Tools to covisualize and coanalyze proteomic data with genomes and transcriptomes: Validation of genes and Alternative mRNA splicing

Journal of Proteome Research

Volumn 13, Issue 1, 2014, Pages 84-98

  Pang, Chi Nam Ignatius ^a   Tay, Aidan P ^a   Aya, Carlos ^b   Twine, Natalie A ^a   Harkness, Linda ^c   Hart Smith, Gene ^a   Chia, Samantha Z ^a   Chen, Zhiliang ^a   Deshpande, Nandan P ^a   Kaakoush, Nadeem O ^a   Mitchell, Hazel M ^a   Kassem, Moustapha ^c   Wilkins, Marc R ^a  

^a UNIVERSITY OF NEW SOUTH WALES   (Australia)

^b Intersect Australia Limited   (Australia)

^c UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

alternative splicing; data integration; RNA seq; splice junction peptides; visualization

Indexed keywords

MESSENGER RNA; PHOSPHOPEPTIDE; TRANSCRIPTOME;

ARTICLE; BACTERIAL GENETICS; BACTERIAL STRAIN; CAMPYLOBACTER; CAMPYLOBACTER CONCISUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEOMICS; RNA ANALYSIS; RNA SPLICING; TIGHT JUNCTION;

CAMPYLOBACTER; GENOME; HUMANS; MASS SPECTROMETRY; PHOSPHOPEPTIDES; PROTEOMICS; RNA SPLICING; RNA, MESSENGER; SACCHAROMYCES CEREVISIAE; TRANSCRIPTOME;

EID: 84891792626     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr400820p     Document Type: Article

References (79)

