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Volumn 2, Issue 4, 2006, Pages 515-528

The abundance of short proteins in the mammalian proteome

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; PROTEOME;

EID: 33646483032     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0020052     Document Type: Article
Times cited : (190)

References (45)
  • 1
  • 2
    • 33646490270 scopus 로고    scopus 로고
    • Transcript annotation in FANTOM3: Mouse gene catalog based on physical cDNAs
    • DOI: 10.1371/journal.pgen.0020052
    • Maeda N, Kasukawa T, Oyama R, Gough J, Frith M, et al. (2006) Transcript annotation in FANTOM3: Mouse gene catalog based on physical cDNAs. PLoS Genet 2: e62. DOI: 10.1371/journal.pgen.0020052
    • (2006) PLoS Genet , vol.2
    • Maeda, N.1    Kasukawa, T.2    Oyama, R.3    Gough, J.4    Frith, M.5
  • 3
    • 3042818018 scopus 로고    scopus 로고
    • The International Protein Index: An integrated database for proteomics experiments
    • Kersey PJ, Duarte J, Williams A, Karavidopoulou Y, Birney E, et al. (2004) The International Protein Index: An integrated database for proteomics experiments. Proteomics 4: 1985-1988.
    • (2004) Proteomics , vol.4 , pp. 1985-1988
    • Kersey, P.J.1    Duarte, J.2    Williams, A.3    Karavidopoulou, Y.4    Birney, E.5
  • 7
    • 0035424711 scopus 로고    scopus 로고
    • On the total number of genes and their length distribution in complete microbial genomes
    • Skovgaard M, Jensen LJ, Brunak S, Ussery D, Krogh A (2001) On the total number of genes and their length distribution in complete microbial genomes. Trends Genet 17: 425-428.
    • (2001) Trends Genet , vol.17 , pp. 425-428
    • Skovgaard, M.1    Jensen, L.J.2    Brunak, S.3    Ussery, D.4    Krogh, A.5
  • 8
    • 0036640957 scopus 로고    scopus 로고
    • Distinguishing the ORFs from the ELFs: Short bacterial genes and the annotation of genomes
    • Ochman H (2002) Distinguishing the ORFs from the ELFs: Short bacterial genes and the annotation of genomes. Trends Genet 18: 335-337.
    • (2002) Trends Genet , vol.18 , pp. 335-337
    • Ochman, H.1
  • 9
    • 0037373525 scopus 로고    scopus 로고
    • When ELFs are ORFs, but don't act like them
    • Lawrence J (2003) When ELFs are ORFs, but don't act like them. Trends Genet 19: 131-132.
    • (2003) Trends Genet , vol.19 , pp. 131-132
    • Lawrence, J.1
  • 10
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
    • (2003) Nature , vol.423 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.S.5
  • 11
    • 0142247622 scopus 로고    scopus 로고
    • A "polyORFomic" analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORFs
    • Harrison PM, Carriero N, Liu Y, Gerstein M (2003) A " polyORFomic" analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORFs. J Mol Biol 333: 885-892.
    • (2003) J Mol Biol , vol.333 , pp. 885-892
    • Harrison, P.M.1    Carriero, N.2    Liu, Y.3    Gerstein, M.4
  • 13
    • 21044431735 scopus 로고    scopus 로고
    • Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution
    • Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, et al. (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308: 1149-1154.
    • (2005) Science , vol.308 , pp. 1149-1154
    • Cheng, J.1    Kapranov, P.2    Drenkow, J.3    Dike, S.4    Brubaker, S.5
  • 14
    • 0031588576 scopus 로고    scopus 로고
    • Construction and characterization of human brain cDNA libraries suitable for analysis of cDNA clones encoding relatively large proteins
    • Ohara O, Nagase T, Ishikawa K, Nakajima D, Ohira M, et al. (1997) Construction and characterization of human brain cDNA libraries suitable for analysis of cDNA clones encoding relatively large proteins. DNA Res 4: 53-59.
    • (1997) DNA Res , vol.4 , pp. 53-59
    • Ohara, O.1    Nagase, T.2    Ishikawa, K.3    Nakajima, D.4    Ohira, M.5
  • 15
    • 0032900737 scopus 로고    scopus 로고
    • CRITICA: Coding region identification tool invoking comparative analysis
    • Badger JH, Olsen GJ (1999) CRITICA: Coding region identification tool invoking comparative analysis. Mol Biol Evol 16: 512-524.
