Proteome TopFIND 3.0 with TopFINDer and PathFINDer: Database and analysis tools for the association of protein termini to pre- and post-translational events

Nucleic Acids Research

Volumn 43, Issue D1, 2015, Pages D290-D297

  Fortelny, Nikolaus ^a   Yang, Sharon ^a   Pavlidis, Paul ^a   Lange, Philipp F ^a   Overall, Christopher M ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME; ISOPROTEIN; PEPTIDE HYDROLASE;

AMINO TERMINAL SEQUENCE; ARABIDOPSIS THALIANA; ARTICLE; BACTERIUM IDENTIFICATION; CARBOXY TERMINAL SEQUENCE; COMPLEX FORMATION; COMPUTER PROGRAM; DATA ANALYSIS; DATA ANALYSIS SOFTWARE; ESCHERICHIA COLI; HUMAN; MEDICAL INFORMATION; MUS MUSCULUS; PATHFINDER SOFTWARE; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROTEIN CLEAVAGE; PROTEIN DATABASE; PROTEIN DEGRADATION; PROTEIN FUNCTION; PROTEIN PROCESSING; PROTEIN STRUCTURE; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; TOPFIND 3.0 DATABASE; TOPFINDER SOFTWARE; VALIDATION PROCESS; ALTERNATIVE RNA SPLICING; ANIMAL; CHEMISTRY; METABOLISM; MOUSE; PROTEOMICS;

ALTERNATIVE SPLICING; ANIMALS; DATABASES, PROTEIN; HUMANS; MICE; PEPTIDE HYDROLASES; PROTEIN ISOFORMS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOME; PROTEOMICS; SOFTWARE;

EID: 84941086837     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1012     Document Type: Article

References (18)

1. Lange, P. F. and Overall, C. M. (2013) Protein TAILS: when termini tel tales of proteolysis and function. Curr. Opin. Chem. Biol, 17, 73-82.
2. Rogers, L. D. and Overall, C. M. (2013) Proteolytic post-translational modification of proteins: proteomic tools and methodology. Mol Cell Proteomics, 12, 3532-3542.
3. auf dem Keller, U., Prudova, A., Eckhard, U., Fingleton, B. and Overall, C. M. (2013) Systems-level analysis of proteolytic events in increased vascular permeability and complement activation in skin inflammation. Sci. Signal, 6, rs2.
4. Lange, P, Huesgen, P, Nguyen, K. and Overall, C. (2014) Annotating N termini for the human proteome project: N termini and Nα-acetylation status differentiate stable cleaved protein species from degradation remnants in the human erythrocyte proteome. J. Proteome Res., 13, 2028-2044.
5. Prudova, A., Serrano, K., Eckhard, U., Fortelny, N., Devine, D. and Overall, C. M. (2014) TAILS N-terminomics of human platelets revea pervasive proteolytic processing and a prominent role of metalloproteinases during storage. Blood, in press.
6. Lange, PF. and Overall, C. M. (2011) TopFIND, a knowledgebase linking protein termini with function. Nat. Methods, 8, 703-704.
7. McQuibban, G. A., Gong, J.-H., Tam, E. M., McCulloch, C. A. G., Clark-Lewis, I. and Overall, C. M. (2000) Inflammation dampened by gelatinase A cleavage of monocyte chemoattractant Protein-3. Science, 289, 1202-1206.
8. Hwang, C.-S., Shemorry, A. and Varshavsky, A. (2010) N-terminal acetylation of cellular proteins creates specific degradation signals. Science, 327, 973-977.
9. Resh, M. D. (2006) Trafficking and signaling by fatty-acylated and prenylatedproteins. Nat. Chem. Biol, 2, 584-590.
10. Pierre, M., Traverso, J. A., Boisson, B., Domenichini, S., Bouchez, D., Giglione, C. and Meinnel, T (2007) N-myristoylation regulates the SnRK1 pathway in arabidopsis. Plant Cell, 19, 2804-2821.
11. Tolstykh, T, Lee, J., Vafai, S. and Stock, J. B. (2000) Carboxyl methylation regulates phosphoprotein phosphatase 2A by controlling the association of regulatory B subunits. EMBO J., 19, 5682-5691.
12. Fortelny, N., Cox, J. H., Kappelhoff, R., Starr, A. E., Lange, PF, Pavlidis, P and Overall, C. M. (2014) Network analyses reveal pervasive functional regulation between proteases in the human protease web. PLoSBiol, 12, e1001869.
13. Lange, PF, Huesgen, PF and Overall, C. M. (2011) TopFIND 2.0-linking protein termini with proteolytic processing and modifications altering protein function. Nucleic Acids Res., 40, D351-D361.
14. Flicek, P., Amode, M. R., Barrell, D., Beal, K., Billis, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fitzgerald, S. et al. (2014) Ensembl 2014. Nucleic Acids Res., 42, D749-D755.
15. Consortium, T. U. (2014) Activities at the universal protein resource (UniProt). Nucleic Acids Res., 42, D191-D198.
16. Wan, J. and Qian, S.-B. (2014) TISdb: a database for alternative translation initiation in mammalian cells. Nucleic Acids Res., 42, D845-850.
17. Östlund, G., Schmitt, T., Forslund, K., Köstler, T., Messina, D. N., Roopra, S., Frings, O. and Sonnhammer, E. L. L. (2010) InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res., 38, D196-D203.
18. Colaert, N., Helsens, K., Martens, L., Vandekerckhove, J. and Gevaert, K. (2009) Improved visualization of protein consensus sequences by iceLogo. Nat. Meth, 6, 786-787.