Global signatures of protein and mRNA expression levels
Open accessAbstract
Cellular states are determined by differential expression of the cell’s proteins. The relationship between protein and mRNA expression levels informs about the combined outcomes of translation and protein degradation which are, in addition to transcription and mRNA stability, essential contributors to gene expression regulation. This review summarizes the state of knowledge about large-scale measurements of absolute protein and mRNA expression levels, and the degree of correlation between the two parameters. We summarize the information that can be derived from comparison of protein and mRNA expression levels and discuss how corresponding sequence characteristics suggest modes of regulation.
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The correlation between proteomes and corresponding transcriptomes was only 0.4 to 0.45, capturing important differences between transcriptome and proteome.
“As the correlation between the proteomes and the corresponding transcriptomes was only 0.4 to 0.45,our analysis captured important differences between transcriptome and proteome30,31 (Fig. 2c).”
From Cell type- and brain region-resolved mouse brain proteome (2015) · cites this paper as [30]
The section ‘Steady-state concentrations of protein molecules per mRNA and their correlates’ (page not provided) reports that several measurements have R² around 0.4 and that much of the variation in protein levels is not explained by mRNA levels. It does not give 0.4–0.45 as a general correlation coefficient: that figure is approximately a squared Pearson correlation, and the reported values vary across organisms. The citing authors’ statement about what their own analysis captured is their inference, not a finding attributed to this source. (LLM, conf=0.86)
Experimental — accuracy not yet measuredThe use of high-resolution MS and RNA-Seq may account for the higher correlations between transcriptomes and proteomes observed here than in previous studies.
“The use of high-resolution MS and RNA-Seq may account for the fact that higher correlations between transcriptomes and proteomes are observed here than in previous studies”
From Deep proteome and transcriptome mapping of a human cancer cell line (2011) · cites this paper as de Sousa Abreu et al, 2009
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Cites
Large-scale analysis of the yeast proteome by multidimensional protein identification technology
Washburn, M. P., Wolters, D. A., & Yates, J. R. (2001) · Nature Biotechnology · doi:10.1038/85686 · Cited by 4,759 · see citing works
Quantitative analysis of complex protein mixtures using isotope-coded affinity tags
Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., & Aebersold, R. (1999) · Nature Biotechnology · doi:10.1038/13690 · Cited by 4,683 · see citing works
The Ubiquitin-Proteasome Proteolytic Pathway: Destruction for the Sake of Construction
Glickman, M. H., & Ciechanover, A. J. (2002) · Physiological Reviews · doi:10.1152/physrev.00027.2001 · Cited by 4,216 · see citing works
Intrinsically unstructured proteins and their functions
Dyson, H. J., & Wright, P. E. (2005) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1589 · Cited by 3,871 · see citing works
Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. S., & Weissman, J. S. (2009) · Science · doi:10.1126/science.1168978 · Cited by 3,853 · see citing works
Correlation between Protein and mRNA Abundance in Yeast
Gygi, S. P., Rochon, Y., Franza, B. R., & Aebersold, R. (1999) · Molecular and Cellular Biology · doi:10.1128/mcb.19.3.1720 · Cited by 3,819 · see citing works
Global analysis of protein expression in yeast
Ghaemmaghami, S., Huh, W.-K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K., & Weissman, J. S. (2003) · Nature · doi:10.1038/nature02046 · Cited by 3,750 · see citing works
Serial Analysis of Gene Expression
Velculescu, V. E., Zhang, L., Vogelstein, B., & Kinzler, K. W. (1995) · Science · doi:10.1126/science.270.5235.484 · Cited by 3,713 · see citing works
The impact of microRNAs on protein output
Baek, D., Villén, J., Shin, C., Camargo, F. D., Gygi, S. P., & Bartel, D. P. (2008) · Nature · doi:10.1038/nature07242 · Cited by 3,592 · see citing works
miR-15 and miR-16 induce apoptosis by targeting BCL2
Cimmino, A., Calin, G. A., Fabbri, M., Iorio, M. V., Ferracin, M., Shimizu, M., Wojcik, S. E., Aqeilan, R. I., Zupo, S., Dono, M., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506654102 · Cited by 3,510 · see citing works
The scanning model for translation: an update.
Kozak, M. (1989) · The Journal of Cell Biology · doi:10.1083/jcb.108.2.229 · Cited by 3,485 · see citing works
Widespread changes in protein synthesis induced by microRNAs
Selbach, M., Schwanhäusser, B., Thierfelder, N., Fang, Z., Khanin, R., & Rajewsky, N. (2008) · Nature · doi:10.1038/nature07228 · Cited by 3,429 · see citing works
Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets
Sonenberg, N., & Hinnebusch, A. G. (2009) · Cell · doi:10.1016/j.cell.2009.01.042 · Cited by 3,304 · see citing works
Regulated Translation Initiation Controls Stress-Induced Gene Expression in Mammalian Cells
Harding, H. P., Novoa, I., Zhang, Y., Zeng, H., Wek, R. C., Schapira, M., & Ron, D. (2000) · Molecular Cell · doi:10.1016/s1097-2765(00)00108-8 · Cited by 3,281 · see citing works
Amino Acid Sequences Common to Rapidly Degraded Proteins: The PEST Hypothesis
Rogers, S. W., Wells, R., & RECHSTEINER, M. C. (1986) · Science · doi:10.1126/science.2876518 · Cited by 2,565 · see citing works
RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO
Hoege, C., Pfander, B., Moldovan, G., Pyrowolakis, G., & Jentsch, S. (2002) · Nature · doi:10.1038/nature00991 · Cited by 2,202 · see citing works
Ishihama, Y., Oda, Y., Tabata, T., Sato, T., Nagasu, T., Rappsilber, J., & Mann, M. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500061-mcp200 · Cited by 2,055 · see citing works
In Vivo Half-Life of a Protein Is a Function of Its Amino-Terminal Residue
Bachmair, A., Finley, D. J., & Varshavsky, A. J. (1986) · Science · doi:10.1126/science.3018930 · Cited by 1,976 · see citing works
Control of translation and mRNA degradation by miRNAs and siRNAs: Table 1.
Valencia-Sanchez, M. A., Liu, J., Hannon, G. J., & Parker, R. (2006) · Genes & Development · doi:10.1101/gad.1399806 · Cited by 1,751 · see citing works
Noise in Gene Expression: Origins, Consequences, and Control
Raser, J. M., & O’Shea, E. K. (2005) · Science · doi:10.1126/science.1105891 · Cited by 1,719 · see citing works
Comparing protein abundance and mRNA expression levels on a genomic scale
Greenbaum, D. (2003) · Genome biology · doi:10.1186/gb-2003-4-9-117 · Cited by 1,692 · see citing works
Fabbri, M., Garzon, R., Cimmino, A., Liu, Z., Zanesi, N. A. O., Callegari, E., Liu, S., Alder, H., Costinean, S., Fernandez-Cymering, C., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0707628104 · Cited by 1,676 · see citing works
Dissecting the regulatory circuitry of a eukaryotic genome
Holstege, F. C. P., Jennings, E. G., Wyrick, J. J., Lee, T. I., Hengartner, C. J., Green, M. R., Golub, T. R., Lander, E. S., & Young, R. A. (1998) · Cell · doi:10.1016/s0092-8674(00)81641-4 · Cited by 1,670 · see citing works
PEST sequences and regulation by proteolysis
RECHSTEINER, M. C., & Rogers, S. W. (1996) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(96)10031-1 · Cited by 1,645 · see citing works
Noise in eukaryotic gene expression
Blake, W. J., Kærn, M., Cantor, C. R., & Collins, J. J. (2003) · Nature · doi:10.1038/nature01546 · Cited by 1,636 · see citing works
An analysis of vertebrate mRNA sequences: intimations of translational control.
