Prediction of lysine ubiquitination with mRMR feature selection and analysis

Amino Acids

Volumn 42, Issue 4, 2012, Pages 1387-1395

  Cai, Yudong ^a,d   Huang, Tao ^b,c   Hu, Lele ^a   Shi, Xiaohe ^e   Xie, Lu ^c   Li, Yixue ^b,c  

^a SHANGHAI UNIVERSITY   (China)

^b Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^c SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

^d FUDAN UNIVERSITY   (China)

^e AGENCY FOR SCIENCE   (Singapore)

Author keywords

Incremental feature selection (IFS); Maximum relevance and minimum redundancy (mRMR); Nearest neighbor algorithm (NNA); Ubiquitination

Indexed keywords

LYSINE;

ALGORITHM; AMINO ACID SEQUENCE; ANALYTICAL PARAMETERS; ARTICLE; BIOCHEMISTRY; CONTROLLED STUDY; CORRELATION COEFFICIENT; JACKKNIFE TEST; MAXIMUM RELEVANCE AND MINIMUM REDUNDANCY; PHYSICAL CHEMISTRY; PREDICTOR VARIABLE; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROCESS OPTIMIZATION; PROTEIN ANALYSIS; PROTEIN DATABASE; SCORING SYSTEM; UBIQUITINATION;

ALGORITHMS; AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; LYSINE; PROTEINS; UBIQUITINATION;

EID: 84862641013     PISSN: 09394451     EISSN: 14382199     Source Type: Journal    
DOI: 10.1007/s00726-011-0835-0     Document Type: Article

References (46)

1. Aguilar RC, Wendland B (2003) Ubiquitin: not just for proteasomes anymore. Curr Opin Cell Biol 15(2):184-190 (Pubitemid 36332193)
2. Ahmad S, Sarai A(2005) Pssm-based prediction ofDNA binding sites in proteins. BMC Bioinform 6:33. doi:10.1186/1471-2105-6-33 (Pubitemid 41357981)
3. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389-3402 (pii:gka562) (Pubitemid 27359211)
4. Atchley WR, Zhao J, Fernandes AD, Druke T (2005) Solving the protein sequence metric problem. Proc Natl Acad Sci USA 102(18):6395-6400. doi:10.1073/pnas.0408677102 (Pubitemid 40617454)
5. Baldi P, Brunak S, Chauvin Y, Andersen CA, Nielsen H (2000) Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 16(5):412-424 (Pubitemid 30487963)
6. Beirlant J, Dudewicz E, Gyorfi L, Meulen Evd (1997) Nonparametric entropy estimation: an overview. Int J Math Stat Sci 6(1):17-39
7. Cai Y, He J, Li X, Lu L, Yang X, Feng K, Lu W, Kong X (2009) A novel computational approach to predict transcription factor DNA binding preference. J Proteome Res 8(2):999-1003. doi: 10.1021/pr800717y
8. Cai YD, Huang T, Feng KY, Hu L, Xie L (2010) A unified 35-gene signature for both subtype classification and survival prediction in diffuse large B cell lymphomas. PLoS One 5(9). doi: 10.1371/journal.pone.0012726
9. Edwards YJ, Lobley AE, Pentony MM, Jones DT (2009) Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data. Genome Biol 10(5):R50. doi:10.1186/gb-2009-10-5-r50
10. Gentry MS, Worby CA, Dixon JE (2005) Insights into lafora disease: Malin is an e3 ubiquitin ligase that ubiquitinates and promotes the degradation of laforin. Proc Natl Acad Sci USA 102(24): 8501-8506 (Pubitemid 40862765)
11. Han L, Wang Y, Bryant SH (2008) Developing and validating predictive decision tree models from mining chemical structural fingerprints and high-throughput screening data in pubchem. BMC Bioinform 9:401. doi:10.1186/1471-2105-9-401
12. Herrmann J, Lerman LO, Lerman A (2007) Ubiquitin and ubiquitinlike proteins in protein regulation. Circ Res 100(9):1276-1291 (Pubitemid 46742918)
13. Hershko A, Ciechanover A (1998) The ubiquitin system. Annu Rev Biochem 67:425-479 (Pubitemid 28411135)
14. Hicke L (2001) Protein regulation by monoubiquitin. Nat Rev Mol Cell Biol 2(3):195-201 (Pubitemid 33675744)
15. Hicke L, Dunn R (2003) Regulation of membrane protein transport by ubiquitin and ubiquitin-binding proteins. Annu Rev Cell Dev Biol 19:141-172 (Pubitemid 37487346)
16. Hoeller D, Hecker CM, Dikic I (2006) Ubiquitin and ubiquitinlike proteins in cancer pathogenesis. Nat Rev Cancer 6(10): 776-788 (Pubitemid 44450466)
17. Huang L, Kinnucan E, Wang G, Beaudenon S, Howley PM, Huibregtse JM, Pavletich NP (1999) Structure of an e6ap-ubch7 complex: insights into ubiquitination by the e2-e3 enzyme cascade. Science 286(5443):1321-1326
18. Huang T, Tu K, Shyr Y, Wei CC, Xie L, Li YX (2008) The prediction of interferon treatment effects based on time series microarray gene expression profiles. J Transl Med 6:44. doi:10.1186/1479-5876-6-44
19. Huang T, Cui W, Hu L, Feng K, Li YX, Cai YD (2009) