메뉴 건너뛰기




Volumn 5, Issue 1, 2010, Pages

An integrated mass-spectrometry pipeline identifies novel protein coding-regions in the human genome

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE; RIBONUCLEOPROTEIN;

EID: 77749282896     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0008949     Document Type: Article
Times cited : (28)

References (58)
  • 3
    • 0037417884 scopus 로고    scopus 로고
    • Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes
    • Guigo R, Dermitzakis ET, Agarwal P, Ponting CP, Parra G, et al. (2003) Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes. PNAS 100: 1140-1145.
    • (2003) PNAS , vol.100 , pp. 1140-1145
    • Guigo, R.1    Dermitzakis, E.T.2    Agarwal, P.3    Ponting, C.P.4    Parra, G.5
  • 5
    • 0035895513 scopus 로고    scopus 로고
    • GENE NUMBER: What If There Are Only 30,000 Human Genes?
    • Claverie J-M (2001) GENE NUMBER: What If There Are Only 30,000 Human Genes? Science 291: 1255-1257.
    • (2001) Science , vol.291 , pp. 1255-1257
    • Claverie, J.-M.1
  • 6
    • 12144287461 scopus 로고    scopus 로고
    • Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22
    • Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S, et al. (2004) Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res 14: 331-342.
    • (2004) Genome Res , vol.14 , pp. 331-342
    • Kampa, D.1    Cheng, J.2    Kapranov, P.3    Yamanaka, M.4    Brubaker, S.5
  • 7
    • 0034204044 scopus 로고    scopus 로고
    • Gene index analysis of the human genome estimates approximately 120,000 genes
    • Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL, et al. (2000) Gene index analysis of the human genome estimates approximately 120,000 genes. Nat Genet 25: 239-240.
    • (2000) Nat Genet , vol.25 , pp. 239-240
    • Liang, F.1    Holt, I.2    Pertea, G.3    Karamycheva, S.4    Salzberg, S.L.5
  • 8
    • 45549088326 scopus 로고    scopus 로고
    • The transcriptional landscape of the yeast genome defined by RNA sequencing
    • Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, et al. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349.
    • (2008) Science , vol.320 , pp. 1344-1349
    • Nagalakshmi, U.1    Wang, Z.2    Waern, K.3    Shou, C.4    Raha, D.5
  • 9
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: A revolutionary tool for transcriptomics
    • Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63.
    • (2009) Nat Rev Genet , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 11
    • 19944376457 scopus 로고    scopus 로고
    • Global Identification of Human Transcribed Sequences with Genome Tiling Arrays
    • Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, et al. (2004) Global Identification of Human Transcribed Sequences with Genome Tiling Arrays. Science 306: 2242-2246.
    • (2004) Science , vol.306 , pp. 2242-2246
    • Bertone, P.1    Stolc, V.2    Royce, T.E.3    Rozowsky, J.S.4    Urban, A.E.5
  • 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
    • 34247644400 scopus 로고    scopus 로고
    • High correspondence between Affymetrix exon and standard expression arrays
    • Okoniewski MJ, Hey Y, Pepper SD, Miller C (2007) High correspondence between Affymetrix exon and standard expression arrays. Biotechniques 42: 181-185.
    • (2007) Biotechniques , vol.42 , pp. 181-185
    • Okoniewski, M.J.1    Hey, Y.2    Pepper, S.D.3    Miller, C.4
  • 15
    • 34447517678 scopus 로고    scopus 로고
    • A Statistical Framework for Genome-Wide Discovery of Biomarker Splice Variations with GeneChip Human Exon 1.0 ST Arrays
    • Ryo Y, Kazuyuki N, Seiya I, Masao N, Atsushi D, et al. (2006) A Statistical Framework for Genome-Wide Discovery of Biomarker Splice Variations with GeneChip Human Exon 1.0 ST Arrays. Genome Informatics 17: 88-99.
