Transcript profiling and expression level mapping

Methods in Molecular Biology

Volumn 513, Issue , 2009, Pages 81-92

  Potokina, Elena ^a   Druka, Arnis ^a   Kearsey, Michael J ^a  

^a UNIVERSITY OF BIRMINGHAM   (United Kingdom)

Author keywords

Affymetrix; Barley; Expression analysis; SNP; Transcript derived markers

Indexed keywords

HORDEUM;

MESSENGER RNA; PLANT RNA;

ARTICLE; BARLEY; CHROMOSOME MAP; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETIC MARKER; GENETICS; METHODOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME MAPPING; GENE EXPRESSION PROFILING; GENETIC MARKERS; HORDEUM; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; RNA, MESSENGER; RNA, PLANT;

EID: 65349174462     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-59745-427-8_5     Document Type: Article

References (13)

1. Ronald, J., Akey, J.M., Whittle, J., Smith, E.N., Yvert, G., and Kruglyak, L. (2005) Simultaneous genotyping gene-expression measurement and detection of allele-specific expression with oligo-nucleotide arrays. Genome Res. 15, 284-291. (Pubitemid 40309393)
2. West, M.A.L., Leeuwen, H., Kozik, A., Kliebenstein, D.K., Doerge, R.W., Clair, D.A., and Michelmore, R.W. (2006) High-density haplotying with microarray-based expression and single feature polymorphism markers in Arabidopsis. Genome Res. 16, 787-795. (Pubitemid 43830699)
3. DeCook, R., Lall, S., Nettleton, D., and Howell, S.H. (2006) Genetic regulation of gene expression during shoot development in Arabidopsis. Genetics 172, 1155-1164. (Pubitemid 43345447)
4. Rostoks, N., Borevitz, J.O., Hedley, P.E., Russell, J., Mudie, S., Morris, J., Cardle, L., Marshall, D.F., and Waugh, R. (2005) Single-feature polymorphism discovery in the barley transcriptome. Genome Biol. 6, R54.
5. Cui, X., Xu, J., Asghar, R., Condamine, P., Svensson, J.T., Wanamaker, S., Stein, N., Roose, M., and Close, T.J. (2005) Detecting single-feature polymorphisms using oligonu-cleotide arrays and robustified projection pursuit. Bioinformatics 21, 3852-3858. (Pubitemid 41535499)
6. Brem, R.B., Yvert, G., Clinton, R., and Kruglyak, L. (2002) Genetic dissection of transcriptional regulation in budding yeast. Science 296, 752-755. (Pubitemid 34442007)
7. Kleinhofs, A., Kilian A., Saghai-Maroof, M.A., Biyashev, R.M., Hayes, P., Chen, F.Q., Lapitan, N., Fenwich, A., Blake, T.K., Kana-zin, V. et al., (1993) A molecular, isozyme and morphological map of the barley genome. Theor. Appl. Genet. 86, 705-712.
8. Caldo, R.A., Nettleton, D., and Wise, R.P. (2004) Interaction-dependent gene expression in Mla-specified response to barley powdery mildew. Plant Cell 16, 2514-2528. (Pubitemid 39247088)
9. Irizarry, R.A., Hobbs, B., Collin, F., Beazer-Barclay, Y.D., Antonellis, K.J., Scherf, U., and Speed, T.P. (2003) Exploration, normalization, and summaries of high density oligo-nucleotide array probe level data. Biostatistics 4 (2), 249-264.
10. Luo, Z.W., Potobina, E., Druka, A., Wise, R., Waugh, R., Kearsey, M.J. (in Press) Robust, high density genotyping from gene-expression data in species with un-sequenced genomes. Genetics
11. Yamashita, S., Wakazono, K., Nomoto, T., Tsujino, Y., Kuramoto, T., et al. (2005) Expression quantitative trait loci analysis of 13 genes in the rat prostate. Genetics 171, 1231-1238. (Pubitemid 43234854)
12. Hubner, N., Wallace, C.A., Zimdahl, H., Petretto, E., Schulz, H., et al. (2005) Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nat. Genet. 37, 243-253. (Pubitemid 41716251)
13. Van Ooijen J.W. and Voorrips R.E. (2001) JoinMap ® 3.0. Software for the calculation of genetic linkage maps. Plant Research International. Wageningen: The Netherlands.