A genome-wide approach to identifying novel-imprinted genes (original) (raw)
References
Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate—a practical and powerful approach to multiple testing. J R Stat Soc Ser B 57:289–300 Google Scholar
Fulmer-Smentek SB, Francke U (2001) Association of acetylated histones with paternally expressed genes in the Prader-Willi deletion region. Hum Mol Genet 10:645–652 ArticlePubMedCAS Google Scholar
Ge B, Gurd S, Gaudin T, Dore C, Lepage P, Harmsen E, Hudson TJ, Pastinen T (2005) Survey of allelic expression using EST mining. Genome Res 15:1584–1591 ArticlePubMedCAS Google Scholar
Grabowski M, Zimprich A, Lorenz-Depiereux B, Kalscheuer V, Asmus F, Gasser T, Meitinger T, Strom TM (2003) The epsilon-sarcoglycan gene (SGCE), mutated in myoclonus-dystonia syndrome, is maternally imprinted. Eur J Hum Genet 11:138–144 ArticlePubMedCAS Google Scholar
Hinds DA, Stuve LL, Nilsen GB, Halperin E, Eskin E, Ballinger DG, Frazer KA, Cox DR (2005) Whole-genome patterns of common DNA variation in three human populations. Science 307:1072–1079 ArticlePubMedCAS Google Scholar
Kamiya M, Judson H, Okazaki Y, Kusakabe M, Muramatsu M, Takada S, Takagi N, Arima T, Wake N, Kamimura K, Satomura K, Hermann R, Bonthron DT, Hayashizaki Y (2000) The cell cycle control gene ZAC/PLAGL1 is imprinted—a strong candidate gene for transient neonatal diabetes. Hum Mol Genet 9:453–460 ArticlePubMedCAS Google Scholar
Lo HS, Wang Z, Hu Y, Yang HH, Gere S, Buetow KH, Lee MP (2003) Genetic variation in gene expression is common in the human genome. Genome Res 13:1855–1862 ArticlePubMedCAS Google Scholar
Luedi PP, Hartemink AJ, Jirtle RL (2005) Genome-wide prediction of imprinted murine genes. Genome Res 15:875–884 ArticlePubMedCAS Google Scholar
Monk D, Arnaud P, Apostolidou S, Hills FA, Kelsey G, Stanier P, Feil R, Moore GE (2006) Limited evolutionary conservation of imprinting in the human placenta. Proc Natl Acad Sci USA 103:6623–6628 ArticlePubMedCAS Google Scholar
Morison IM, Ramsay JP, Spencer HG (2005) Evolution of mammalian imprinting. Trends Genet 21:457–465 ArticlePubMedCAS Google Scholar
Murphy SK, Jirtle RL (2003) Imprinting evolution and the price of silence. BioEssays 25:577–588 ArticlePubMedCAS Google Scholar
Nikaido I, Saito C, Mizuno Y, Meguro M, Bono H, Kadomura M, Kono T, Morris GA, Lyons PA, Oshimura M, RIKEN GER Group, GSL Members, Hayashizaki Y, Okazaki Y (2003) Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling. Genome Res 13:1402–1409 ArticlePubMedCAS Google Scholar
Pant PV, Tao H, Beilharz EJ, Ballinger DG, Cox DR, Frazer KA (2006) Analysis of allelic differential expression in human white blood cells. Genome Res 16:331–339 ArticlePubMedCAS Google Scholar
Pastinen T, Sladek R, Gurd S, Sammak A, Ge B, Lepage P, Lavergne K, Villeneuve A, Gaudin T, Brandstrom H, Beck A, Verner A, Kingsley J, Harmsen E, Labuda D, Morgan K, Vohl MC, Naumova AK, Sinnett D, Hudson TJ (2004) A survey of genetic and epigenetic variation affecting human gene expression. Physiol Genomics 16:184–193 PubMedCAS Google Scholar
Pastinen T, Ge B, Gurd S, Gaudin T, Dore C, Lemire M, Lepage P, Harmsen E, Hudson TJ (2005) Mapping common regulatory variants to human haplotypes. Hum Mol Genet 14:3963–3971 ArticlePubMedCAS Google Scholar
Reik W, Walter J (2001) Evolution of imprinting mechanisms: the battle of the sexes begins in the zygote. Nat Genet 27:255–256 ArticlePubMedCAS Google Scholar
Ruf N, Dunzinger U, Brinckmann A, Haaf T, Nurnberg P, Zechner U (2006) Expression profiling of uniparental mouse embryos is inefficient in identifying novel imprinted genes. Genomics 87:509–519 ArticlePubMedCAS Google Scholar
Ruf N, Bahring S, Galetska D, Pliushch G, Luft F, Nurnberg P, Haaf T, Kelsey G, Zechner U (2007) Sequence-based bioinformatic prediction and QUASEP identify genomic imprinting of the KCNK9 potassium channel gene in mouse and human. Hum Mol Genet 16:2591–2599 ArticlePubMedCAS Google Scholar
Schweizer J, Zynger D, Francke U (1999) In vivo nuclease hypersensitivity studies reveal multiple sites of parental origin-dependent differential chromatin conformation in the 150 kb SNRPN transcription unit. Hum Mol Genet 8:555–566 ArticlePubMedCAS Google Scholar
Spencer HG, Feldman MW, Clark AG (1998) Genetic conflicts, multiple paternity and the evolution of genomic imprinting. Genetics 148:893–904 PubMedCAS Google Scholar
Spielman RS, Bastone LA, BurdickJT, Morely M, Ewens WJ, Cheung VG (2007) Common genetic variants account for differences in gene expression among ethnic groups. Nat Genet 39:226–231 ArticlePubMedCAS Google Scholar
Storey JD, Madeoy J, Strout JL, Wurfel M, Ronald J, Akey JM (2007) Gene-expression variation within and among human populations. Am J Hum Genet 80:502–509 ArticlePubMedCAS Google Scholar
Stranger BE, Forrest MS, Clark AG, Minichiello MJ, Deutsch S, Lyle R, Hunt S, Kahl B, Antonarakis SE, Tavaré S, Deloukas P, Dermitzakis ET (2005) Genome-wide associations of gene expression variation in humans. PLoS Genet 1:e78 ArticlePubMed Google Scholar
Tao H, Cox DR, Frazer KA (2006) Allele-specific KRT1 expression is a complex trait. PLoS Genet 2:e93 ArticlePubMed Google Scholar
Valleley EM, Cordery SF, Bonthron DT (2007) Tissue-specific imprinting of the ZAC/PLAGL1 tumour suppressor gene results from variable utilization of monoallelic and biallelic promoters. Hum Mol Genet 16:972–981 ArticlePubMedCAS Google Scholar
Yan H, Yuan W, Velculescu VE, Vogelstein B, Kinzler KW (2002) Allelic variation in human gene expression. Science 297:1143 ArticlePubMedCAS Google Scholar
Zhou H, Brockington M, Jungbluth H, Monk D, Stanier P, Sewry CA, Moore GE, Muntoni F (2006) Epigenetic allele silencing unveils recessive RYR1 mutations in core myopathies. Am J Hum Genet 79:859–868 ArticlePubMedCAS Google Scholar