-
1
-
-
84904872156
-
The growing landscape of lysine acetylation links metabolism and cell signalling
-
Choudhary, C., Weinert, B. T., Nishida, Y., Verdin, E., and Mann, M. (2014) The growing landscape of lysine acetylation links metabolism and cell signalling. Nat. Rev. 15, 536-550
-
(2014)
Nat. Rev.
, vol.15
, pp. 536-550
-
-
Choudhary, C.1
Weinert, B.T.2
Nishida, Y.3
Verdin, E.4
Mann, M.5
-
2
-
-
57749170458
-
The many roles of histone deacetylases in development and physiology: Implications for disease and therapy
-
Haberland, M., Montgomery, R. L., and Olson, E. N. (2009) The many roles of histone deacetylases in development and physiology: implications for disease and therapy. Nat. Rev. 10, 32-42
-
(2009)
Nat. Rev.
, vol.10
, pp. 32-42
-
-
Haberland, M.1
Montgomery, R.L.2
Olson, E.N.3
-
3
-
-
0034912742
-
Histone acetyltransferases
-
Roth, S. Y., Denu, J. M., and Allis, C. D. (2001) Histone acetyltransferases. Ann. Rev. Biochem. 70, 81-120
-
(2001)
Ann. Rev. Biochem.
, vol.70
, pp. 81-120
-
-
Roth, S.Y.1
Denu, J.M.2
Allis, C.D.3
-
4
-
-
0034051227
-
Acetylation of histones and transcription-related factors
-
Sterner, D. E., and Berger, S. L. (2000) Acetylation of histones and transcription-related factors. Microbiol. Mol. Biol. Rev. 64, 435-459
-
(2000)
Microbiol. Mol. Biol. Rev.
, vol.64
, pp. 435-459
-
-
Sterner, D.E.1
Berger, S.L.2
-
5
-
-
79954415619
-
Comprehensive lysine acetylomes emerging from bacteria to humans
-
Kim, G. W., and Yang, X. J. (2011) Comprehensive lysine acetylomes emerging from bacteria to humans. Trends Biochem. Sci. 36, 211-220
-
(2011)
Trends Biochem. Sci.
, vol.36
, pp. 211-220
-
-
Kim, G.W.1
Yang, X.J.2
-
6
-
-
33746992118
-
Substrate and functional diversity of lysine acetylation revealed by a proteomics survey
-
Kim, S. C., Sprung, R., Chen, Y., Xu, Y., Ball, H., Pei, J., Cheng, T., Kho, Y., Xiao, H., Xiao, L., Grishin, N. V., White, M., Yang, X. J., and Zhao, Y. (2006) Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol. Cell 23, 607-618
-
(2006)
Mol. Cell
, vol.23
, pp. 607-618
-
-
Kim, S.C.1
Sprung, R.2
Chen, Y.3
Xu, Y.4
Ball, H.5
Pei, J.6
Cheng, T.7
Kho, Y.8
Xiao, H.9
Xiao, L.10
Grishin, N.V.11
White, M.12
Yang, X.J.13
Zhao, Y.14
-
7
-
-
84905378213
-
Stoichiometry of site-specific lysine acetylation in an entire proteome
-
Baeza, J., Dowell, J. A., Smallegan, M. J., Fan, J., Amador-Noguez, D., Khan, Z., and Denu, J. M. (2014) Stoichiometry of site-specific lysine acetylation in an entire proteome. J. Biol. Chem. 289, 21326-21338
-
(2014)
J. Biol. Chem.
, vol.289
, pp. 21326-21338
-
-
Baeza, J.1
Dowell, J.A.2
Smallegan, M.J.3
Fan, J.4
Amador-Noguez, D.5
Khan, Z.6
Denu, J.M.7
-
8
-
-
84898012537
-
Acetylation dynamics and stoichiometry in Saccharomyces cerevisiae
-
Weinert, B. T., Iesmantavicius, V., Moustafa, T., Scholz, C., Wagner, S. A., Magnes, C., Zechner, R., and Choudhary, C. (2014) Acetylation dynamics and stoichiometry in Saccharomyces cerevisiae. Mol. Syst. Biol. 10, 716
-
(2014)
Mol. Syst. Biol.
