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[41] Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC,
Baldwin J, et al. Initial sequencing and analysis of the human
genome. Nature 2001;409:860
e
921.
[42] Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG,
et al. The sequence of the human genome. Science 2001;291:
1304
e
51.
[43] Ewing B, Green P. Analysis of expressed sequence tags indicates
35,000 human genes. Nat Genet 2000;25:232
e
4.
[44] Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL,
Quackenbush J. Gene index analysis of the human genome
estimates approximately 120,000 genes. Nat Genet 2000;25:
239
e
40.
[45] Hogenesch JB, Ching KA, Batalov S, Su AI, Walker JR, Zhou Y,
et al. A comparison of the Celera and Ensembl predicted gene sets
reveals little overlap in novel genes. Cell 2001;106:413
e
5.
[46] Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, et al. Dis-
tinguishing protein-coding and noncoding genes in the human
genome. Proc Natl Acad Sci U S A 2007;104:19428
e
33.
[47] Venter J, Adams M, Myers E, Li P, Mural R, Sutton G, et al. The
sequence of the human genome. Science 2001;291:1304
e
51.
[48] Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC,
Baldwin J, et al. Initial sequencing and analysis of the human
genome. Nature 2001;409:860
e
921.
[49] Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, et al.
Ensembl 2008. Nucleic acids research 2008;36:D707
ENCODE protein complement. Proc Natl Acad Sci U S A
2007;104:5495
500.
[62] Brockdorff N, Ashworth A, Kay GF, McCabe VM, Norris DP,
Cooper PJ, et al. The product of the mouse Xist gene is a 15 kb
inactive X-specific transcript containing no conserved ORF and
located in the nucleus. Cell 1992;71:515
e
26.
[63] Gabory A, Ripoche MA, Le Digarcher A, Watrin F, Ziyyat A, Forne T,
et al. H19 acts as a trans regulator of the imprinted gene network
controlling growth in mice. Development 2009;136:3413
e
21.
[64] Mancini-Dinardo D, Steele SJ, Levorse JM, Ingram RS,
Tilghman SM. Elongation of the Kcnq1ot1 transcript is required
for genomic imprinting of neighboring genes. Genes Dev 2006;20:
1268
e
82.
[65] Ponting CP, Oliver PL, Reik W. Evolution and functions of long
noncoding RNAs. Cell 2009;136:629
e
41.
[66] Mattick JS. The genetic signatures of noncoding RNAs. PLoS
Genet 2009;5:e1000459.
[67] Lipovich L, Johnson R, Lin CY. MacroRNA underdogs in
a microRNA world: evolutionary, regulatory, and biomedical
significance of mammalian long non-protein-coding RNA. Bio-
chim Biophys Acta 2010;1799:597
e
615.
[68] Mattick JS, Mehler MF. RNA editing, DNA recoding and the
evolution of human cognition. Trends Neurosci 2008;31:227
e
33.
[69] Yu W, Gius D, Onyango P, Muldoon-Jacobs K, Karp J,
Feinberg AP, et al. Epigenetic silencing of tumour suppressor gene
p15 by its antisense RNA. Nature 2008;451:202
e
14.
[50] Karolchik D, Hinrichs AS, Kent WJ, et al. The UCSC Genome
Browser. Current protocols in bioinformatics/editoral board,
Andreas D. Baxevanis. [et al.]; 2007. Chapter 1, Unit 1.4.
[51] Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences
(RefSeq): a curated non-redundant sequence database of genomes,
transcripts and proteins. Nucleic Acids Res 2007;35:D61
e
5.
[52] Maglott DR, Katz KS, Sicotte H, Pruitt KD. NCBI's LocusLink
and RefSeq. Nucleic Acids Res 2000;28:126
e
8.
[53] Wilming LG, Gilbert JGR, Howe K, Trevanion S, Hubbard T,
Harrow JL. The vertebrate genome annotation (Vega) database.
Nucleic Acids Res 2008;36:D753
e
60.
[54] Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R,
Gingeras TR, Margulies EH, et al. Identification and analysis of
functional elements in 1% of the human genome by the ENCODE
pilot project. Nature 2007;447:799
e
816.
[55] Myers RM, Stamatoyannopoulos J, Snyder M, Dunham I,
Hardison RC, Bernstein BE, et al. A user's guide to the encyclo-
pedia of DNA elements (ENCODE). PLoS Biol 2011;9:e1001046.
[56] TheENCODEProjectConsortium. An integrated encyclopedia of
DNA elements in the human genome. Nature (in review) 2012.
[57] The1000GenomesProjectConsortium. A map of human genome
variation from population-scale sequencing. Nature 2010;467:
1061
e
73.
[58] Hudson TJ, Anderson W, Artez A, Barker AD, Bell C,
Bernabe RR, et al. International network of cancer genome
projects. Nature 2010;464:993
e
6.
[70] Pasmant E, Sabbagh A, Vidaud M, Bieche I. ANRIL, a long,
noncoding RNA, is an unexpected major hotspot in GWAS. FASEB
J 2011;25:444
e
8.
[71] Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ,
Kenzelmann-Broz D, et al. A large intergenic noncoding RNA
induced by p53 mediates global gene repression in the p53
response. Cell 2010;142:409
e
19.
[72] Zhou Y, Zhong Y, Wang Y, Zhang X, Batista DL, Gejman R, et al.
Activation of p53 by MEG3 non-coding RNA. J Biol Chem
2007;282:24731
e
42.
[73] Daughters RS, Tuttle DL, Gao W, Ikeda Y, Moseley ML, Ebner TJ,
et al. RNA gain-of-function in spinocerebellar ataxia type 8. PLoS
Genet 2009;5:e1000600.
[74] Faghihi MA, Modarresi F, Khalil AM, Wood DE, Sahagan BG,
Morgan TE, et al. Expression of a noncoding RNA is elevated in
Alzheimer's disease and drives rapid feed-forward regulation of
beta-secretase. Nat Med 2008;14:723
e
30.
[75] Maeda N, Kasukawa T, Oyama R, Gough J, Frith M, Engstrom PG,
et al. Transcript annotation in FANTOM3: mouse gene catalog
based on physical cDNAs. PLoS Genet 2006;2:e62.
e
[76]
Jia H, Osak M, Bogu GK, Stanton LW, Johnson R, Lipovich L.
Genome-wide computational identification and manual annotation
of human long noncoding RNA genes. RNA 2010;16:1478
87.
[77] Orom UA, Derrien T, Beringer M, Gumireddy K, Gardini A,
Bussotti G, et al. Long noncoding RNAs with enhancer-like
function in human cells. Cell 2010;143:46
e
8.
[59] Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM,
et al. Evidence for transcript networks composed of chimeric
RNAs in human cells. PLoS One 2012;7:e28213.
[60] Bian S, T., S.. Functions of noncoding RNAs in neural development
and neurological diseases. Mol Neurobiol 2011;44:359
e
73.
[61] Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ,
Yeats C, et al. The implications of alternative splicing in the
e
58.
[78] Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A,
et al. Integrative annotation of human large intergenic noncoding
RNAs reveals global properties and specific subclasses. Genes Dev
2011;25:1915
e
27.
[79] Derrien T, Johnson R, Bussoti G, Tanzer A, Djebali S, Tilgner H,
et al. The GENCODE v7 catalogue of human long non-coding
e