    • (1999) Mol Biol Evol , vol.16 , pp. 512-524
    • Badger, J.H.1    Olsen, G.J.2
  • 16
    • 0037121050 scopus 로고    scopus 로고
    • Pushing the limits of the scanning mechanism for initiation of translation
    • Kozak M (2002) Pushing the limits of the scanning mechanism for initiation of translation. Gene 299: 1-34.
    • (2002) Gene , vol.299 , pp. 1-34
    • Kozak, M.1
  • 17
    • 0037062982 scopus 로고    scopus 로고
    • Alternative pre-mRNA splicing and proteome expansion in metazoans
    • Maniatis T, Tasic B (2002) Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature 418: 236-243.
    • (2002) Nature , vol.418 , pp. 236-243
    • Maniatis, T.1    Tasic, B.2
  • 18
    • 0037673675 scopus 로고    scopus 로고
    • Targeting a complex transcriptome: The construction of the mouse full-length cDNA encyclopedia
    • Carninci P, Waki K, Shiraki T, Konno H, Shibata K, et al. (2003) Targeting a complex transcriptome: The construction of the mouse full-length cDNA encyclopedia. Genome Res 13: 1273-1289.
    • (2003) Genome Res , vol.13 , pp. 1273-1289
    • Carninci, P.1    Waki, K.2    Shiraki, T.3    Konno, H.4    Shibata, K.5
  • 21
    • 0036731660 scopus 로고    scopus 로고
    • The RAY1/ST7 tumor-suppressor locus on chromosome 7q31 represents a complex multi-transcript system
    • Vincent JB, Petek E, Thevarkunnel S, Kolozsvari D, Cheung J, et al. (2002) The RAY1/ST7 tumor-suppressor locus on chromosome 7q31 represents a complex multi-transcript system. Genomics 80: 283-294.
    • (2002) Genomics , vol.80 , pp. 283-294
    • Vincent, J.B.1    Petek, E.2    Thevarkunnel, S.3    Kolozsvari, D.4    Cheung, J.5
  • 22
    • 0032971571 scopus 로고    scopus 로고
    • Genomic organization of the KCNQ1 K+ channel gene and identification of C-terminal mutations in the long-QT syndrome
    • Neyroud N, Richard P, Vignier N, Donger C, Denjoy I, et al. (1999) Genomic organization of the KCNQ1 K+ channel gene and identification of C-terminal mutations in the long-QT syndrome. Circ Res 84: 290-297.
    • (1999) Circ Res , vol.84 , pp. 290-297
    • Neyroud, N.1    Richard, P.2    Vignier, N.3    Donger, C.4    Denjoy, I.5
  • 23
    • 0032900772 scopus 로고    scopus 로고
    • An untranslated CTG expansion causes a novel form of spinocerebellar ataxia (SCA8)
    • Koob MD, Moseley ML, Schut LJ, Benzow KA, Bird TD, et al. (1999) An untranslated CTG expansion causes a novel form of spinocerebellar ataxia (SCA8). Nat Genet 21: 379-384.
    • (1999) Nat Genet , vol.21 , pp. 379-384
    • Koob, M.D.1    Moseley, M.L.2    Schut, L.J.3    Benzow, K.A.4    Bird, T.D.5
  • 24
    • 0036482846 scopus 로고    scopus 로고
    • Identification of a novel osteoblastic gene, inducible by C-type natriuretic peptide, whose transcript might function in mineralization as a noncoding RNA
    • Inoue A, Kobayashi Y, Ishizuka M, Hirose S, Hagiwara H (2002) Identification of a novel osteoblastic gene, inducible by C-type natriuretic peptide, whose transcript might function in mineralization as a noncoding RNA. Calcif Tissue Int 70: 111-116.
    • (2002) Calcif Tissue Int , vol.70 , pp. 111-116
    • Inoue, A.1    Kobayashi, Y.2    Ishizuka, M.3    Hirose, S.4    Hagiwara, H.5
  • 25
    • 0035912773 scopus 로고    scopus 로고
    • Endogenous Msx1 antisense transcript: In vivo and in vitro evidences, structure, and potential involvement in skeleton development in mammals
    • U S A
    • Blin-Wakkach C, Lezot F, Ghoul-Mazgar S, Hotton D, Monteiro S, et al. (2001) Endogenous Msx1 antisense transcript: In vivo and in vitro evidences, structure, and potential involvement in skeleton development in mammals. Proc Natl Acad Sci U S A 98: 7336-7341.