, vol.10
, pp. 716
-
-
Weinert, B.T.1
Iesmantavicius, V.2
Moustafa, T.3
Scholz, C.4
Wagner, S.A.5
Magnes, C.6
Zechner, R.7
Choudhary, C.8
-
9
-
-
84867186480
-
Quantitative acetylome analysis reveals the roles of SIRT1 in regulating diverse substrates and cellular pathways
-
Chen, Y., Zhao, W., Yang, J. S., Cheng, Z., Luo, H., Lu, Z., Tan, M., Gu, W., and Zhao, Y. (2012) Quantitative acetylome analysis reveals the roles of SIRT1 in regulating diverse substrates and cellular pathways. Mol. Cell. Proteomics 11, 1048-1062
-
(2012)
Mol. Cell. Proteomics
, vol.11
, pp. 1048-1062
-
-
Chen, Y.1
Zhao, W.2
Yang, J.S.3
Cheng, Z.4
Luo, H.5
Lu, Z.6
Tan, M.7
Gu, W.8
Zhao, Y.9
-
10
-
-
68949212379
-
Lysine acetylation targets protein complexes and co-regulates major cellular functions
-
Choudhary, C., Kumar, C., Gnad, F., Nielsen, M. L., Rehman, M., Walther, T. C., Olsen, J. V., and Mann, M. (2009) Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325, 834-840
-
(2009)
Science
, vol.325
, pp. 834-840
-
-
Choudhary, C.1
Kumar, C.2
Gnad, F.3
Nielsen, M.L.4
Rehman, M.5
Walther, T.C.6
Olsen, J.V.7
Mann, M.8
-
11
-
-
84872276165
-
Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome
-
Hebert, A. S., Dittenhafer-Reed, K. E., Yu, W., Bailey, D. J., Selen, E. S., Boersma, M. D., Carson, J. J., Tonelli, M., Balloon, A. J., Higbee, A. J., Westphall, M. S., Pagliarini, D. J., Prolla, T. A., Assadi-Porter, F., Roy, S., Denu, J. M., and Coon, J. J. (2013) Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome. Mol. Cell 49, 186-199
-
(2013)
Mol. Cell
, vol.49
, pp. 186-199
-
-
Hebert, A.S.1
Dittenhafer-Reed, K.E.2
Yu, W.3
Bailey, D.J.4
Selen, E.S.5
Boersma, M.D.6
Carson, J.J.7
Tonelli, M.8
Balloon, A.J.9
Higbee, A.J.10
Westphall, M.S.11
Pagliarini, D.J.12
Prolla, T.A.13
Assadi-Porter, F.14
Roy, S.15
Denu, J.M.16
Coon, J.J.17
-
12
-
-
84865726581
-
Proteomic analysis of lysine acetylation sites in rat tissues reveals organ specificity and subcellular patterns
-
Lundby, A., Lage, K., Weinert, B. T., Bekker-Jensen, D. B., Secher, A., Skovgaard, T., Kelstrup, C. D., Dmytriyev, A., Choudhary, C., Lundby, C., and Olsen, J. V. (2012) Proteomic analysis of lysine acetylation sites in rat tissues reveals organ specificity and subcellular patterns. Cell Reports 2, 419-431
-
(2012)
Cell Reports
, vol.2
, pp. 419-431
-
-
Lundby, A.1
Lage, K.2
Weinert, B.T.3
Bekker-Jensen, D.B.4
Secher, A.5
Skovgaard, T.6
Kelstrup, C.D.7
Dmytriyev, A.8
Choudhary, C.9
Lundby, C.10
Olsen, J.V.11
-
13
-
-
84879637572
-
Integrated proteomic analysis of post-translational modifications by serial enrichment
-
Mertins, P., Qiao, J. W., Patel, J., Udeshi, N. D., Clauser, K. R., Mani, D. R., Burgess, M. W., Gillette, M. A., Jaffe, J. D., and Carr, S. A. (2013) Integrated proteomic analysis of post-translational modifications by serial enrichment. Nat. Methods 10, 634-637
-
(2013)
Nat. Methods
, vol.10
, pp. 634-637
-
-
Mertins, P.1
Qiao, J.W.2
Patel, J.3
Udeshi, N.D.4
Clauser, K.R.5
Mani, D.R.6
Burgess, M.W.7
Gillette, M.A.8
Jaffe, J.D.9
Carr, S.A.10
-
14
-
-
79952276306
-
Generation of acetyllysine antibodies and affinity enrichment of acetylated peptides
-
Guan, K. L., Yu, W., Lin, Y., Xiong, Y., and Zhao, S. (2010) Generation of acetyllysine antibodies and affinity enrichment of acetylated peptides. Nat. Protocols 5, 1583-1595
-
(2010)
Nat. Protocols
, vol.5
, pp. 1583-1595
-
-
Guan, K.L.1
Yu, W.2
Lin, Y.3
Xiong, Y.4
Zhao, S.5
-
15
-
-
84885012783
-
Large-scale identification of ubiquitination sites by mass spectrometry
-
Udeshi, N. D., Mertins, P., Svinkina, T., and Carr, S. A. (2013) Large-scale identification of ubiquitination sites by mass spectrometry. Nat. Protocols 8, 1950-1960