    • (2006) Genome Informatics , vol.17 , pp. 88-99
    • Ryo, Y.1    Kazuyuki, N.2    Seiya, I.3    Masao, N.4    Atsushi, D.5
  • 16
    • 0035865260 scopus 로고    scopus 로고
    • Experimental annotation of the human genome using microarray technology
    • Shoemaker DD, Schadt EE, Armour CD, He YD, Garrett-Engele P, et al. (2001) Experimental annotation of the human genome using microarray technology. Nature 409: 922-927.
    • (2001) Nature , vol.409 , pp. 922-927
    • Shoemaker, D.D.1    Schadt, E.E.2    Armour, C.D.3    He, Y.D.4    Garrett-Engele, P.5
  • 17
    • 12344302543 scopus 로고    scopus 로고
    • A comprehensive transcript index of the human genome generated using microarrays and computational approaches
    • Schadt E, Edwards S, GuhaThakurta D, Holder D, Ying L, et al. (2004) A comprehensive transcript index of the human genome generated using microarrays and computational approaches. Genome Biology 5: R73.
    • (2004) Genome Biology , vol.5
    • Schadt, E.1    Edwards, S.2    GuhaThakurta, D.3    Holder, D.4    Ying, L.5
  • 18
    • 0027751663 scopus 로고
    • The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
    • Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854.
    • (1993) Cell , vol.75 , pp. 843-854
    • Lee, R.C.1    Feinbaum, R.L.2    Ambros, V.3
  • 19
    • 57149107578 scopus 로고    scopus 로고
    • Dinger ME, Pang KC, Mercer TR, Mattick JS (2008) Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities. PLoS Computational Biology 4: e1000176.
    • Dinger ME, Pang KC, Mercer TR, Mattick JS (2008) Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities. PLoS Computational Biology 4: e1000176.
  • 20
    • 0035346719 scopus 로고    scopus 로고
    • Interrogating the human genome using uninterpreted mass spectrometry data
    • Choudhary JS, Blackstock WP, Creasy DM, Cottrell JS (2001) Interrogating the human genome using uninterpreted mass spectrometry data. Proteomics 1: 651-667.
    • (2001) Proteomics , vol.1 , pp. 651-667
    • Choudhary, J.S.1    Blackstock, W.P.2    Creasy, D.M.3    Cottrell, J.S.4
  • 21
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
    • Eng JK, McCormack AL, Yates IIIJR (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. Journal of the American Society for Mass Spectrometry 5: 976-989.
    • (1994) Journal of the American Society for Mass Spectrometry , vol.5 , pp. 976-989
    • Eng, J.K.1    McCormack, A.L.2    IIIJR, Y.3
  • 22
    • 0037108887 scopus 로고    scopus 로고
    • Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    • Keller A, Nesvizhskii AI, Kolker E, Aebersold R (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem 74: 5383-5392.
    • (2002) Anal Chem , vol.74 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 23
    • 0035350894 scopus 로고    scopus 로고
    • Mass spectrometry allows direct identification of proteins in large genomes
    • Kuster B, Mortensen P, Andersen JS, Mann M (2001) Mass spectrometry allows direct identification of proteins in large genomes. Proteomics 1: 641-650.
    • (2001) Proteomics , vol.1 , pp. 641-650
    • Kuster, B.1    Mortensen, P.2    Andersen, J.S.3    Mann, M.4
  • 24
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • Perkins DN, Pappin DJ, Creasy DM, Cottrell JS (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20: 3551-3567.
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.2    Creasy, D.M.3    Cottrell, J.S.4
  • 26
    • 34848889259 scopus 로고    scopus 로고
    • The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra
    • Shilov IV, Seymour SL, Patel AA, Loboda A, Tang WH, et al. (2007) The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra. Mol Cell Proteomics 6: 1638-1655.
    • (2007) Mol Cell Proteomics , vol.6 , pp. 1638-1655
    • Shilov, I.V.1    Seymour, S.L.2    Patel, A.A.3    Loboda, A.4    Tang, W.H.5
  • 27
    • 44249091879 scopus 로고    scopus 로고
    • Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics
    • Baerenfaller K, Grossmann J, Grobei MA, Hull R, Hirsch-Hoffmann M, et al. (2008) Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science 320: 938-941.
