Statistical similarities between transcriptomics and quantitative shotgun proteomics data

Molecular and Cellular Proteomics

Volumn 7, Issue 4, 2008, Pages 631-644

  Pavelka, Norman ^a   Fournier, Marjorie L ^a   Swanson, Selene K ^a   Pelizzola, Mattia ^b,d   Ricciardi Castagnoli, Paola ^c   Florens, Laurence ^a   Washburn, Michael P ^a  

^a STOWERS INSTITUTE FOR MEDICAL RESEARCH   (United States)

^b UNIVERSITY OF MILANO BICOCCA   (Italy)

^c AGENCY FOR SCIENCE   (Singapore)

^d YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME;

CELL LYSATE; CONFERENCE PAPER; CONTROLLED STUDY; HUMAN; IMMUNOPRECIPITATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN MICROARRAY; PROTEOMICS; QUANTITATIVE ANALYSIS; SACCHAROMYCES CEREVISIAE; STATISTICAL ANALYSIS; TRANSCRIPTOMICS; YEAST;

DATA INTERPRETATION, STATISTICAL; GENE EXPRESSION PROFILING; HUMANS; IMMUNOPRECIPITATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEINS; PROTEOME; PROTEOMICS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 42649131100     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M700240-MCP200     Document Type: Conference Paper

References (58)