Kozak, M. (1991) · The Journal of Cell Biology · doi:10.1083/jcb.115.4.887 · Cited by 1,623 · see citing works
Regulation of noise in the expression of a single gene
Özbudak, E. M., Thattai, M., Kurtser, I., Grossman, A. D., & van Oudenaarden, A. (2002) · Nature Genetics · doi:10.1038/ng869 · Cited by 1,559 · see citing works
Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
Newman, J. R. S., Ghaemmaghami, S., Ihmels, J., Breslow, D. K., Noble, M., DeRisi, J. L., & Weissman, J. S. (2006) · Nature · doi:10.1038/nature04785 · Cited by 1,483 · see citing works
Coding-Sequence Determinants of Gene Expression in <i>Escherichia coli</i>
Kudla, G., Murray, A. W., Tollervey, D., & Plotkin, J. B. (2009) · Science · doi:10.1126/science.1170160 · Cited by 1,458 · see citing works
Control of Stochasticity in Eukaryotic Gene Expression
Raser, J. M., & O'Shea, E. K. (2004) · Science · doi:10.1126/science.1098641 · Cited by 1,425 · see citing works
Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs
Bartel, D. P., & Chen, C. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1328 · Cited by 1,417 · see citing works
Initiation of translation in prokaryotes and eukaryotes
Kozak, M. (1999) · Gene · doi:10.1016/s0378-1119(99)00210-3 · Cited by 1,364 · see citing works
A comparison of selected mRNA and protein abundances in human liver
Anderson, L., & Seilhamer, J. (1997) · Electrophoresis · doi:10.1002/elps.1150180333 · Cited by 1,266 · see citing works
The <i>let-7</i> MicroRNA Represses Cell Proliferation Pathways in Human Cells
Johnson, C. D., Esquela-Kerscher, A., Stefani, G., Byrom, M., Kelnar, K., Ovcharenko, D., Wilson, M., Wang, X., Shelton, J., Shingara, J., et al. (2007) · Cancer Research · doi:10.1158/0008-5472.can-07-1083 · Cited by 1,224 · see citing works
Lu, P., Vogel, C., Wang, R., Yao, X., & Marcotte, E. M. (2007) · Nature Biotechnology · doi:10.1038/nbt1270 · Cited by 1,139 · see citing works
Self-citationA translational profiling approach for the molecular characterization of CNS cell types
Heiman, M., Schaefer, A., Gong, S., Peterson, J. D., Day, M., Ramsey, K. E., Suárez-Fariñas, M., Schwarz, C., Stephan, D. A., Surmeier, D. J., et al. (2008) · Cell · doi:10.1016/j.cell.2008.10.028 · Cited by 1,134 · see citing works
Proteolysis: from the lysosome to ubiquitin and the proteasome
Ciechanover, A. (2005) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1552 · Cited by 1,133 · see citing works
Gene Regulation at the Single-Cell Level
Rosenfeld, N., Young, J. W., Alon, U., Swain, P. S., & Elowitz, M. B. (2005) · Science · doi:10.1126/science.1106914 · Cited by 1,104 · see citing works
Welcker, M., & Clurman, B. E. (2008) · Nature Reviews Cancer · doi:10.1038/nrc2290 · Cited by 1,084 · see citing works
Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation
López-Maury, L., Marguerat, S., & Bähler, J. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2398 · Cited by 1,061 · see citing works
Molecular mechanisms of translational control
Gebauer, F., & Hentze, M. W. (2004) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1488 · Cited by 991 · see citing works
Untranslated regions of mRNAs.
(2002) · Genome biology · doi:10.1186/gb-2002-3-3-reviews0004 · Cited by 987 · see citing works
The Cdk inhibitor p27 in human cancer: prognostic potential and relevance to anticancer therapy
Chu, I. M., Hengst, L., & Slingerland, J. M. (2008) · Nature reviews. Cancer · doi:10.1038/nrc2347 · Cited by 986 · see citing works
Fragile X mental retardation protein targets G quartet mRNAs important for neuronal function
Darnell, J. C., Jensen, K. B., Jin, P., Brown, V., Warren, S. T., & Darnell, R. B. (2001) · Cell · doi:10.1016/s0092-8674(01)00566-9 · Cited by 952 · see citing works
Discordant Protein and mRNA Expression in Lung Adenocarcinomas
Chen, G., Gharib, T. G., Huang, C.-C., Taylor, J. M. G., Misek, D. E., Kardia, S. L. R., Giordano, T. J., Iannettoni, M. D., Orringer, M. B., Hanash, S., et al. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m200008-mcp200 · Cited by 946 · see citing works
Calvo, S. E., Pagliarini, D. J., & Mootha, V. K. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0810916106 · Cited by 914 · see citing works
Application of a translational profiling approach for the comparative analysis of CNS cell types
Doyle, J. P., Dougherty, J. D., Heiman, M., Schmidt, E. F., Stevens, T. R., Ma, G., Bupp, S., Shrestha, P., Shah, R. D., Doughty, M. L., et al. (2008) · Cell · doi:10.1016/j.cell.2008.10.029 · Cited by 912 · see citing works
Deregulated proteolysis by the F-box proteins SKP2 and β-TrCP: tipping the scales of cancer
Frescas, D., & Pagano, M. (2008) · Nature reviews. Cancer · doi:10.1038/nrc2396 · Cited by 886 · see citing works
Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
de Godoy, L. M. F., Olsen, J. V., Cox, J., Nielsen, M. L., Hubner, N. C., Fröhlich, F., Walther, T. C., & Mann, M. (2008) · Nature · doi:10.1038/nature07341 · Cited by 873 · see citing works
Diversity of degradation signals in the ubiquitin–proteasome system
Ravid, T., & Hochstrasser, M. (2008) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2468 · Cited by 831 · see citing works
Why highly expressed proteins evolve slowly
Drummond, D. A., Bloom, J. D., Adami, C., Wilke, C. O., & Arnold, F. H. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504070102 · Cited by 815 · see citing works
Duret, L., & Mouchiroud, D. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.8.4482 · Cited by 808 · see citing works
Targeting the PI3K/Akt/mTOR pathway: Effective combinations and clinical considerations
LoPiccolo, J., Blumenthal, G. M., Bernstein, W. B., & Dennis, P. A. (2008) · Drug Resistance Updates · doi:10.1016/j.drup.2007.11.003 · Cited by 804 · see citing works
Integrated Genomic and Proteomic Analyses of Gene Expression in Mammalian Cells
Tian, Q., Stepaniants, S., Mao, M., Weng, L., Feetham, M. C., Doyle, M. J., Yi, E. C., Dai, H. A., Thórsson, V., Eng, J. K., et al. (2004) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m400055-mcp200 · Cited by 778 · see citing works