    • (2008) Science , vol.320 , pp. 938-941
    • Baerenfaller, K.1    Grossmann, J.2    Grobei, M.A.3    Hull, R.4    Hirsch-Hoffmann, M.5
  • 29
    • 58249110387 scopus 로고    scopus 로고
    • Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer
    • Menon R, Zhang Q, Zhang Y, Fermin D, Bardeesy N, et al. (2009) Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer. Cancer Res 69: 300-309.
    • (2009) Cancer Res , vol.69 , pp. 300-309
    • Menon, R.1    Zhang, Q.2    Zhang, Y.3    Fermin, D.4    Bardeesy, N.5
  • 30
    • 33846884410 scopus 로고    scopus 로고
    • Improving gene annotation using peptide mass spectrometry
    • Tanner S, Shen Z, Ng J, Florea L, Guigo R, et al. (2007) Improving gene annotation using peptide mass spectrometry. Genome Res 17: 231-239.
    • (2007) Genome Res , vol.17 , pp. 231-239
    • Tanner, S.1    Shen, Z.2    Ng, J.3    Florea, L.4    Guigo, R.5
  • 32
    • 33745054329 scopus 로고    scopus 로고
    • Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics
    • Fermin D, Allen B, Blackwell T, Menon R, Adamski M, et al. (2006) Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biology 7: R35.
    • (2006) Genome Biology , vol.7
    • Fermin, D.1    Allen, B.2    Blackwell, T.3    Menon, R.4    Adamski, M.5
  • 33
    • 0029645432 scopus 로고
    • Mining genomes: Correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases
    • Yates JR, Eng JK, McCormack AL (1995) Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases. Anal Chem 67: 3202-3210.
    • (1995) Anal Chem , vol.67 , pp. 3202-3210
    • Yates, J.R.1    Eng, J.K.2    McCormack, A.L.3
  • 34
    • 34548452940 scopus 로고    scopus 로고
    • Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation
    • Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, et al. (2007) Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res 17: 1362-1377.
    • (2007) Genome Res , vol.17 , pp. 1362-1377
    • Gupta, N.1    Tanner, S.2    Jaitly, N.3    Adkins, J.N.4    Lipton, M.5
  • 35
    • 3042735127 scopus 로고    scopus 로고
    • The Need for Guidelines in Publication of Peptide and Protein Identification Data: Working Group On Publication Guidelines For Peptide And Protein Identification Data
    • Carr S, Aebersold R, Baldwin M, Burlingame A, Clauser K, et al. (2004) The Need for Guidelines in Publication of Peptide and Protein Identification Data: Working Group On Publication Guidelines For Peptide And Protein Identification Data. Mol Cell Proteomics 3: 531-533.
    • (2004) Mol Cell Proteomics , vol.3 , pp. 531-533
    • Carr, S.1    Aebersold, R.2    Baldwin, M.3    Burlingame, A.4    Clauser, K.5
  • 36
    • 33847630405 scopus 로고    scopus 로고
    • Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    • Elias JE, Gygi SP (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods 4: 207-214.
    • (2007) Nat Methods , vol.4 , pp. 207-214
    • Elias, J.E.1    Gygi, S.P.2
  • 37
    • 63049120021 scopus 로고    scopus 로고
    • Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines
    • Jones AR, Siepen JA, Hubbard SJ, Paton NW (2009) Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines. Proteomics 9: 1220-1229.
    • (2009) Proteomics , vol.9 , pp. 1220-1229
    • Jones, A.R.1    Siepen, J.A.2    Hubbard, S.J.3    Paton, N.W.4
  • 38
    • 38649083118 scopus 로고    scopus 로고
    • Assigning significance to peptides identified by tandem mass spectrometry using decoy databases
    • Kall L, Storey JD, MacCoss MJ, Noble WS (2008) Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J Proteome Res 7: 29-34.
    • (2008) J Proteome Res , vol.7 , pp. 29-34
    • Kall, L.1    Storey, J.D.2    MacCoss, M.J.3    Noble, W.S.4
  • 40
    • 55249121202 scopus 로고    scopus 로고
    • Nonlinear Fitting Method for Determining Local False Discovery Rates from Decoy Database Searches
    • Tang W, Shilov I, Seymour S (2008) Nonlinear Fitting Method for Determining Local False Discovery Rates from Decoy Database Searches. J Proteome Res 7: 3661-3667.