1. Harrow, J.; Frankish, A.; Gonzalez, J. M.; Tapanari, E.; Diekhans, M.; Kokocinski, F.; Aken, B. L.; Barrell, D.; Zadissa, A.; Searle, S.; Barnes, I.; Bignell, A.; Boychenko, V.; Hunt, T.; Kay, M.; Mukherjee, G.; Rajan, J.; Despacio-Reyes, G.; Saunders, G.; Steward, C.; Harte, R.; Lin, M.; Howald, C.; Tanzer, A.; Derrien, T.; Chrast, J.; Walters, N.; Balasubramanian, S.; Pei, B.; Tress, M.; Rodriguez, J. M.; Ezkurdia, I.; van Baren, J.; Brent, M.; Haussler, D.; Kellis, M.; Valencia, A.; Reymond, A.; Gerstein, M.; Guigo, R.; Hubbard, T. J. GENCODE: the reference human genome annotation for The ENCODE Project Genome Res. 2012, 22 (9) 1760-74
2. Brosch, M.; Saunders, G. I.; Frankish, A.; Collins, M. O.; Yu, L.; Wright, J.; Verstraten, R.; Adams, D. J.; Harrow, J.; Choudhary, J. S.; Hubbard, T. Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome Genome Res. 2011, 21 (5) 756-67
3. Gupta, N.; Benhamida, J.; Bhargava, V.; Goodman, D.; Kain, E.; Kerman, I.; Nguyen, N.; Ollikainen, N.; Rodriguez, J.; Wang, J.; Lipton, M. S.; Romine, M.; Bafna, V.; Smith, R. D.; Pevzner, P. A. Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes Genome Res. 2008, 18 (7) 1133-42
4. Sheynkman, G. M.; Shortreed, M. R.; Frey, B. L.; Smith, L. M. Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq Mol. Cell. Proteomics 2013, 12 (8) 2341-53
5. Howald, C.; Tanzer, A.; Chrast, J.; Kokocinski, F.; Derrien, T.; Walters, N.; Gonzalez, J. M.; Frankish, A.; Aken, B. L.; Hourlier, T.; Vogel, J. H.; White, S.; Searle, S.; Harrow, J.; Hubbard, T. J.; Guigo, R.; Reymond, A. Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome Genome Res. 2012, 22 (9) 1698-710
6. Nagaraj, N.; Wisniewski, J. R.; Geiger, T.; Cox, J.; Kircher, M.; Kelso, J.; Paabo, S.; Mann, M. Deep proteome and transcriptome mapping of a human cancer cell line Mol. Syst. Biol. 2011, 7, 548
7. Ederveen, T. H.; Overmars, L.; van Hijum, S. A. Reduce manual curation by combining gene predictions from multiple annotation engines, a case study of start codon prediction PLoS One 2013, 8 (5) e63523
8. Goli, B.; Nair, A. S. The elusive short gene-an ensemble method for recognition for prokaryotic genome Biochem. Biophys. Res. Commun. 2012, 422 (1) 36-41
9. Christie-Oleza, J. A.; Miotello, G.; Armengaud, J. High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade BMC Genomics 2012, 13, 73
10. Peterson, E. S.; McCue, L. A.; Schrimpe-Rutledge, A. C.; Jensen, J. L.; Walker, H.; Kobold, M. A.; Webb, S. R.; Payne, S. H.; Ansong, C.; Adkins, J. N.; Cannon, W. R.; Webb-Robertson, B. J. VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data BMC Genomics 2012, 13, 131
11. Deshpande, N. P.; Kaakoush, N. O.; Mitchell, H.; Janitz, K.; Raftery, M. J.; Li, S. S.; Wilkins, M. R. Sequencing and validation of the genome of a Campylobacter concisus reveals intra-species diversity PLoS One 2011, 6 (7) e22170
12. Yates, J. R., 3rd; Eng, J. K.; McCormack, A. L. Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases Anal. Chem. 1995, 67 (18) 3202-10
13. Berghoff, B. A.; Konzer, A.; Mank, N. N.; Looso, M.; Rische, T.; Förstner, K. U.; Krüger, M.; Klug, G. Integrative "omics"- approach discovers dynamic and regulatory features of bacterial stress responses PLoS Genet. 2013, 9 (6) e1003576
14. Payne, S. H.; Huang, S. T.; Pieper, R. A proteogenomic update to Yersinia: enhancing genome annotation BMC Genomics 2010, 11, 460
15. Feng, Y.; Chien, K. Y.; Chen, H. L.; Chiu, C. H. Pseudogene recoding revealed from proteomic analysis of salmonella serovars J. Proteome Res. 2012, 11 (3) 1715-9