1. Ideker, T., Thorsson, V., Ranish, J. A., Christmas, R., Buhler, J., Eng, J. K., Bumgarner, R., Goodlett, D. R., Aebersold, R., and Hood, L. (2001) Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292, 929-934
2. Kitano, H. (2002) Systems biology: a brief overview. Science 295, 1662-1664
3. Albeck, J. G., MacBeath, G., White, F. M., Sorger, P. K., Lauffenburger, D. A., and Gaudet, S. (2006) Collecting and organizing systematic sets of protein data. Nat. Rev. Mol. Cell. Biol. 7, 803-812
4. Lipshutz, R. J., Fodor, S. P., Gingeras, T. R., and Lockhart, D. J. (1999) High density synthetic oligonucleotide arrays. Nat. Genet. 21, 20-24
5. David, L., Huber, W., Granovskaia, M., Toedling, J., Palm, C. J., Bofkin, L., Jones, T., Davis, R. W., and Steinmetz, L. M. (2006) A high-resolution map of transcription in the yeast genome. Proc. Natl. Acad. Sci. U. S. A. 103, 5320-5325
6. Washburn, M. P., Wolters, D., and Yates, J. R., III (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242-247
7. Aebersold, R., and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198 -207
8. Csete, M. E., and Doyle, J. C. (2002) Reverse engineering of biological complexity. Science 295, 1664-1669
9. Golub, T. R., Slonim, D. K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, J. P., Collar, H., Loh, M. L., Downing, J. R., Caligiuri, M. A., Bloomfield, C. D., and Lander, E. S. (1999) Molecular classification of cancer. class discovery and class prediction by gene expression monitoring. Science 286, 531-537
10. Hughes, T. R., Marton, M. J., Jones, A. R., Roberts, C. J., Stoughton, R., Armour, C. D., Bennett, H. A., Coffey, E., Dai, H., He, Y. D., Kidd, M. J., King, A. M., Meyer, M. R., Slade, D., Lum, P. Y., Stepaniants, S. B., Shoemaker, D. D., Gachotte, D., Chakraburtty, K., Simon, J., Bard, M., and Friend, S. H. (2000) Functional discovery via a compendium of expression profiles. Cell 102 109-126
11. Granucci, F., Vizzardelli, C., Pavelka, N., Feau, S., Persico, M., Virzi, E., Rescigno, M., Moro, G., and Ricciardi-Castagnoli, P. (2001) Inducible IL-2 production by dendritic cells revealed by global gene expression analysis. Nat. Immunol. 2, 882-888
12. Florens, L., Washburn, M. P., Raine, J. D., Anthony, R. M., Grainger, M., Haynes, J. D., Moch, J. K, Muster, N., Sacci, J. B., Tabb, D. L., Witney, A. A., Wolters, D., Wu, Y., Gardner, M. J., Holder, A. A., Sinden, R. E., Yates, J. R., and Carucci, D. J. (2002) A proteomic view of the Plasmodium falciparum life cycle. Nature 419, 520-526
13. Listgarten, J., and Emili, A. (2005) Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. Mol. Cell. Proteomics 4, 419-434
14. Wang, E. (2005) RNA amplification for successful gene profiling analysis. J. Transl. Med. 3, 28
15. Lonnstedt, I., and Speed, T. (2002) Replicated microarray data. Stat. Sin. 12, 31-46
16. Huang, X., and Pan, W. (2002) Comparing three methods for variance estimation with duplicated high density oligonucleotide arrays. Funct. Integr. Genomics 2, 126-133
17. Ideker, T., Thorsson, V., Siegel, A. F., and Hood, L. E. (2000) Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data. J. Comput. Biol. 7, 805-817
18. Baggerly, K. A., Coombes, K. R., Hess, K. R., Stivers, D. N., Abruzzo, L. V., and Zhang, W. (2001) Identifying differentially expressed genes in cDNA microarray experiments. J. Comput. Biol. 8, 639-659
19. Tusher, V. G., Tibshirani, R., and Chu, G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. U. S. A. 98, 5116-5121
20. Pavelka, N., Pelizzola, M., Vizzardelli, C., Capozzoli, M., Splendiani, A., Granucci, F., and Ricciardi-Castagnoli, P. (2004) A power law global error model for the identification of differentially expressed genes in microarray data. BMC Bioinformatics 5, 203
21. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., and Aebersold, R. (1999) Quantitative analysis of complex protein mixtures usJng isotope-coded affinity tags. Nat. Biotechnol. 17, 994-999
22. Tao, W. A., and Aebersold, R. (2003) Advances in quantitative proteomics via stable isotope tagging and mass spectrometry. Curr. Opin. Biotechnol. 14, 110-118
23. Liu, H., Sadygov, R. G., and Yates, J. R., III (2004) A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 76, 4193-4201
24. Old, W. M., Meyer-Arendt, K., Aveline-Wolf, L., Pierce, K. G., Mendoza, A., Sevinsky, J. R., Rasing, K. A., and Ahn, N. G. (2005) Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol. Cell. Proteomics 4, 1487-1502
25. Zhang, B., Verberkmoes, N. C., Langston, M. A., Uberbacher, E., Hettich, R. L., and Samatova, N. F. (2006) Detecting differential and correlated protein expression in label-free shotgun proteomics. J. Proteome Res. 5, 2909-2918
26. Paoletti, A. C., Parmely, T. J., Tomomori-Sato, C., Sato, S., Zhu, D., Conaway, R. C., Conaway, J. W., Florens, L, and Washburn, M. P. (2006) Quantitative proteomic, analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors. Proc. Natl. Acad. Sci. U. S. A. 103, 18928-18933
27. Zybailov, B., Mosley, A. L, Sardiu, M. E., Coleman, M. K., Florens, L, and Washburn, M. P. (2006) Statistical analysis of membrane proteome expression changes in Saccharomyces cerevislae. J. Proteome Res. 5, 2339-2347
28. Chen, Y., Dougherty, E. R., and Bittrier, M. L. (1997) Ratio-based decisions and the quantitative analysis of cDNA microarray images. J. Biomed. Opt. 2, 364-374
29. Rocke, D. M., and Durbin, B. (2001) A model for measurement error for gene expression arrays. J. Comput. Biol. 8, 557-569