Regulation of translation via mRNA structure in prokaryotes and eukaryotes
Kozak, M. (2005) · Gene · doi:10.1016/j.gene.2005.06.037 · Cited by 747 · see citing works
Gene-Specific Regulation by General Translation Factors
Dever, T. E. (2002) · Cell · doi:10.1016/s0092-8674(02)00642-6 · Cited by 720 · see citing works
Precision and functional specificity in mRNA decay
Wang, Y., Liu, C. L., Storey, J. D., Tibshirani, R. J., Herschlag, D., & Brown, P. O. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.092538799 · Cited by 708 · see citing works
Regulation of stability and function of the epithelial Na+ channel (ENaC) by ubiquitination
Staub, O., Gautschi, I., Ishikawa, T., Breitschopf, K., Ciechanover, A. J., Schild, L., & Rotin, D. (1997) · The EMBO Journal · doi:10.1093/emboj/16.21.6325 · Cited by 697 · see citing works
Quantification of protein half-lives in the budding yeast proteome
Belle, A., Tanay, A., Bitincka, L., Shamir, R., & O’Shea, E. K. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605420103 · Cited by 678 · see citing works
Genome-wide analysis of mRNA translation profiles in <i>Saccharomyces</i> <i>cerevisiae</i>
Arava, Y., Wang, Y., Storey, J. D., Liu, C. L., Brown, P. O., & Herschlag, D. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0635171100 · Cited by 663 · see citing works
Gerber, A. P., Herschlag, D., & Brown, P. O. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020079 · Cited by 651 · see citing works
Hogan, D. J., Riordan, D. P., Gerber, A. P., Herschlag, D., & Brown, P. O. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060255 · Cited by 609 · see citing works
A Sampling of the Yeast Proteome
Futcher, B., Latter, G. I., Monardo, P., McLaughlin, C. S., & Garrels, J. I. (1999) · Molecular and Cellular Biology · doi:10.1128/mcb.19.11.7357 · Cited by 606 · see citing works
Decay Rates of Human mRNAs: Correlation With Functional Characteristics and Sequence AttributesPreprint
Yang, E., van Nimwegen, E., Zavolan, M., Rajewsky, N., Schroeder, M., Magnasco, M., & Darnell, J. E., Jr. (2003) · Genome Research · doi:10.1101/gr.1272403 · Cited by 598 · see citing works
Dynamic Proteomics of Individual Cancer Cells in Response to a Drug
Cohen, A., Geva‐Zatorsky, N., Eden, E., Frenkel‐Morgenstern, M., Issaeva, I., Sigal, A., Milo, R., Cohen‐Saidon, C., Liron, Y., Kam, Z., et al. (2008) · Science · doi:10.1126/science.1160165 · Cited by 594 · see citing works
Stochastic modelling for quantitative description of heterogeneous biological systems
Wilkinson, D. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2509 · Cited by 573 · see citing works
The Molecular Mechanics of Eukaryotic Translation
Kapp, L. D., & Lorsch, J. R. (2004) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.73.030403.080419 · Cited by 540 · see citing works
Tumor necrosis factor or tumor promoting factor?
Balkwill, F. (2002) · Cytokine & Growth Factor Reviews · doi:10.1016/s1359-6101(01)00020-x · Cited by 520 · see citing works
NF-κB Family of Transcription Factors: Central Regulators of Innate and Adaptive Immune Functions
Caamaño, J., & Hunter, C. A. (2002) · Clinical Microbiology Reviews · doi:10.1128/cmr.15.3.414-429.2002 · Cited by 513 · see citing works
Dissecting eIF4E action in tumorigenesis.Preprint
Wendel, H., Silva, R. L. A., Malina, A., Mills, J., Zhu, H., Ueda, T., Watanabe‐Fukunaga, R., Fukunaga, R., Teruya-Feldstein, J., Pelletier, J., et al. (2007) · Genes & Development · doi:10.1101/gad.1604407 · Cited by 512 · see citing works
TIA‐1 is a translational silencer that selectively regulates the expression of TNF‐α
Piecyk, M., Wax, S. D., Beck, A., Kedersha, N., Gupta, M., Maritim, B., Chen, S., Gueydan, C., Kruys, V., Streuli, M., et al. (2000) · The EMBO Journal · doi:10.1093/emboj/19.15.4154 · Cited by 509 · see citing works
RNA-Seq—quantitative measurement of expression through massively parallel RNA-sequencing
Wilhelm, B. T., & Landry, J. (2009) · Methods · doi:10.1016/j.ymeth.2009.03.016 · Cited by 500 · see citing works
Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics
Baerenfaller, K., Grossmann, J., Grobei, M. A., Hull, R., Hirsch‐Hoffmann, M., Yalovsky, S., Zimmermann, P., Grossniklaus, U., Gruissem, W., & Baginsky, S. (2008) · Science · doi:10.1126/science.1157956 · Cited by 483 · see citing works
Global Protein Stability Profiling in Mammalian Cells
Yen, H.-C. S., Xu, Q., Chou, D. M., Zhao, Z., & Elledge, S. J. (2008) · Science · doi:10.1126/science.1160489 · Cited by 482 · see citing works
Regulation of peptide‐chain elongation in mammalian cells
Browne, G. J., & Proud, C. G. (2002) · European Journal of Biochemistry · doi:10.1046/j.1432-1033.2002.03290.x · Cited by 469 · see citing works
Tight Regulation of Unstructured Proteins: From Transcript Synthesis to Protein Degradation
Gsponer, J., Futschik, M. E., Teichmann, S. A., & Babu, M. M. (2008) · Science · doi:10.1126/science.1163581 · Cited by 466 · see citing works
Disassembly and Reassembly of the Yeast Vacuolar H+-ATPase in Vivo
Kane, P. M. (1995) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)46944-4 · Cited by 462 · see citing works
eIF4E – from translation to transformation
Mamane, Y., Petroulakis, E., Rong, L., Yoshida, K., Ler, L. W., & Sonenberg, N. (2004) · Oncogene · doi:10.1038/sj.onc.1207549 · Cited by 452 · see citing works
Global analysis of transcript and protein levels across the Plasmodium falciparum life cyclePreprint
Roch, K. G. L., Johnson, J. R., Florens, L., Zhou, Y., Santrosyan, A., Grainger, M., Yan, S. F., Williamson, K. C., Holder, A. A., Carucci, D. J., et al. (2004) · Genome Research · doi:10.1101/gr.2523904 · Cited by 437 · see citing works
Guo, Y.-F., Xiao, P., Lei, S., Deng, F., Xiao, G. G., Liu, Y., Chen, X., Li, L., Wu, S., Chen, Y., et al. (2008) · Acta Biochimica et Biophysica Sinica · doi:10.1111/j.1745-7270.2008.00418.x · Cited by 424 · see citing works