16. Risk, B. A.; Spitzer, W. J.; Giddings, M. C. Peppy: proteogenomic search software J. Proteome Res. 2013, 12 (6) 3019-25
17. Thorvaldsdottir, H.; Robinson, J. T.; Mesirov, J. P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration Briefings Bioinf. 2013, 14 (2) 178-92
18. Buljan, M.; Chalancon, G.; Eustermann, S.; Wagner, G. P.; Fuxreiter, M.; Bateman, A.; Babu, M. M. Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks Mol. Cell 2012, 46 (6) 871-83
19. Salomonis, N.; Schlieve, C. R.; Pereira, L.; Wahlquist, C.; Colas, A.; Zambon, A. C.; Vranizan, K.; Spindler, M. J.; Pico, A. R.; Cline, M. S.; Clark, T. A.; Williams, A.; Blume, J. E.; Samal, E.; Mercola, M.; Merrill, B. J.; Conklin, B. R. Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation Proc. Natl. Acad. Sci. U. S. A. 2010, 107 (23) 10514-9
20. Davis, M. J.; Shin, C. J.; Jing, N.; Ragan, M. A. Rewiring the dynamic interactome Mol. BioSyst. 2012, 8 (8) 2054-66
21. Colak, R.; Kim, T.; Michaut, M.; Sun, M.; Irimia, M.; Bellay, J.; Myers, C. L.; Blencowe, B. J.; Kim, P. M. Distinct types of disorder in the human proteome: functional implications for alternative splicing PLoS Comput. Biol. 2013, 9 (4) e1003030
22. Djebali, S.; Davis, C. A.; Merkel, A.; Dobin, A.; Lassmann, T.; Mortazavi, A.; Tanzer, A.; Lagarde, J.; Lin, W.; Schlesinger, F.; Xue, C.; Marinov, G. K.; Khatun, J.; Williams, B. A.; Zaleski, C.; Rozowsky, J.; Roder, M.; Kokocinski, F.; Abdelhamid, R. F.; Alioto, T.; Antoshechkin, I.; Baer, M. T.; Bar, N. S.; Batut, P.; Bell, K.; Bell, I.; Chakrabortty, S.; Chen, X.; Chrast, J.; Curado, J.; Derrien, T.; Drenkow, J.; Dumais, E.; Dumais, J.; Duttagupta, R.; Falconnet, E.; Fastuca, M.; Fejes-Toth, K.; Ferreira, P.; Foissac, S.; Fullwood, M. J.; Gao, H.; Gonzalez, D.; Gordon, A.; Gunawardena, H.; Howald, C.; Jha, S.; Johnson, R.; Kapranov, P.; King, B.; Kingswood, C.; Luo, O. J.; Park, E.; Persaud, K.; Preall, J. B.; Ribeca, P.; Risk, B.; Robyr, D.; Sammeth, M.; Schaffer, L.; See, L. H.; Shahab, A.; Skancke, J.; Suzuki, A. M.; Takahashi, H.; Tilgner, H.; Trout, D.; Walters, N.; Wang, H.; Wrobel, J.; Yu, Y.; Ruan, X.; Hayashizaki, Y.; Harrow, J.; Gerstein, M.; Hubbard, T.; Reymond, A.; Antonarakis, S. E.; Hannon, G.; Giddings, M. C.; Ruan, Y.; Wold, B.; Carninci, P.; Guigo, R.; Gingeras, T. R. Landscape of transcription in human cells Nature 2012, 489 (7414) 101-8
23. Merkin, J.; Russell, C.; Chen, P.; Burge, C. B. Evolutionary dynamics of gene and isoform regulation in Mammalian tissues Science 2012, 338 (6114) 1593-9
24. Ezkurdia, I.; del Pozo, A.; Frankish, A.; Rodriguez, J. M.; Harrow, J.; Ashman, K.; Valencia, A.; Tress, M. L. Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function Mol. Biol. Evol. 2012, 29 (9) 2265-83
25. Khatun, J.; Yu, Y.; Wrobel, J. A.; Risk, B. A.; Gunawardena, H. P.; Secrest, A.; Spitzer, W. J.; Xie, L.; Wang, L.; Chen, X.; Giddings, M. C. Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions BMC Genomics 2013, 14, 141
26. Wang, X.; Slebos, R. J.; Wang, D.; Halvey, P. J.; Tabb, D. L.; Liebler, D. C.; Zhang, B. Protein identification using customized protein sequence databases derived from RNA-Seq data J. Proteome Res. 2012, 11 (2) 1009-17
27. Blakeley, P.; Siepen, J. A.; Lawless, C.; Hubbard, S. J. Investigating protein isoforms via proteomics: a feasibility study Proteomics 2010, 10 (6) 1127-40
28. Goode, R. J.; Yu, S.; Kannan, A.; Christiansen, J. H.; Beitz, A.; Hancock, W. S.; Nice, E.; Smith, A. I. The proteome browser web portal J. Proteome Res. 2013, 12 (1) 172-8
