ruff, T. G., Milligan, S. B., Lamb, J. R., Cavet, G., Linsley, P. S., Mao, M., Stoughton, R. B., & Friend, S. H. (2003). Genetics of gene expression surveyed in maize, mouse and man. Nature, 422, 297–302.CrossRef

39.

Schreve, J., Sin, J., & Garrett, J. (1998). The Saccharomyces cerevisiae YCC5 (YCL025c) gene encodes an amino acid permease, Agp1, which transports asparagine and glutamine. Journal of Bacteriology, 180, 2556–2559.

40.

Stranger, B. E., Forrest, M. S., Clark, A. G., Minichiello, M. J., Deutsch, S., Lyle, R., Hunt, S., Kahl, B., Antonarakis, S. E., Tavare, S., Deloukas, P., & Dermitzakis, E. T. (2005). Genome-wide associations of gene expression variation in humans. PLoS Genetics, 1(6), e78.CrossRef

41.

Sun, W., Yu, T., & Li, K. C. (2007). Detection of eQTL modules mediated by activity levels of transcription factors. Bioinformatics, 23, 2290–2297.CrossRef

42.

Sun, W., Yuan, S., & Li, K. C. (2008). Trait-trait dynamic interaction: 2D-trait eQTL mapping for genetic variation study. BMC Genomics, 9, 242.CrossRef

43.

Tenreiro, S., Nunes, P., Viegas, C., Neves, M., Teixeira, M., Cabral, M., & Sá-Correia, I. (2002). AQR1 gene (ORF YNL065w) encodes a plasma membrane transporter of the major facilitator superfamily that confers resistance to short-chain monocarboxylic acids and quinidine in Saccharomyces cerevisiae. Biochemical and Biophysical Research Communications, 292, 741–748.CrossRef

44.

Troyanskaya, O., Cantor, M., Sherlock, G., Brown, P., Hastie, T., Tibshirani, R., Botstein, D., & Altman, R. B. (2001). Missing value estimation methods for DNA microarrays. Bioinformatics, 17, 520–525.CrossRef

45.

Velasco, I., Tenreiro, S., Calderon, I., & André, B. (2004). Saccharomyces cerevisiae Aqr1 is an internal-membrane transporter involved in excretion of amino acids. Eukaryotic Cell, 3, 1492–1503.CrossRef

46.

Wang, S., Yehya, N., Schadt, E. E., Wang, H., Drake, T. A., & Lusis, A. J. (2006). Genetic and genomic analysis of a fat mass trait with complex inheritance reveals marked sex specificity. PLoS Genetics, 2(2), e15.CrossRef

47.

Wang, Y., & Dohlman, H. (2004). Pheromone signaling mechanisms in yeast: A prototypical sex machine. Science, 306, 1508–1509.CrossRef

48.

Wu, C., Delano, D. L., Mitro, N., Su, S. V., Janes, J., McClurg, P., Batalov, S., Welch, G. L., Zhang, J., Orth, A. P., Walker, J. R., Glynne, R. J., Cooke, M. P., Takahashi, J. S., Shimomura, K., Kohsaka, A., Bass, J., Saez, E., Wiltshrie, T., & Su, A. I. (2008). Gene set enrichment in eQTL identifies novel annotations and pathway regulators. PLoS Genetics, 4(5), e1000,070.

49.

Yvert, G., Brem, R. B., Whittle, J., Akey, J. M., Foss, E., Smith, E. N., Mackelprang, R., & Kruglyak, L. (2003). Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nature Genetics, 35, 57–64.CrossRef

Title: eQTL Mapping for Functional Classes of Saccharomyces cerevisiae Genes with Multivariate Sparse Partial Least Squares Regression
Authors: Dongjun Chung
Sündüz Keleş
Publisher: Springer Berlin Heidelberg
Book: Handbook of Statistical Bioinformatics
Print ISBN: 978-3-642-16344-9

Electronic ISBN: 978-3-642-16345-6

Copyright Year: 2011
DOI: https://doi.org/10.1007/978-3-642-16345-6_13

Springer Professional

Abstract

Please log in to get access to your license.

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Springer Professional "Technik"

Springer Professional "Wirtschaft"

Premium Partner