O’Connor, T., Sadleir, K. R., Maus, E., Velliquette, R. A., Zhao, J., Cole, S. L., Eimer, W. A., Hitt, B. D., Bembinster, L. A., Lammich, S., et al. (2008) · Neuron · doi:10.1016/j.neuron.2008.10.047 · Cited by 422 · see citing works
Rajasekhar, V. K., Viale, A., Socci, N. D., Wiedmann, M., Hu, X., & Holland, E. C. (2003) · Molecular Cell · doi:10.1016/s1097-2765(03)00395-2 · Cited by 420 · see citing works
Noise Minimization in Eukaryotic Gene Expression
Fraser, H. B., Hirsh, A. E., Giaever, G. N., Kumm, J., & Eisen, M. B. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020137 · Cited by 419 · see citing works
Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays
Tenenbaum, S. A., Carson, C. C., Lager, P. J., & Keene, J. D. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.26.14085 · Cited by 397 · see citing works
Jordanova, A., Irobi, J., Thomas, F. P., Dijck, P. V., Meerschaert, K., Dewil, M., Dierick, I., Jacobs, A., Vriendt, E. D., Guergueltcheva, V., et al. (2006) · Nature Genetics · doi:10.1038/ng1727 · Cited by 378 · see citing works
Ubiquitin-Like Protein Involved in the Proteasome Pathway of Mycobacterium tuberculosis
Pearce, M. J., Mintseris, J., Ferreyra, J. A., Gygi, S. P., & Darwin, K. H. (2008) · Science · doi:10.1126/science.1163885 · Cited by 377 · see citing works
The role of mRNA and protein stability in gene expression
Hargrove, J. L., & Schmidt, F. H. (1989) · The FASEB Journal · doi:10.1096/fasebj.3.12.2676679 · Cited by 371 · see citing works
ELAV/Hu proteins inhibit p27 translation via an IRES element in the p27 5′UTR
Kullmann, M., Göpfert, U., Siewe, B., & Hengst, L. (2002) · Genes & Development · doi:10.1101/gad.248902 · Cited by 327 · see citing works
Kempe, S. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki836 · Cited by 284 · see citing works
Gerber, A. P., Luschnig, S., Krasnow, M. A., Brown, P. O., & Herschlag, D. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0509260103 · Cited by 277 · see citing works
Dual function of the messenger RNA cap structure in poly(A)-tail-promoted translation in yeast
Preiß, T., & Hentze, M. W. (1998) · Nature · doi:10.1038/33192 · Cited by 270 · see citing works
Pascal, L. E., True, L. D., Campbell, D. S., Deutsch, E. W., Risk, M. C., Coleman, I. M., Eichner, L. J., Nelson, P. S., & Liu, A. Y. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-246 · Cited by 267 · see citing works
Wnt-5a has tumor suppressor activity in thyroid carcinoma
Kremenevskaja, N., von Wasielewski, R., Rao, A., Schöfl, C., Andersson, T., & Brabant, G. E. (2005) · Oncogene · doi:10.1038/sj.onc.1208370 · Cited by 260 · see citing works
Abdelmohsen, K., Kuwano, Y., Kim, H. H., & Gorospe, M. (2008) · Biological Chemistry · doi:10.1515/bc.2008.022 · Cited by 258 · see citing works
Codon usage and genome evolution
Sharp, P. M., & Matassi, G. (1994) · Current Opinion in Genetics & Development · doi:10.1016/0959-437x(94)90070-1 · Cited by 253 · see citing works
Immunopurification of Polyribosomal Complexes of Arabidopsis for Global Analysis of Gene Expression
Zanetti, M. E., Chang, I., Gong, F., Galbraith, D. W., & Bailey-Serres, J. N. (2005) · PLANT PHYSIOLOGY · doi:10.1104/pp.105.059477 · Cited by 251 · see citing works
Mechanism of ubiquitin activation revealed by the structure of a bacterial MoeB–MoaD complex
Lake, M. W., Wuebbens, M. M., Rajagopalan, K. V., et al. (2001) · Nature · doi:10.1038/35104586 · Cited by 251 · see citing works
Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale
Beyer, A., Hollunder, J., Nasheuer, H.-P., & Wilhelm, T. (2004) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m400099-mcp200 · Cited by 248 · see citing works
Nie, L., Wu, G., & Zhang, W. (2006) · Genetics · doi:10.1534/genetics.106.065862 · Cited by 245 · see citing works
MicroRNAs: Control and Loss of Control in Human Physiology and Disease
Li, M., Marín‐Müller, C., Bharadwaj, U., Chow, K.-H., Yao, Q. C., & Chen, C. (2008) · World Journal of Surgery · doi:10.1007/s00268-008-9836-x · Cited by 241 · see citing works
Schwartz, D. C., & Parker, R. (1999) · Molecular and Cellular Biology · doi:10.1128/mcb.19.8.5247 · Cited by 235 · see citing works
Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes
Raghavan, A. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf682 · Cited by 233 · see citing works
Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes
Schrimpf, S. P., Weiss, M., Reiter, L., Ahrens, C. H., Jovanovic, M., Malmström, J., Brunner, E., Mohanty, S., Lercher, M. J., Hunziker, P. E., et al. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000048 · Cited by 229 · see citing works
Translation initiation: structures, mechanisms and evolution
Marintchev, A., & Wagner, G. (2004) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583505004026 · Cited by 223 · see citing works
Translational pathophysiology: a novel molecular mechanism of human disease
Cazzola, M., & Skoda, R. C. (2000) · Blood · doi:10.1182/blood.v95.11.3280 · Cited by 222 · see citing works
Toward a structural understanding of IRES RNA function
Filbin, M., & Kieft, J. S. (2009) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2009.03.005 · Cited by 219 · see citing works
Lehner, B. (2008) · Molecular Systems Biology · doi:10.1038/msb.2008.11 · Cited by 218 · see citing works
A novel function for fragile X mental retardation protein in translational activation
Bechara, E. G., Didiot, M. C., Melko, M., Davidovic, L., Bensaid, M., Martin, P., Castets, M., Pognonec, P., Khandjian, E. W., Moine, H., et al. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000016 · Cited by 206 · see citing works
A Network of Multiple Regulatory Layers Shapes Gene Expression in Fission Yeast
Lackner, D. H., Beilharz, T. H., Marguerat, S., Mata, J., Watt, S., Schubert, F., Preiss, T., & Bähler, J. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.03.002 · Cited by 204 · see citing works
Posttranscriptional expression regulation: what determines translation rates?