29. Guo, F.; Wang, D.; Liu, Z.; Lu, L.; Zhang, W.; Sun, H.; Zhang, H.; Ma, J.; Wu, S.; Li, N.; Jiang, Y.; Zhu, W.; Qin, J.; Xu, P.; Li, D.; He, F. CAPER: a chromosome-assembled human proteome browser J. Proteome Res. 2013, 12 (1) 179-86
30. Chang, K. Y.; Georgianna, D. R.; Heber, S.; Payne, G. A.; Muddiman, D. C. Detection of alternative splice variants at the proteome level in Aspergillus flavus J. Proteome Res. 2010, 9 (3) 1209-17
31. Chang, K. Y.; Muddiman, D. C. Identification of alternative splice variants in Aspergillus flavus through comparison of multiple tandem MS search algorithms BMC Genomics 2011, 12, 358
32. Severing, E. I.; van Dijk, A. D.; van Ham, R. C. Assessing the contribution of alternative splicing to proteome diversity in Arabidopsis thaliana using proteomics data BMC Plant Biol. 2011, 11 (1) 82
33. Pruitt, K. D.; Tatusova, T.; Brown, G. R.; Maglott, D. R. NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy Nucleic Acids Res. 2012, 40 (Database issue) D130-5
34. Consortium, U. Reorganizing the protein space at the Universal Protein Resource (UniProt) Nucleic Acids Res. 2012, 40 (Database issue) D71-5
35. Elzanowski, A.; Ostell, J. The Genetic Codes. http://www.ncbi.nlm.nih. gov/Taxonomy/Utils/wprintgc.cgi (accessed May 10, 2013).
36. Delcher, A. L.; Bratke, K. A.; Powers, E. C.; Salzberg, S. L. Identifying bacterial genes and endosymbiont DNA with Glimmer Bioinformatics 2007, 23 (6) 673-9
37. Cherry, J. M.; Hong, E. L.; Amundsen, C.; Balakrishnan, R.; Binkley, G.; Chan, E. T.; Christie, K. R.; Costanzo, M. C.; Dwight, S. S.; Engel, S. R.; Fisk, D. G.; Hirschman, J. E.; Hitz, B. C.; Karra, K.; Krieger, C. J.; Miyasato, S. R.; Nash, R. S.; Park, J.; Skrzypek, M. S.; Simison, M.; Weng, S.; Wong, E. D. Saccharomyces Genome Database: the genomics resource of budding yeast Nucleic Acids Res. 2012, 40 (Database issue) D700-5
38. de Godoy, L. M.; Olsen, J. V.; Cox, J.; Nielsen, M. L.; Hubner, N. C.; Frohlich, F.; Walther, T. C.; Mann, M. Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast Nature 2008, 455 (7217) 1251-4
39. Deutsch, E. W. The PeptideAtlas Project Methods Mol. Biol. 2010, 604, 285-96
40. Cox, M. P.; Peterson, D. A.; Biggs, P. J. SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data BMC Bioinf. 2010, 11, 485
41. Trapnell, C.; Roberts, A.; Goff, L.; Pertea, G.; Kim, D.; Kelley, D. R.; Pimentel, H.; Salzberg, S. L.; Rinn, J. L.; Pachter, L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks Nat. Protoc. 2012, 7 (3) 562-78
42. Langmead, B.; Salzberg, S. L. Fast gapped-read alignment with Bowtie 2 Nat. Methods 2012, 9 (4) 357-9
43. Flicek, P.; Amode, M. R.; Barrell, D.; Beal, K.; Brent, S.; Carvalho-Silva, D.; Clapham, P.; Coates, G.; Fairley, S.; Fitzgerald, S.; Gil, L.; Gordon, L.; Hendrix, M.; Hourlier, T.; Johnson, N.; Kahari, A. K.; Keefe, D.; Keenan, S.; Kinsella, R.; Komorowska, M.; Koscielny, G.; Kulesha, E.; Larsson, P.; Longden, I.; McLaren, W.; Muffato, M.; Overduin, B.; Pignatelli, M.; Pritchard, B.; Riat, H. S.; Ritchie, G. R.; Ruffier, M.; Schuster, M.; Sobral, D.; Tang, Y. A.; Taylor, K.; Trevanion, S.; Vandrovcova, J.; White, S.; Wilson, M.; Wilder, S. P.; Aken, B. L.; Birney, E.; Cunningham, F.; Dunham, I.; Durbin, R.; Fernandez-Suarez, X. M.; Harrow, J.; Herrero, J.; Hubbard, T. J.; Parker, A.; Proctor, G.; Spudich, G.; Vogel, J.; Yates, A.; Zadissa, A.; Searle, S. M. Ensembl 2012 Nucleic Acids Res. 2012, 40 (Database issue) D84-90