30. Huber, W., von Heydebreck, A., Sultmann, H., Poustka, A., and Vingron, M. (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18, Suppl. 1, S96-S104
31. Wright, G. W., and Simon, R. M. (2003) A random variance model for detection of differential gene expression in small microarray experiments. Bioinformatics 19, 2448-2455
32. Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L, Ge, Y., Gentry, J., Homik, K., Hathom, T., Huber, W., lacus, S., Irizarry, R., Leisch, F., Li, C., Maechler, M., Rossini A. J., Sawitzki, G., Smith, C., Smyth, G., Tiemey, L, Yang, J. Y., and Zhang, J. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80
33. Pelizzola, M., Pavelka, N., Foti, M., and Ricciardi-Castagnoli, P. (2006) AMDA: an R package for the automated microarray data analysis. BMC Bioinformatics 7, 335
34. Vizzardelli, C., Pavelka, N., Luchini, A., Zanoni, I., Bendickson, L, Pelizzola, M., Beretta, O., Foti, M., Granucci, F., Nilsen-Hamilton, M., and Ricciardi-Castagnoli, P. (2006) Effects of dexamethazone on LPS-Induced activation and migration of mouse dendritic cells revealed by a genome-wide transcriptional analysis. Eur. J. Immunol. 36, 1504-1515
35. lovino, F., Lentini, L, Amato, A., and Di Leonardo, A. (2006) RB acute loss induces centrosome amplification and aneuploidy in murine primary fibroblasts. Mol. Cancer 5, 38
36. Anderle, M., Roy, S., Lin, H., Becker, C., and Joho, K. (2004) Quantifying reproducibility for differential proteomics: noise analysis for protein liquid chromatography-mass spectrometry of human serum. Bioinformatics 20, 3575-3582
37. Brachmann, C. B., Davies, A., Cost, G. J., Caputo, E., Li, J., Hieter, P., and Boeke, J. D. (1998) Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14, 115-132
38. Sato, S., Tomomori-Sato, C., Parmely, T. J., Florens, L., Zybailov, B., Swanson, S. K., Banks, C. A., Jin, J., Cai, Y., Washburn, M. P., Conaway, J. W., and Conaway, R. C. (2004) A set of consensus mammalian mediator subunits identified by multidimensional protein identification technology. Mol, Cell 14, 685-691
39. McDonald, W. H., Ohi, R., Miyamoto, D. T., Mitchlson, T. J., and Yates, J. R., III (2002) Comparison of three directly coupled HPLC MS/MS strategies for identification of proteins from complex mixtures: Single-dimension LC-MS/MS, 2-phase MudPIT, and 3-phase MudPIT. Int. J. Mass Spectrom. 219, 245-251
40. Florens, L., and Washburn, M. P. (2006) Proteomic analysis by multidimensionall protein identification technology. Methods Mol. Biol. 328, 159-175
41. Eng, J. K., McCormack, A. L, and Yates, J. R. (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Sac. Mass Spectrom. 5, 976-989
42. Tabb, D. L, McDonald, W. H., and Yates, J. R., III (2002) DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J. Proteome Res. 1, 21-26
43. Florens, L, Carozza, M. J., Swanson, S. K., Fournier, M., Coleman, M. K., Workman, J. L., and Washburn, M. P. (2006) Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors. Methods 40, 303-311
44. Elias, J. E., Haas, W., Faherty, B. K., and Gygi, S. P. (2005) Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat. Methods 2, 667-675
45. Trottein, F., Pavelka, N., Vizzardelli, C., Angell, V., Zouain, C. S., Pelizzola, M., Capozzoli, M., Urbano, M., Capron, M., Belardelli, F., Granucci, F., and Ricciardi-Castagnoli, P. (2004) A type I IFN-dependent pathway induced by Schistosoma mansoni eggs in mouse myeloid dendritic cells generates an inflammatory signature. J. Immunol. 172, 3011-3017
46. Edgar, R., Domrachev, M., and Lash, A. E. (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30, 207-210
47. Ihaka, R., and Gentleman, R. (1996) R: a language for data analysis and graphics. J. Comput. Graph. Stat. 5, 299-314
48. Baldi, P., and Long, A. D. (2001) A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 17. 509-519
49. Hoyle, D. C., Rattray, M., Jupp, R., and Brass, A. (2002) Making sense of microarray data distributions. Bioinformafics 18, 576-584
50. Wemer-Washbume, M., Braun, E., Johnston, G. C., and Singer, R. A. (1993) Stationary phase in the yeast Saccharomyces cerevisiae. Microbiol. Rev. 57, 383-401
51. Al-Shahrour, F., Minguez, P., Tarraga, J., Montaner, D., Alloza, E., Vaquerizas, J. M., Conde, L., Blaschke, C., Vera, J., and Dopazo, J. (2006) BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. Nucleic Acids Res. 34, W472-W476
52. Fuge, E. K., Braun, E. L., and Wemer-Washbume, M. (1994) Protein synthesis in long-term stationary-phase cultures of Saccharomyces cerevisiae. J. Bacteriol. 176, 5802-5813
53. Sehgal, M. S., Gondal, I., and Dooley, L S. (2005) Collateral missing value imputation: a new robust missing value estimation algorithm for microarray data. Bioinformatics 21, 2417-2423
54. Kim, H., Golub, G. H., and Park, H. (2005) Missing value estimation for DNA microarray gene expression data: local least squares imputation. Bioinformatics 21, 187-198
55. Troyanskaya, O., Cantor, M., Sherlock, G., Brown, P., Hastie, T., Tibshirani, R., Botstein, D., and Altman, R. B. (2001) Missing value estimation methods for DNA microarrays. Bioinformatics 17, 520-525
56. Dudoit, S., Yang, Y. H., Callow, M. J., and Speed, T. P. (2002) Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Stat. Sin. 12, 111-139
57. Storey, J. D., and Tibshirani, R. (2003) Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. U. S. A 100, 9440-9445
58. Rocke, D. M., and Lorenzato, S. (1995) A two-component model for measurement error in analytical chemistry. Technometrics 37, 176-184