Brockmann, R., Beyer, A., Heinisch, J. J., & Wilhelm, T. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030057 · Cited by 201 · see citing works
Regulation of Cyclooxygenase-2 Expression by the Translational Silencer TIA-1
Dixon, D. A., Balch, G. C., Kedersha, N., Anderson, P. J., Zimmerman, G. A., Beauchamp, R. D., & Prescott, S. M. (2003) · The Journal of Experimental Medicine · doi:10.1084/jem.20030616 · Cited by 197 · see citing works
Neural RNA-binding protein Musashi1 inhibits translation initiation by competing with eIF4G for PABP
Kawahara, H., Imai, T., Imataka, H., Tsujimoto, M., Matsumoto, K., & Okano, H. (2008) · The Journal of Cell Biology · doi:10.1083/jcb.200708004 · Cited by 196 · see citing works
mRNA sequence features that contribute to translational regulation in Arabidopsis
Kawaguchi, R. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki240 · Cited by 195 · see citing works
SCF-mediated protein degradation and cell cycle control
Cambronne, X. A., & Harper, J. W. (2005) · Oncogene · doi:10.1038/sj.onc.1208614 · Cited by 193 · see citing works
Nie, L., Wu, G., & Zhang, W. (2006) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2005.11.055 · Cited by 191 · see citing works
Gene Expression Analyzed by High-resolution State Array Analysis and Quantitative Proteomics
MacKay, V. L., Li, X., Flory, M. R., Turcott, E., Law, G. L., Serikawa, K. A., Xu, X. L., Lee, H., Goodlett, D. R., Aebersold, R. H., et al. (2004) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m300129-mcp200 · Cited by 189 · see citing works
Grolleau‐Julius, A., Bowman, J., Pradet‐Balade, B., Puravs, E., Hanash, S., García‐Sanz, J. A., & Beretta, L. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m202014200 · Cited by 187 · see citing works
Floyd, Z. E., & Stephens, J. M. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m108473200 · Cited by 187 · see citing works
Phosphorylation of a Pest Sequence in ABCA1 Promotes Calpain Degradation and Is Reversed by ApoA-I
Martinez, L. O., Agerholm-Larsen, B., Wang, N., Chen, W., & Tall, A. R. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m307161200 · Cited by 186 · see citing works
Expression of stem cell markers in human astrocytomas of different WHO grades
Ma, Y.-H., Mentlein, R., Knerlich‐Lukoschus, F., Kruse, M., Mehdorn, H. M., & Held‐Feindt, J. (2007) · Journal of Neuro-Oncology · doi:10.1007/s11060-007-9439-7 · Cited by 178 · see citing works
Toward a protein profile of Escherichia coli : Comparison to its transcription profile
Corbin, R. W., Paliy, O., Yang, F., Shabanowitz, J., Platt, M., Lyons, C. E., Root, K. E., McAuliffe, J., Jordan, M. I., Kustu, S. G., et al. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1533294100 · Cited by 177 · see citing works
Unwin, R. D., Smith, D. L., Blinco, D., Wilson, C., Miller, C. J., Evans, C. A., Jaworska, E., Baldwin, S. A., Barnes, K., Pierce, A., et al. (2006) · Blood · doi:10.1182/blood-2005-12-4995 · Cited by 173 · see citing works
Cell-to-Cell Stochastic Variation in Gene Expression Is a Complex Genetic Trait
Ansel, J., Duplus‐Bottin, H., Rodriguez-Beltran, C., Damon‐Soubeyrand, C., Nagarajan, M., Fehrmann, S., François, J., & Yvert, G. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000049 · Cited by 169 · see citing works
Kierzek, A. M., Zaim, J., & Zielenkiewicz, P. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m006264200 · Cited by 167 · see citing works
FMRP interferes with the Rac1 pathway and controls actin cytoskeleton dynamics in murine fibroblasts
Castets, M., Schaeffer, C., Bechara, E., Schenck, A., Khandjian, E. W., Luche, S., Moine, H., Rabilloud, T., Mandel, J.-L., & Bardoni, B. (2005) · Human Molecular Genetics · doi:10.1093/hmg/ddi077 · Cited by 162 · see citing works
Preiß, T., Baron-Benhamou, J., Ansorge, W. J., & Hentze, M. W. (2003) · Nature Structural & Molecular Biology · doi:10.1038/nsb1015 · Cited by 158 · see citing works
microRNAs and muscle disorders
Chen, J., Callis, T. E., & Wang, D. (2008) · Journal of Cell Science · doi:10.1242/jcs.041723 · Cited by 158 · see citing works
Rogers, J. T., Bush, A. I., Cho, H.-H., Smith, D. H., Thomson, A. M., Friedlich, A. L., Lahiri, D. K., Leedman, P. J., Huang, X., & Cahill, C. M. (2008) · Biochemical Society Transactions · doi:10.1042/bst0361282 · Cited by 148 · see citing works
Hierarchy of Sequence-Dependent Features Associated With Prokaryotic TranslationPreprint
Lithwick, G. (2003) · Genome Research · doi:10.1101/gr.1485203 · Cited by 146 · see citing works
Modulation of a Transcription Factor Counteracts Heterochromatic Gene Silencing in Drosophila
Ahmad, K., & Henikoff, S. (2001) · Cell · doi:10.1016/s0092-8674(01)00281-1 · Cited by 141 · see citing works
Chappell, S. A., LeQuesne, J., Paulin, F., et al. (2000) · Oncogene · doi:10.1038/sj.onc.1203791 · Cited by 140 · see citing works
Lichtinghagen, R., Musholt, P. B., Lein, M., et al. (2002) · European Urology · doi:10.1016/s0302-2838(02)00324-x · Cited by 139 · see citing works
Folding Free Energies of 5′-UTRs Impact Post-Transcriptional Regulation on a Genomic Scale in Yeast
Ringnér, M., & Krogh, M. (2005) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0010072 · Cited by 139 · see citing works
One-step affinity purification of the yeast ribosome and its associated proteins and mRNAs
Inada, T., Winstall, É., Tarun, S. Z., Yates, J. R., SCHIELTZ, D., & Sachs, A. B. (2002) · RNA · doi:10.1017/s1355838202026018 · Cited by 137 · see citing works
Kanemura, Y., Yamasaki, M., Mori, K., Fujikawa, H., Hayashi, H., Nakano, A., Matsumoto, T., Tamura, K., Arita, N., Sakakibara, S., et al. (2001) · Differentiation · doi:10.1046/j.1432-0436.2001.680208.x · Cited by 134 · see citing works
Man, O., & Pilpel, Y. (2007) · Nature Genetics · doi:10.1038/ng1967 · Cited by 133 · see citing works
FMRP RNA targets: identification and validation
Darnell, J. C., Mostovetsky, O., & Darnell, R. B. (2005) · Genes Brain & Behavior · doi:10.1111/j.1601-183x.2005.00144.x · Cited by 132 · see citing works
Paul, S. (2008) · BioEssays · doi:10.1002/bies.20852 · Cited by 131 · see citing works
Dissecting eukaryotic translation and its control by ribosome density mapping