44. Wall, L.; Christiansen, T.; Orwant, J., Programming Perl, 3 rd ed.; O'Reilly Media: Cambridge, 2000.
45. Olsen, J. V.; Blagoev, B.; Gnad, F.; Macek, B.; Kumar, C.; Mortensen, P.; Mann, M. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks Cell 2006, 127 (3) 635-48
46. Daub, H.; Olsen, J. V.; Bairlein, M.; Gnad, F.; Oppermann, F. S.; Korner, R.; Greff, Z.; Keri, G.; Stemmann, O.; Mann, M. Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle Mol. Cell 2008, 31 (3) 438-48
47. Oppermann, F. S.; Gnad, F.; Olsen, J. V.; Hornberger, R.; Greff, Z.; Keri, G.; Mann, M.; Daub, H. Large-scale proteomics analysis of the human kinome Mol. Cell. Proteomics 2009, 8 (7) 1751-64
48. Olsen, J. V.; Vermeulen, M.; Santamaria, A.; Kumar, C.; Miller, M. L.; Jensen, L. J.; Gnad, F.; Cox, J.; Jensen, T. S.; Nigg, E. A.; Brunak, S.; Mann, M. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis Sci. Signaling 2010, 3 (104) ra3
49. Gnad, F.; Gunawardena, J.; Mann, M. PHOSIDA 2011: the posttranslational modification database Nucleic Acids Res. 2011, 39 (Database issue) D253-60
50. Simonsen, J. L.; Rosada, C.; Serakinci, N.; Justesen, J.; Stenderup, K.; Rattan, S. I.; Jensen, T. G.; Kassem, M. Telomerase expression extends the proliferative life-span and maintains the osteogenic potential of human bone marrow stromal cells Nat. Biotechnol. 2002, 20 (6) 592-6
51. Abdallah, B. M.; Haack-Sorensen, M.; Burns, J. S.; Elsnab, B.; Jakob, F.; Hokland, P.; Kassem, M. Maintenance of differentiation potential of human bone marrow mesenchymal stem cells immortalized by human telomerase reverse transcriptase gene despite extensive proliferation Biochem. Biophys. Res. Commun. 2005, 326 (3) 527-38
52. Al-Nbaheen, M.; Vishnubalaji, R.; Ali, D.; Bouslimi, A.; Al-Jassir, F.; Megges, M.; Prigione, A.; Adjaye, J.; Kassem, M.; Aldahmash, A. Human stromal (mesenchymal) stem cells from bone marrow, adipose tissue and skin exhibit differences in molecular phenotype and differentiation potential Stem Cell Rev. 2013, 9 (1) 32-43
53. Shevchenko, A.; Wilm, M.; Vorm, O.; Mann, M. Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels Anal. Chem. 1996, 68 (5) 850-8
54. Hart-Smith, G.; Raftery, M. J. Detection and characterization of low abundance glycopeptides via higher-energy C-trap dissociation and orbitrap mass analysis J. Am. Soc. Mass Spectrom. 2012, 23 (1) 124-40
55. Zou, L.; Zou, X.; Chen, L.; Li, H.; Mygind, T.; Kassem, M.; Bunger, C. Multilineage differentiation of porcine bone marrow stromal cells associated with specific gene expression pattern J. Orthop. Res. 2008, 26 (1) 56-64
56. Twine, N. A.; Janitz, C.; Wilkins, M. R.; Janitz, M. Sequencing of hippocampal and cerebellar transcriptomes provides new insights into the complexity of gene regulation in the human brain Neurosci. Lett. 2013, 541, 263-8
57. FastQC. http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Accessed October 14, 2013.
58. Kim, D.; Pertea, G.; Trapnell, C.; Pimentel, H.; Kelley, R.; Salzberg, S. L. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Genome Biol. 2013, 14 (4) R36
59. Trapnell, C.; Hendrickson, D. G.; Sauvageau, M.; Goff, L.; Rinn, J. L.; Pachter, L. Differential analysis of gene regulation at transcript resolution with RNA-seq Nat. Biotechnol. 2013, 31 (1) 46-53
60. Cufflinks Manual. http://cufflinks.cbcb.umd.edu/manual.html#cufflinks. Accessed October 14, 2013.
61. Goecks, J.; Nekrutenko, A.; Taylor, J. Galaxy Team, Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences Genome Biol. 2010, 11 (8) R86
