mRNA expression datasets

Data typeOrganismNumber of ORFsMethodRel./Abs.Citation
mRNA yeast 6250 Affymetrix GeneChip A Greenbaum, D., Colangelo, C., Williams, K. and Gerstein, M. (2003) Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biology, 4, 117
mRNA yeast 5442 Affymetrix GeneChip A Holstege, F.C. and Jennings, E.G., et al. (1998) Dissecting the regulatory circuitry of a eukaryotic genome. Cell, 95, 717-728.
mRNA yeast 6090 Affymetrix GeneChip A Jelinsky, S.A. and Samson, L.D. (1999) Global response of Saccharomyces cerevisiae to an alkylating agent. PNAS USA, 96, 1486-1491.
mRNA yeast 6214 Affymetrix GeneChip A Roth, F.P. and Hughes, J.D., et al. (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nature Biotechnology, 16, 939-945.
mRNA yeast 2961 SAGE A Velculescu, V.E. and Zhang, L., et al. (1997) Characterization of the yeast transcriptome. Cell, 88, 243-251.
mRNA rat 8799 Affymetrix RGU34A arrays A Walker, J.R., Su, A.I., Self, D.W., Hogenesch, J.B., Lapp, H., Maier, R., Hoyer, D. and Bilbe, G. (2004) Applications of a rat multiple tissue gene expression data set. Genome Research, 14, 742-749.
mRNA yeast 5935 DNA microarray R Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L. (2001) Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science, 292, 929-934.
mRNA yeast 245 DNA microarray R Griffin TJ, Gygi SP, Ideker T, Rist B, Eng J, Hood L, Aebersold R. (2002) Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol. Cell Proteomics, 4, 323-333.
mRNA mouse 150 DNA microarray R Tian Q, Stepaniants SB, Mao M, Weng L, Feetham MC, Doyle MJ, Yi EC, Dai H, Thorsson V, Eng J, Goodlett D, Berger JP, Gunter B, Linseley PS, Stoughton RB, Aebersold R, Collins SJ, Hanlon WA, Hood LE. (2004) Integrated genomic and proteomic analyses of gene expression in Mammalian cells. Mol. Cell Proteomics, 10, 960-969.
mRNA Halobacterium 157 DNA microarray R Baliga NS, Pan M, Goo YA, Yi EC, Goodlett DR, Dimitrov K, Shannon P, Aebersold R, Ng WV, Hood L. (2002) Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proc. Natl. Acad. Sci. USA, 99, 14913-14918.

Protein abundance datasets

Data typeOrganismNumber of ORFsMethodRel./Abs.Citation
protein yeast 2042 MuDPIT A Greenbaum, D., Jansen, R. and Gerstein, M. (2002) Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts. Bioinformatics, 18, 585-596.
protein yeast 66 35S-labeled proteins, 2D gel electrophoresis A Futcher, B., Latter, G.I., Monardo, P., McLaughlin, C.S. and Garrels, J.I. (1999) A sampling of the yeast proteome. Mol. Cell Biol., 19, 7357-7368.
protein yeast 3868 TAP-tag, SDS-PAGE/Western blot A Ghaemmaghami, S., Huh, W.K., Bower, K., Howson, R.W., Belle, A., Dephoure, N., O'Shea, E.K. and Weissman, J.S. (2003) Global analysis of protein expression in yeast. Nature, 425, 737-741.
protein yeast 125 Metabolic labeling, 2DE and liq. scintillation counting, LC-MS/MS A Gygi, S.P., Rochon, Y., Franza, B.R. and Aebersold, R. (1999) Correlation between protein and mRNA abundance in yeast. Mol. Cell Biol., 19, 1720-1730.
protein yeast 1478 LC/LC-MS/MS A Peng, J., Elias, J.E., Thoreen, C.C., Licklider, L.J. and Gygi, S.P. (2003) Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J. Proteome Res., 2, 43-50.
protein yeast 1417 MuDPIT A Washburn, M.P., Wolters, D., and Yates, J. R. 3rd. (2001) Large-scale analysis of the yeast proteome by multidimensional protein identificatino technology. Nature Biotechnology, 19, 242-247.
protein rat 227 SDS-PAGE, MS/MS A Girard, M., Allaire, P. D.,  McPherson, P. S., and Blondeau, F. (2005) Non-stoichiometric relationship between clathrin heavy and light chains revealed by subcellular proteomics of clathrin-coated vesicles from brain and liver. Mol. Cell Proteomics, 4, 1145-1154.
protein yeast 289 ICAT, LC-MS/MS R Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L. (2001) Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science, 292, 929-934.
protein yeast 245 ICAT, LC-MS/MS R Griffin TJ, Gygi SP, Ideker T, Rist B, Eng J, Hood L, Aebersold R. (2002) Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol. Cell Proteomics, 4, 323-333.
protein mouse 150 ICAT, LC-MS/MS; DIGE R Tian Q, Stepaniants SB, Mao M, Weng L, Feetham MC, Doyle MJ, Yi EC, Dai H, Thorsson V, Eng J, Goodlett D, Berger JP, Gunter B, Linseley PS, Stoughton RB, Aebersold R, Collins SJ, Hanlon WA, Hood LE. (2004) Integrated genomic and proteomic analyses of gene expression in Mammalian cells. Mol. Cell Proteomics, 10, 960-969.
protein Halobacterium 52 ICAT, LC-MS/MS R Baliga NS, Pan M, Goo YA, Yi EC, Goodlett DR, Dimitrov K, Shannon P, Aebersold R, Ng WV, Hood L. (2002) Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proc. Natl. Acad. Sci. USA, 99, 14913-14918.



Created by Anne Counterman Burba
Yale University
Last modified June 6, 2006
For comments please email to
proteomics@bioinfo.mbb.yale.edu