Arava, Y. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki331 · Cited by 129 · see citing works
Foth, B. J., Zhang, N., Mok, S., Preiser, P. R., & Bozdech, Z. (2008) · Genome biology · doi:10.1186/gb-2008-9-12-r177 · Cited by 128 · see citing works
Ubiquitination of PCNA and the Polymerase Switch in Human Cells
Kannouche, P. L., & Lehmann, A. R. (2004) · Cell Cycle · doi:10.4161/cc.3.8.1074 · Cited by 127 · see citing works
Determinants of Protein Abundance and Translation Efficiency in S. cerevisiae
Tuller, T., Kupiec, M., & Ruppin, E. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030248 · Cited by 124 · see citing works
Antonellis, A., Lee-Lin, S.-Q., Wasterlain, A. S., et al. (2006) · Journal of Neuroscience · doi:10.1523/jneurosci.1671-06.2006 · Cited by 122 · see citing works
Mehra, A., Lee, K. H., & Vassily Hatzimanikatis, A. (2003) · Biotechnology and Bioengineering · doi:10.1002/bit.10860 · Cited by 120 · see citing works
Harris, M. N., Özpolat, B., Abdi, F. A., Gu, S., Legler, A., Mawuenyega, K. G., Tírado-Gómez, M., Lopez‐Berestein, G., & Chen, X. (2004) · Blood · doi:10.1182/blood-2004-01-0046 · Cited by 115 · see citing works
Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe
Schmidt, M. W., Houseman, A., Ivanov, A. R., & Wolf, D. A. (2007) · Molecular Systems Biology · doi:10.1038/msb4100117 · Cited by 114 · see citing works
Uncovering Genes with Divergent mRNA-Protein Dynamics in Streptomyces coelicolor
Jayapal, K. P., Philp, R. J., Kok, Y. J., Yap, M. G. S., Sherman, D. H., Griffin, T. J., & Hu, W. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002097 · Cited by 113 · see citing works
Role of two upstream open reading frames in the translational control of oncogene mdm2
Brown, C. Y., Mize, G. J., Pineda, M. J., George, D. L., & Morris, D. (1999) · Oncogene · doi:10.1038/sj.onc.1202949 · Cited by 110 · see citing works
Overexpression of ribosomal protein L15 is associated with cell proliferation in gastric cancer
Wang, H., Zhao, L., Li, K.-Z., Ling, R., Li, X., & Wang, L. (2006) · BMC Cancer · doi:10.1186/1471-2407-6-91 · Cited by 108 · see citing works
Structural disorder serves as a weak signal for intracellular protein degradation
Tompa, P., Prilusky, J., Silman, I., & Sussman, J. L. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21773 · Cited by 107 · see citing works
Cahill, C. M., Lahiri, D. K., Huang, X., & Rogers, J. T. (2008) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2008.12.001 · Cited by 107 · see citing works
Lin, B., White, J. T., Lu, W., Xie, T., Utleg, A. G., Yan, X. S., Yi, E. C., Shannon, P. T., Khrebtukova, I., Lange, P. H., et al. (2005) · Cancer Research · doi:10.1158/0008-5472.can-04-3218 · Cited by 102 · see citing works
The fragile X syndrome: exploring its molecular basis and seeking a treatment
Bardoni, B., Davidovic, L., Bensaid, M., & Khandjian, É. W. (2006) · Expert Reviews in Molecular Medicine · doi:10.1017/s1462399406010751 · Cited by 100 · see citing works
Solution structure of ThiS and implications for the evolutionary roots of ubiquitin.
Nicholson, L. K., Wang, C., Xi, J., & Begley, T. P. (2001) · Nature Structural Biology · doi:10.1038/83041 · Cited by 100 · see citing works
Orntoft, T. F., Thykjær, T., Waldman, F. M., Wolf, H., & Celis, J. E. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m100019-mcp200 · Cited by 99 · see citing works
Differential Expression of Ribosomal Proteins in Human Normal and Neoplastic Colorectum
Kasai, H., Nadano, D., Hidaka, E., Higuchi, K., Kawakubo, M., Sato, T., & Nakayama, J. (2003) · Journal of Histochemistry & Cytochemistry · doi:10.1177/002215540305100502 · Cited by 97 · see citing works
The involvement of mRNA secondary structure in protein synthesis
Pelletier, J., & Sonenberg, N. (1987) · Biochemistry and Cell Biology · doi:10.1139/o87-074 · Cited by 97 · see citing works
Meijer, H. A., Bushell, M., Hill, K., Gant, T. W., Willis, A. E., Jones, P., & de Moor, C. H. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm830 · Cited by 96 · see citing works
Howson, R. W., Huh, W., Ghaemmaghami, S., Falvo, J. V., Bower, K., Belle, A., Dephoure, N., Wykoff, D. D., Weissman, J. S., & O’Shea, E. K. (2005) · Comparative and Functional Genomics · doi:10.1002/cfg.449 · Cited by 93 · see citing works
Wnt-5a mRNA translation is suppressed by the Elav-like protein HuR in human breast epithelial cells
Leandersson, K., Riesbeck, K., & Andersson, T. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl571 · Cited by 92 · see citing works
Low expression of Wnt-5a gene is associated with high-risk neuroblastoma
Blanc, É., Roux, G. L., Bénard, J., & Raguénez, G. (2004) · Oncogene · doi:10.1038/sj.onc.1208255 · Cited by 91 · see citing works
Schulenburg, A., Cech, P., Herbacek, I., et al. (2007) · The Journal of Pathology · doi:10.1002/path.2220 · Cited by 81 · see citing works
Integrating shotgun proteomics and mRNA expression data to improve protein identification
Ramakrishnan, S. R., Vogel, C., Prince, J. T., Wang, R., Li, Z., Penalva, L. O. F., Myers, M., Marcotte, E. M., & Miranker, D. P. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp168 · Cited by 79 · see citing works
Self-citationJin, X., Turcott, E., Englehardt, S., Mize, G. J., & Morris, D. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m300316200 · Cited by 79 · see citing works
Wu, G., Nie, L., & Zhang, W. (2008) · Current Microbiology · doi:10.1007/s00284-008-9145-5 · Cited by 77 · see citing works
Thrombopoietin Production Is Inhibited by a Translational Mechanism
Ghilardi, N., Wiestner, A. C., & Skoda, R. C. (1998) · Blood · doi:10.1182/blood.v92.11.4023 · Cited by 77 · see citing works
Cap-independent regulation of gene expression in apoptosis
Graber, T. E., & Holčı́k, M. (2007) · Molecular BioSystems · doi:10.1039/b708867a · Cited by 75 · see citing works
Spencer, M. L., Theodosiou, M., & Noonan, D. J. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m402507200 · Cited by 74 · see citing works
Regulation of COX-2 Expression in Human Cancers
Dixon, D. A. (2003) · KARGER eBooks · doi:10.1159/000071363 · Cited by 73 · see citing works
Evolutionary constraints on yeast protein size
Warringer (2006) · BMC Evolutionary Biology · doi:10.1186/1471-2148-6-61 · Cited by 71 · see citing works