-
(2013)
Nat. Protocols
, vol.8
, pp. 1950-1960
-
-
Udeshi, N.D.1
Mertins, P.2
Svinkina, T.3
Carr, S.A.4
-
16
-
-
82455179484
-
Systematic and quantitative assessment of the ubiquitin-modified proteome
-
Kim, W., Bennett, E. J., Huttlin, E. L., Guo, A., Li, J., Possemato, A., Sowa, M. E., Rad, R., Rush, J., Comb, M. J., Harper, J. W., and Gygi, S. P. (2011) Systematic and quantitative assessment of the ubiquitin-modified proteome. Mol. Cell 44, 325-340
-
(2011)
Mol. Cell
, vol.44
, pp. 325-340
-
-
Kim, W.1
Bennett, E.J.2
Huttlin, E.L.3
Guo, A.4
Li, J.5
Possemato, A.6
Sowa, M.E.7
Rad, R.8
Rush, J.9
Comb, M.J.10
Harper, J.W.11
Gygi, S.P.12
-
17
-
-
84906841343
-
Time-resolved dissection of early phosphoproteome and ensuing proteome changes in response to TGF-beta
-
D'Souza, R. C., Knittle, A. M., Nagaraj, N., van Dinther, M., Choudhary, C., ten Dijke, P., Mann, M., and Sharma, K. (2014) Time-resolved dissection of early phosphoproteome and ensuing proteome changes in response to TGF-beta. Sci. Signaling 7, rs5
-
(2014)
Sci. Signaling
, vol.7
, pp. rs5
-
-
D'Souza, R.C.1
Knittle, A.M.2
Nagaraj, N.3
Van Dinther, M.4
Choudhary, C.5
Ten Dijke, P.6
Mann, M.7
Sharma, K.8
-
18
-
-
78650466243
-
A tissue-specific atlas of mouse protein phosphorylation and expression
-
Huttlin, E. L., Jedrychowski, M. P., Elias, J. E., Goswami, T., Rad, R., Beausoleil, S. A., Villen, J., Haas, W., Sowa, M. E., and Gygi, S. P. (2010) A tissue-specific atlas of mouse protein phosphorylation and expression. Cell 143, 1174-1189
-
(2010)
Cell
, vol.143
, pp. 1174-1189
-
-
Huttlin, E.L.1
Jedrychowski, M.P.2
Elias, J.E.3
Goswami, T.4
Rad, R.5
Beausoleil, S.A.6
Villen, J.7
Haas, W.8
Sowa, M.E.9
Gygi, S.P.10
-
19
-
-
0037131411
-
Phosphoprotein analysis using antibodies broadly reactive against phosphorylated motifs
-
Zhang, H., Zha, X., Tan, Y., Hornbeck, P. V., Mastrangelo, A. J., Alessi, D. R., Polakiewicz, R. D., and Comb, M. J. (2002) Phosphoprotein analysis using antibodies broadly reactive against phosphorylated motifs. J. Biol. Chem. 277, 39379-39387
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 39379-39387
-
-
Zhang, H.1
Zha, X.2
Tan, Y.3
Hornbeck, P.V.4
Mastrangelo, A.J.5
Alessi, D.R.6
Polakiewicz, R.D.7
Comb, M.J.8
-
20
-
-
84874619400
-
Refined preparation and use of anti-diglycine remnant (K-epsilon-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments
-
Udeshi, N. D., Svinkina, T., Mertins, P., Kuhn, E., Mani, D. R., Qiao, J. W., and Carr, S. A. (2013) Refined preparation and use of anti-diglycine remnant (K-epsilon-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments. Mol. Cell. Proteomics 12, 825-831
-
(2013)
Mol. Cell. Proteomics
, vol.12
, pp. 825-831
-
-
Udeshi, N.D.1
Svinkina, T.2
Mertins, P.3
Kuhn, E.4
Mani, D.R.5
Qiao, J.W.6
Carr, S.A.7
-
21
-
-
84891801106
-
Immunoaffinity enrichment and mass spectrometry analysis of protein methylation
-
Guo, A., Gu, H., Zhou, J., Mulhern, D., Wang, Y., Lee, K. A., Yang, V., Aguiar, M., Kornhauser, J., Jia, X., Ren, J., Beausoleil, S. A., Silva, J. C., Vemulapalli, V., Bedford, M. T., and Comb, M. J. (2014) Immunoaffinity enrichment and mass spectrometry analysis of protein methylation. Mol. Cell. Proteomics 13, 372-387
-
(2014)
Mol. Cell. Proteomics
, vol.13
, pp. 372-387
-
-
Guo, A.1
Gu, H.2
Zhou, J.3
Mulhern, D.4
Wang, Y.5
Lee, K.A.6
Yang, V.7
Aguiar, M.8
Kornhauser, J.9
Jia, X.10
Ren, J.11
Beausoleil, S.A.12
Silva, J.C.13
Vemulapalli, V.14
Bedford, M.T.15
Comb, M.J.16
-
22
-
-
57449099865
-
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
-
Cox, J., and Mann, M. (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotech. 26, 1367-1372
-
(2008)
Nat. Biotech.