    • (2008) J Proteome Res , vol.7 , pp. 3661-3667
    • Tang, W.1    Shilov, I.2    Seymour, S.3
  • 41
    • 34548824879 scopus 로고    scopus 로고
    • An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data
    • Okoniewski M, Yates T, Dibben S, Miller C (2007) An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data. Genome Biology 8: R79.
    • (2007) Genome Biology , vol.8
    • Okoniewski, M.1    Yates, T.2    Dibben, S.3    Miller, C.4
  • 43
  • 46
    • 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. Journal of Molecular Biology 268: 78-94.
    • (1997) Journal of Molecular Biology , vol.268 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 47
    • 53649088131 scopus 로고    scopus 로고
    • Applications of next-generation sequencing technologies in functional genomics
    • Morozova O, Marra MA (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics 92: 255-264.
    • (2008) Genomics , vol.92 , pp. 255-264
    • Morozova, O.1    Marra, M.A.2
  • 48
  • 49
    • 43549094212 scopus 로고    scopus 로고
    • Déjà vu in proteomics. A hit parade of repeatedly identified differentially expressed proteins
    • Jiri P, Ivanek R, Toman O, Cmejla R, Cmejlova J, et al. (2008) Déjà vu in proteomics. A hit parade of repeatedly identified differentially expressed proteins. PROTEOMICS 8: 1744-1749.
    • (2008) PROTEOMICS , vol.8 , pp. 1744-1749
    • Jiri, P.1    Ivanek, R.2    Toman, O.3    Cmejla, R.4    Cmejlova, J.5
  • 50
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422: 198-207.
    • (2003) Nature , vol.422 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 51
    • 33645813378 scopus 로고    scopus 로고
    • Mass Spectrometry and Protein Analysis
    • Domon B, Aebersold R (2006) Mass Spectrometry and Protein Analysis. Science 312: 212-217.
    • (2006) Science , vol.312 , pp. 212-217
    • Domon, B.1    Aebersold, R.2
  • 52
    • 24944440037 scopus 로고    scopus 로고
    • Quantitative proteomic analysis using isobaric protein tags enables rapid comparison of changes in transcript and protein levels in transformed cells
    • Unwin RD, Pierce A, Watson RB, Sternberg DW, Whetton AD (2005) Quantitative proteomic analysis using isobaric protein tags enables rapid comparison of changes in transcript and protein levels in transformed cells. Mol Cell Proteomics 4: 924-935.
    • (2005) Mol Cell Proteomics , vol.4 , pp. 924-935
    • Unwin, R.D.1    Pierce, A.2    Watson, R.B.3    Sternberg, D.W.4    Whetton, A.D.5
  • 54
    • 28744458859 scopus 로고    scopus 로고
    • Bioconductor: Open software development for computational biology and bioinformatics
    • Gentleman R, Carey V, Bates D, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biology 5: R80.
    • (2004) Genome Biology , vol.5
    • Gentleman, R.1    Carey, V.2    Bates, D.3    Bolstad, B.4    Dettling, M.5
  • 55
    • 0142121516 scopus 로고    scopus 로고
    • Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    • Irizarry R, Hobbs B, Collin F, Beazer-Barclay Y, Antonellis K, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.
    • (2003) Biostatistics , vol.4 , pp. 249-264
    • Irizarry, R.1    Hobbs, B.2    Collin, F.3    Beazer-Barclay, Y.4    Antonellis, K.5
  • 57
    • 32144432437 scopus 로고    scopus 로고
    • The SWISS-MODEL workspace: A web-based environment for protein structure homology modelling
    • Arnold K, Bordoli L, Kopp J, Schwede T (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22: 195-201.
    • (2006) Bioinformatics , vol.22 , pp. 195-201
    • Arnold, K.1    Bordoli, L.2    Kopp, J.3    Schwede, T.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.