62. Perkins, D. N.; Pappin, D. J.; Creasy, D. M.; Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 1999, 20 (18) 3551-67
63. The SAM Format Specification (v1.4-r985). http://samtools.sourceforge. net/SAM1.pdf (accessed May 9, 2013).
64. HyperSQL: HSQLDB-100% Java Database. http://hsqldb.org/ (accessed May 9, 2013).
65. Stein, L. Generic Feature Format Version 3 (GFF3). http://www. sequenceontology.org/gff3.shtml (accessed May 9, 2013).
66. Jones, A. R.; Eisenacher, M.; Mayer, G.; Kohlbacher, O.; Siepen, J.; Hubbard, S. J.; Selley, J. N.; Searle, B. C.; Shofstahl, J.; Seymour, S. L.; Julian, R.; Binz, P. A.; Deutsch, E. W.; Hermjakob, H.; Reisinger, F.; Griss, J.; Vizcaino, J. A.; Chambers, M.; Pizarro, A.; Creasy, D. The mzIdentML data standard for mass spectrometry-based proteomics results Mol. Cell. Proteomics 2012, 11 (7) M111.014381
67. Arthur, J. W.; Wilkins, M. R. Using proteomics to mine genome sequences J. Proteome Res. 2004, 3 (3) 393-402
68. Gupta, N.; Tanner, S.; Jaitly, N.; Adkins, J. N.; Lipton, M.; Edwards, R.; Romine, M.; Osterman, A.; Bafna, V.; Smith, R. D.; Pevzner, P. A. Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation Genome Res. 2007, 17 (9) 1362-77
69. Tress, M. L.; Bodenmiller, B.; Aebersold, R.; Valencia, A. Proteomics studies confirm the presence of alternative protein isoforms on a large scale Genome Biol. 2008, 9 (11) R162
70. Meyer, L. R.; Zweig, A. S.; Hinrichs, A. S.; Karolchik, D.; Kuhn, R. M.; Wong, M.; Sloan, C. A.; Rosenbloom, K. R.; Roe, G.; Rhead, B.; Raney, B. J.; Pohl, A.; Malladi, V. S.; Li, C. H.; Lee, B. T.; Learned, K.; Kirkup, V.; Hsu, F.; Heitner, S.; Harte, R. A.; Haeussler, M.; Guruvadoo, L.; Goldman, M.; Giardine, B. M.; Fujita, P. A.; Dreszer, T. R.; Diekhans, M.; Cline, M. S.; Clawson, H.; Barber, G. P.; Haussler, D.; Kent, W. J. The UCSC Genome Browser database: extensions and updates 2013 Nucleic Acids Res. 2013, 41 (Database issue) D64-9
71. Woo, S.; Cha, S. W.; Merrihew, G.; He, Y.; Castellana, N.; Guest, C.; Maccoss, M.; Bafna, V. Proteogenomic database construction driven from large scale RNA-seq data J. Proteome Res. 2013, 10.1021/pr400294c
72. Blakeley, P.; Overton, I. M.; Hubbard, S. J. Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies J. Proteome Res. 2012, 11 (11) 5221-34
73. Menon, R.; Zhang, Q.; Zhang, Y.; Fermin, D.; Bardeesy, N.; DePinho, R. A.; Lu, C.; Hanash, S. M.; Omenn, G. S.; States, D. J. Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer Cancer Res. 2009, 69 (1) 300-9
74. Lee, Y.; Lee, Y.; Kim, B.; Shin, Y.; Nam, S.; Kim, P.; Kim, N.; Chung, W. H.; Kim, J.; Lee, S. ECgene: an alternative splicing database update Nucleic Acids Res. 2007, 35 (Database issue) D99-103
75. Bianchi, V.; Colantoni, A.; Calderone, A.; Ausiello, G.; Ferre, F.; Helmer-Citterich, M. DBATE: database of alternative transcripts expression Database (Oxford) 2013, 2013, bat050
76. Schulz, M. H.; Zerbino, D. R.; Vingron, M.; Birney, E. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels Bioinformatics 2012, 28 (8) 1086-92
77. Chu, H. T.; Hsiao, W. W.; Chen, J. C.; Yeh, T. J.; Tsai, M. H.; Lin, H.; Liu, Y. W.; Lee, S. A.; Chen, C. C.; Tsao, T. T.; Kao, C. Y. EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection Bioinformatics 2013, 29 (8) 1004-10
78. Ning, K.; Nesvizhskii, A. I. The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment BMC Bioinf. 2010, 11 (Suppl 11) S14
79. Mo, F.; Hong, X.; Gao, F.; Du, L.; Wang, J.; Omenn, G. S.; Lin, B. A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data BMC Bioinf. 2008, 9, 537