, vol.26
, pp. 1367-1372
-
-
Cox, J.1
Mann, M.2
-
23
-
-
79953701087
-
Andromeda: A peptide search engine integrated into the MaxQuant environment
-
Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, J. V., and Mann, M. (2011) Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 10, 1794-1805
-
(2011)
J. Proteome Res.
, vol.10
, pp. 1794-1805
-
-
Cox, J.1
Neuhauser, N.2
Michalski, A.3
Scheltema, R.A.4
Olsen, J.V.5
Mann, M.6
-
24
-
-
84861151032
-
Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition
-
Udeshi, N. D., Mani, D. R., Eisenhaure, T., Mertins, P., Jaffe, J. D., Clauser, K. R., Hacohen, N., and Carr, S. A. (2012) Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. Mol. Cell. Proteomics 11, 148-159
-
(2012)
Mol. Cell. Proteomics
, vol.11
, pp. 148-159
-
-
Udeshi, N.D.1
Mani, D.R.2
Eisenhaure, T.3
Mertins, P.4
Jaffe, J.D.5
Clauser, K.R.6
Hacohen, N.7
Carr, S.A.8
-
25
-
-
4544341015
-
Linear models and empirical bayes methods for assessing differential expression in microarray experiments
-
Smyth, G. K. (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stati. Appl. Gen. Mol. Biol. 3, Article3
-
(2004)
Stati. Appl. Gen. Mol. Biol.
, vol.3
-
-
Smyth, G.K.1
-
26
-
-
61449172037
-
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
-
Huang, D. W., Sherman, B. T., and Lempicki, R. A. (2008) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protocols 4, 44-57
-
(2008)
Nat. Protocols
, vol.4
, pp. 44-57
-
-
Huang, D.W.1
Sherman, B.T.2
Lempicki, R.A.3
-
27
-
-
84940529935
-
-
Department of Medical Protein Research, Department of Biochemistry Ghent University, Ghent, Belgium
-
Colaert, N., Helsens, K., Vandekerchove, J., Gevaert, K., and Martens, L., IceLogo Manual. Department of Medical Protein Research, Department of Biochemistry Ghent University, Ghent, Belgium
-
IceLogo Manual
-
-
Colaert, N.1
Helsens, K.2
Vandekerchove, J.3
Gevaert, K.4
Martens, L.5
-
29
-
-
79959923522
-
g:Profiler - A web server for functional interpretation of gene lists (2011 update)
-
Reimand, J., Arak, T., and Vilo, J. (2011) g:Profiler-a web server for functional interpretation of gene lists (2011 update). Nucleic Acids Res. 39, W307-W315
-
(2011)
Nucleic Acids Res
, vol.39
, pp. W307-W315
-
-
Reimand, J.1
Arak, T.2
Vilo, J.3
-
30
-
-
9144269670
-
EnsMart: A generic system for fast and flexible access to biological data
-
Kasprzyk, A., Keefe, D., Smedley, D., London, D., Spooner, W., Melsopp, C., Hammond, M., Rocca-Serra, P., Cox, T., and Birney, E. (2004) EnsMart: a generic system for fast and flexible access to biological data. Genome Res. 14, 160-169
-
(2004)
Genome Res
, vol.14
, pp. 160-169
-
-
Kasprzyk, A.1
Keefe, D.2
Smedley, D.3
London, D.4
Spooner, W.5
Melsopp, C.6
Hammond, M.7
Rocca-Serra, P.8
Cox, T.9
Birney, E.10
-
31
-
-
84904111890
-
Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels
-
Mertins, P., Yang, F., Liu, T., Mani, D. R., Petyuk, V. A., Gillette, M. A., Clauser, K. R., Qiao, J. W., Gritsenko, M. A., Moore, R. J., Levine, D. A., Townsend, R., Erdmann-Gilmore, P., Snider, J. E., Davies, S. R., Ruggles, K. V., Fenyo, D., Kitchens, R. T., Li, S., Olvera, N., Dao, F., Rodriguez, H., Chan, D. W., Liebler, D., White, F., Rodland, K. D., Mills, G. B., Smith, R. D., Paulovich, A. G., Ellis, M., and Carr, S. A. (2014) Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels. Mol. Cell. Proteomics 13, 1690-1704
-
(2014)
Mol. Cell. Proteomics
, vol.13
, pp. 1690-1704
-
-
Mertins, P.1
Yang, F.2
Liu, T.3
Mani, D.R.4
Petyuk, V.A.5
Gillette, M.A.6
Clauser, K.R.7
Qiao, J.W.8
Gritsenko, M.A.9
Moore, R.J.10
Levine, D.A.11
Townsend, R.12
Erdmann-Gilmore, P.13
Snider, J.E.14
Davies, S.R.15
Ruggles, K.V.16
Fenyo, D.17
Kitchens, R.T.18
Li, S.19
Olvera, N.20
Dao, F.21
Rodriguez, H.22
Chan, D.W.23
Liebler, D.24
White, F.25
Rodland, K.D.26
Mills, G.B.27
Smith, R.D.28
Paulovich, A.G.29
Ellis, M.30
Carr, S.A.31
more..