    • (2001) Proc Natl Acad Sci , vol.98 , pp. 7336-7341
    • Blin-Wakkach, C.1    Lezot, F.2    Ghoul-Mazgar, S.3    Hotton, D.4    Monteiro, S.5
  • 26
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genomic DNA
    • Burge C, Karlin S (1997) Prediction of complete gene structures in human genomic DNA. J Mol Biol 268: 78-94.
    • (1997) J Mol Biol , vol.268 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 28
    • 17444437765 scopus 로고    scopus 로고
    • Integrating genomic homology into gene structure prediction
    • Korf I, Flicek P, Duan D, Brent MR (2001) Integrating genomic homology into gene structure prediction. Bioinformatics 17: S140-S148.
    • (2001) Bioinformatics , vol.17
    • Korf, I.1    Flicek, P.2    Duan, D.3    Brent, M.R.4
  • 31
    • 17844407888 scopus 로고    scopus 로고
    • ECgene: Genome-based EST clustering and gene modeling for alternative splicing
    • Kim N, Shin S, Lee S (2005) ECgene: Genome-based EST clustering and gene modeling for alternative splicing. Genome Res 15: 566-576.
    • (2005) Genome Res , vol.15 , pp. 566-576
    • Kim, N.1    Shin, S.2    Lee, S.3
  • 34
    • 0141815478 scopus 로고    scopus 로고
    • Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes
    • U S A
    • Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D (2003) Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A 100: 11484-11489.
    • (2003) Proc Natl Acad Sci , vol.100 , pp. 11484-11489
    • Kent, W.J.1    Baertsch, R.2    Hinrichs, A.3    Miller, W.4    Haussler, D.5
  • 35
    • 11144358198 scopus 로고    scopus 로고
    • A gene atlas of the mouse and human protein-encoding transcriptomes
    • U S A
    • Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 101: 6062-6067.
    • (2004) Proc Natl Acad Sci , vol.101 , pp. 6062-6067
    • Su, A.I.1    Wiltshire, T.2    Batalov, S.3    Lapp, H.4    Ching, K.A.5
  • 36
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
    • Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J Mol Biol 305: 567-580.
    • (2001) J Mol Biol , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    Von Heijne, G.3    Sonnhammer, E.L.4
  • 37
    • 7444252784 scopus 로고    scopus 로고
    • Human ORFeome version 1.1: A platform for reverse proteomics
    • Rual JF, Hirozane-Kishikawa T, Hao T, Bertin N, Li S, et al. (2004) Human ORFeome version 1.1: A platform for reverse proteomics. Genome Res 14: 2128-2135.
    • (2004) Genome Res , vol.14 , pp. 2128-2135
    • Rual, J.F.1    Hirozane-Kishikawa, T.2    Hao, T.3    Bertin, N.4    Li, S.5
  • 38
    • 2942521197 scopus 로고    scopus 로고
    • Recent advances in gene structure prediction
    • Brent MR, Guigo R (2004) Recent advances in gene structure prediction. Curr Opin Struct Biol 14: 264-272.
    • (2004) Curr Opin Struct Biol , vol.14 , pp. 264-272
    • Brent, M.R.1    Guigo, R.2
  • 39
    • 7444253965 scopus 로고    scopus 로고
    • Analysis of small human proteins reveals the translation of upstream open reading frames of mRNAs
    • Oyama M, Itagaki C, Hata H, Suzuki Y, Izumi T, et al. (2004) Analysis of small human proteins reveals the translation of upstream open reading frames of mRNAs. Genome Res 14: 2048-2052.
    • (2004) Genome Res , vol.14 , pp. 2048-2052
    • Oyama, M.1    Itagaki, C.2    Hata, H.3    Suzuki, Y.4    Izumi, T.5
  • 42
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5
  • 43
    • 0001514262 scopus 로고
    • Statistics of local complexity in amino acid sequences and sequence databases
    • Wootton JC, Federhen S (1993) Statistics of local complexity in amino acid sequences and sequence databases. Comput Chem 17: 149-163.
    • (1993) Comput Chem , vol.17 , pp. 149-163
    • Wootton, J.C.1    Federhen, S.2
  • 45
    • 0034565285 scopus 로고    scopus 로고
    • Combinatorial approaches to finding subtle signals in DNA sequences
    • Pevzner PA, Sze SH (2000) Combinatorial approaches to finding subtle signals in DNA sequences. Proc Int Conf Intell Syst Mol Biol 8: 269-278.
    • (2000) Proc Int Conf Intell Syst Mol Biol , vol.8 , pp. 269-278
    • Pevzner, P.A.1    Sze, S.H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.