Activation of the ribosomal protein L13 gene in human gastrointestinal cancer
Kobayashi, T., Sasaki, Y., Oshima, Y., Yamamoto, H., Mita, H., Suzuki, H., Toyota, M., Tokino, T., Itoh, F., Imai, K., et al. (2006) · International Journal of Molecular Medicine · doi:10.3892/ijmm.18.1.161 · Cited by 66 · see citing works
Trading translation with RNA-binding proteins
Abaza, I., & Gebauer, F. (2008) · RNA · doi:10.1261/rna.848208 · Cited by 62 · see citing works
Nie, L., Wu, G., Brockman, F. J., & Zhang, W. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl134 · Cited by 58 · see citing works
Chapter 5 Translational Control of Gene Expression
Lackner, D. H., & Bähler, J. (2008) · International review of cytology · doi:10.1016/s1937-6448(08)01205-7 · Cited by 58 · see citing works
Targeting the eIF4F translation initiation complex for cancer therapy
Konicek, B. W., Dumstorf, C. A., & Graff, J. R. (2008) · Cell Cycle · doi:10.4161/cc.7.16.6464 · Cited by 57 · see citing works
Ciechanover, A. J. (2007) · Annals of the New York Academy of Sciences · doi:10.1196/annals.1402.078 · Cited by 51 · see citing works
An Algorithmic Framework for Genome-Wide Modeling and Analysis of Translation Networks
Mehra, A., & Hatzimanikatis, V. (2005) · Biophysical Journal · doi:10.1529/biophysj.105.062521 · Cited by 49 · see citing works
Quantitative Aspects of Protein Induction
Yagil, G. (1975) · Current topics in cellular regulation · doi:10.1016/b978-0-12-152809-6.50013-5 · Cited by 44 · see citing works
Expression of the Neural RNA-Binding Protein Musashi1 in Pediatric Brain Tumors
Nakano, A., Kanemura, Y., Mori, K., et al. (2007) · Pediatric Neurosurgery · doi:10.1159/000103307 · Cited by 42 · see citing works
Miyasaka, H. (2002) · Journal of Molecular Evolution · doi:10.1007/s00239-001-0090-1 · Cited by 34 · see citing works
Common gene expression strategies revealed by genome-wide analysis in yeast
García‐Martínez, J., Gónzález‐Candelas, F., & Pérez-Ortín, J. E. (2007) · Genome biology · doi:10.1186/gb-2007-8-10-r222 · Cited by 33 · see citing works
Biotinylated Tags for Recovery and Characterization of Ribonucleoprotein Complexes
Penalva, L. O. F., & Keene, J. D. (2004) · BioTechniques · doi:10.2144/04374st05 · Cited by 31 · see citing works
Self-citationEames, M., & Kortemme, T. (2007) · Structure · doi:10.1016/j.str.2007.09.010 · Cited by 30 · see citing works
The ubiquitin‐proteasome pathway and enhanced activity of NF‐κB in gastric carcinoma
Wu, L., Pu, Z., Feng, J., et al. (2007) · Journal of Surgical Oncology · doi:10.1002/jso.20952 · Cited by 25 · see citing works
On the origin of the cap-dependent initiation of translation in eukaryotes
Hernández, G. (2009) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2009.02.001 · Cited by 21 · see citing works
Coleman, J., & Miskimins, W. K. (2009) · RNA Biology · doi:10.4161/rna.6.1.7572 · Cited by 21 · see citing works
Divergence in cis-regulatory networks: taking the 'species' out of cross-species analysis
Zinzen, R. P., & Furlong, E. E. M. (2008) · Genome biology · doi:10.1186/gb-2008-9-11-240 · Cited by 10 · see citing works
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- [24]Ralston A Nat. Educ 2008 1 1 http://www.nature.com/scitable/topicpage/Simultaneous-Gene-Transcription-and-Translation-in-Bacteria-1025.
- [40]Vijay-Kumar S Bugg CE Wilkinson KD Vierstra RD Hatfield PM Cook WJ J. Biol. Chem 1987 262 13 6396 6399 3032965
- [157]Seigel GM Hackam AS Ganguly A Mandell LM Gonzalez-Fernandez F Mol. Vision 2007 13 823 832 PMC2768758 17615543
- [163]Kondoh N Shuda M Tanaka K Wakatsuki T Hada A Yamamoto M Anticancer Res 2001 21 4A 2429 2433 11724303
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Global quantification of mammalian gene expression control
Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., & Selbach, M. (2011) · Nature · doi:10.1038/nature10098 · Cited by 6,566 · see citing works
Insights into the regulation of protein abundance from proteomic and transcriptomic analyses
Vogel, C., & Marcotte, E. M. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3185 · Cited by 4,195 · see citing works
Self-citationA survey of best practices for RNA-seq data analysis
Conesa, A., Madrigal, P., Tarazona, S., Gomez-Cabrero, D., Cervera, A., McPherson, A., Szcześniak, M. W., Gaffney, D. J., Elo, L. L., Zhang, X., et al. (2016) · Genome Biology · doi:10.1186/s13059-016-0881-8 · Cited by 2,794 · see citing works
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CPTAC, T. N., Zhang, B., Wang, J., Wang, X., Zhu, J., Liu, Q., Shi, Z., Chambers, M. C., Zimmerman, L. J., Shaddox, K. F., et al. (2014) · Nature · doi:10.1038/nature13438 · Cited by 1,462 · see citing works
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Liu, Y., Yang, M., Deng, Y., Su, G., Enninful, A., Guo, C. C., Tebaldi, T., Zhang, D., Kim, D., Bai, Z., et al. (2020) · Cell · doi:10.1016/j.cell.2020.10.026 · Cited by 966 · see citing works
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Nagaraj, N., Wisniewski, J. R., Geiger, T., Cox, J., Kircher, M., Kelso, J., Pääbo, S., & Mann, M. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.81 · Cited by 979 · see citing works
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Sharma, K., Schmitt, S., Bergner, C. G., Tyanova, S., Kannaiyan, N., Manrique-Hoyos, N., Kongi, K., Cantuti, L., Hanisch, U.-K., Philips, M.-A., et al. (2015) · Nature Neuroscience · doi:10.1038/nn.4160 · Cited by 871 · see citing works
Vogel, C., de Sousa Abreu, R., Ko, D., Le, S., Shapiro, B. A., Burns, S. C., Sandhu, D., Boutz, D. R., Marcotte, E. M., & Penalva, L. O. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.59 · Cited by 608 · see citing works
Self-citationSeyfried, N. T., Dammer, E. B., Swarup, V., Nandakumar, D., Duong, D. M., Yin, L., Deng, Q., Nguyen, T., Hales, C. M., Wingo, T., et al. (2017) · Cell Systems · doi:10.1016/j.cels.2016.11.006 · Cited by 477 · see citing works
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Guneykaya, D., Ivanov, A., Hernandez, D. P., Haage, V., Wojtas, B., Meyer, N., Maricos, M., Jordan, P., Buonfiglioli, A., Gielniewski, B., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.08.001 · Cited by 477 · see citing works