-
32
-
-
84876217035
-
Label-free quantitative proteomics of the lysine acetylome in mitochondria identifies substrates of SIRT3 in metabolic pathways
-
Rardin, M. J., Newman, J. C., Held, J. M., Cusack, M. P., Sorensen, D. J., Li, B., Schilling, B., Mooney, S. D., Kahn, C. R., Verdin, E., and Gibson, B. W. (2013) Label-free quantitative proteomics of the lysine acetylome in mitochondria identifies substrates of SIRT3 in metabolic pathways. Proc. Natl. Acad. Sci. USA 110, 6601-6606
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 6601-6606
-
-
Rardin, M.J.1
Newman, J.C.2
Held, J.M.3
Cusack, M.P.4
Sorensen, D.J.5
Li, B.6
Schilling, B.7
Mooney, S.D.8
Kahn, C.R.9
Verdin, E.10
Gibson, B.W.11
-
33
-
-
84910601317
-
Suberoylanilide hydroxamic acid (SAHA)-induced dynamics of a human histone deacetylase protein interaction network
-
Sardiu, M. E., Smith, K. T., Groppe, B. D., Gilmore, J. M., Saraf, A., Egidy, R., Peak, A., Seidel, C. W., Florens, L., Workman, J. L., and Washburn, M. P. (2014) Suberoylanilide hydroxamic acid (SAHA)-induced dynamics of a human histone deacetylase protein interaction network. Mol. Cell. Proteomics 13, 3114-3125
-
(2014)
Mol. Cell. Proteomics
, vol.13
, pp. 3114-3125
-
-
Sardiu, M.E.1
Smith, K.T.2
Groppe, B.D.3
Gilmore, J.M.4
Saraf, A.5
Egidy, R.6
Peak, A.7
Seidel, C.W.8
Florens, L.9
Workman, J.L.10
Washburn, M.P.11
-
34
-
-
84907830955
-
SAHA regulates histone acetylation, butyrylation, and protein expression in neuroblastoma
-
Xu, G., Wang, J., Wu, Z., Qian, L., Dai, L., Wan, X., Tan, M., Zhao, Y., and Wu, Y. (2014) SAHA regulates histone acetylation, butyrylation, and protein expression in neuroblastoma. J. Proteome Res. 13, 4211-4219
-
(2014)
J. Proteome Res.
, vol.13
, pp. 4211-4219
-
-
Xu, G.1
Wang, J.2
Wu, Z.3
Qian, L.4
Dai, L.5
Wan, X.6
Tan, M.7
Zhao, Y.8
Wu, Y.9
-
35
-
-
79960797509
-
Proteome-wide mapping of the Drosophila acetylome demonstrates a high degree of conservation of lysine acetylation
-
Weinert, B. T., Wagner, S. A., Horn, H., Henriksen, P., Liu, W. R., Olsen, J. V., Jensen, L. J., and Choudhary, C. (2011) Proteome-wide mapping of the Drosophila acetylome demonstrates a high degree of conservation of lysine acetylation. Sci. Signaling 4, ra48
-
(2011)
Sci. Signaling
, vol.4
, pp. ra48
-
-
Weinert, B.T.1
Wagner, S.A.2
Horn, H.3
Henriksen, P.4
Liu, W.R.5
Olsen, J.V.6
Jensen, L.J.7
Choudhary, C.8
|