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Lundberg, E., Fagerberg, L., Klevebring, D., Matic, I., Geiger, T., Cox, J., Älgenäs, C., Lundeberg, J., Mann, M., & Uhlen, M. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.106 · Cited by 373 · see citing works
Variation and genetic control of protein abundance in humans
Wu, L., Candille, S. I., Choi, Y., Xie, D., Jiang, L., Li-Pook-Than, J., Tang, H., & Snyder, M. (2013) · Nature · doi:10.1038/nature12223 · Cited by 364 · see citing works
Quantification of mRNA and protein and integration with protein turnover in a bacterium
Maier, T., Schmidt, A., Güell, M., Kühner, S., Gavin, A., Aebersold, R., & Serrano, L. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.38 · Cited by 297 · see citing works
Li, J. J., Bickel, P. J., & Biggin, M. D. (2014) · PeerJ · doi:10.7717/peerj.270 · Cited by 279 · see citing works
The Size of the Human Proteome: The Width and Depth
Ponomarenko, E. A., Poverennaya, E. V., Ilgisonis, E. V., Pyatnitskiy, M. A., Kopylov, A. T., Zgoda, V. G., Lisitsa, A. V., & Archakov, A. I. (2016) · International Journal of Analytical Chemistry · doi:10.1155/2016/7436849 · Cited by 267 · see citing works
Csárdi, G., Franks, A., Choi, D. S., Airoldi, E. M., & Drummond, D. A. (2015) · PLOS Genetics · doi:10.1371/journal.pgen.1005206 · Cited by 181 · see citing works
Protein abundances are more conserved than mRNA abundances across diverse taxa
Laurent, J. M., Vogel, C., Kwon, T., Craig, S. A., Boutz, D. R., Huse, H. K., Nozue, K., Walia, H., Whiteley, M., Ronald, P. C., et al. (2010) · PROTEOMICS · doi:10.1002/pmic.201000327 · Cited by 156 · see citing works
Self-citationEvolution at two levels of gene expression in yeast
Artieri, C. G., & Fraser, H. B. (2014) · Genome Research · doi:10.1101/gr.165522.113 · Cited by 138 · see citing works
Multi-omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency
Yang, P., Humphrey, S. J., Cinghu, S., Pathania, R., Oldfield, A. J., Kumar, D., Perera, D., Yang, J. Y. H., James, D. E., Mann, M., et al. (2019) · Cell Systems · doi:10.1016/j.cels.2019.03.012 · Cited by 146 · see citing works
Systems-based proteomics to resolve the biology of Alzheimer’s disease beyond amyloid and tau
Rayaprolu, S., Higginbotham, L., Bagchi, P., Watson, C. M., Zhang, T., Levey, A. I., Rangaraju, S., & Seyfried, N. T. (2021) · Neuropsychopharmacology · doi:10.1038/s41386-020-00840-3 · Cited by 118 · see citing works
“These findings, consistent with previous comparisons of protein and mRNA data [65], strongly support the utility of protein profiling in AD and its complementarity with transcriptomic studies.”
ResultGenetic control of the human brain proteome
Robins, C., Wingo, A. P., Fan, W., Duong, D. M., Meigs, J., Gerasimov, E. S., Dammer, E. B., Cutler, D. J., Jager, P. L. D., Bennett, D. A., et al. (2019) · doi:10.1101/816652 · Cited by 104 · see citing works
Thévenin, A., Ein-Dor, L., Ozery-Flato, M., & Shamir, R. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku667 · Cited by 84 · see citing works
Beck, M., Claassen, M., & Aebersold, R. (2011) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2010.09.002 · Cited by 83 · see citing works
Rayaprolu, S., Gao, T., Xiao, H., Ramesha, S., Weinstock, L. D., Shah, J., Duong, D. M., Dammer, E. B., Webster, J. A., Lah, J. J., et al. (2019) · doi:10.1101/802694 · Cited by 71 · see citing works
Xiong, Q., Feng, J., Li, S.-T., Zhang, G.-Y., Qiao, Z.-X., Chen, Z., Wu, Y., Lin, Y., Li, T., Ge, F., et al. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.046003 · Cited by 64 · see citing works
Altered Myokine Secretion Is an Intrinsic Property of Skeletal Muscle in Type 2 Diabetes
Ciaraldi, T. P., Ryan, A. J., Mudaliar, S. R., & Henry, R. R. (2016) · PLOS ONE · doi:10.1371/journal.pone.0158209 · Cited by 66 · see citing works
A practical data processing workflow for multi-OMICS projects
Kohl, M., Megger, D. A., Trippler, M., Meckel, H., Ahrens, M., Bracht, T., Weber, F., Hoffmann, A.-C., Baba, H. A., Sitek, B., et al. (2014) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2013.02.029 · Cited by 60 · see citing works
Transcriptional responses to DNA damage
Silva, E., & Ideker, T. (2019) · DNA repair · doi:10.1016/j.dnarep.2019.05.002 · Cited by 31 · see citing works
Kaulich, E., Waselenchuk, Q., Fürst, N., Desch, K., Mosbacher, J., Ciirdaeva, E., Juengling, M., Tushev, G., Langer, J., & Schuman, E. M. (2024) · doi:10.1101/2024.08.05.606570 · Cited by 22 · see citing works
Sullivan, D. I., Jiang, M., Hinchie, A. M., Roth, M. G., Bahudhanapati, H., Nouraie, M., Liu, J., McDyer, J. F., Mallampalli, R. K., Zhang, Y., et al. (2021) · Frontiers in Medicine · doi:10.3389/fmed.2021.600626 · Cited by 16 · see citing works
- Authors
- de Sousa Abreu, R., Penalva, L. O., Marcotte, E. M., & Vogel, C.
- Affiliations
- Children’s Cancer Research Institute, University of Texas Health Science Center at San Antonio a , TX, USA
- The University of Texas at San Antonio Health Science Center (US)
- The University of Texas at Austin (US)
- Corresponding author
- Vogel, Christine
- Venue
- Molecular BioSystems
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-10-01
- Volume
- 5
- Issue
- 12
- Pages
- 1512-1526
- ISSN
- 1742-2051 (ISSN-L)
- 1742-206X
- PMC
- PMC4089977
- OpenAlex
- W2056710301
- Cited by
- 1,248
- References
- 187
- Citations by year
- 2026: 32 · 2025: 58 · 2024: 76 · 2023: 99 · 2022: 108 · 2021: 91 · 2020: 99 · 2019: 104 · 2018: 93 · 2017: 85 · 2016: 78 · 2015: 85 · 2014: 85 · 2013: 60 · 2012: 43
- FWCI
- 2.42
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Molecular BioSystems (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Cancer Research Institute
- National Institute of General Medical Sciences (R01GM076536)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- protein abundance, mRNA levels, mRNA-protein correlation, gene expression regulation, translation (biology), protein degradation, mRNA stability, large-scale proteomics
- MeSH terms
- Escherichia coli, Humans, Proteins, RNA, Messenger, Protein Biosynthesis, Yeasts, Computational Biology, Ubiquitination
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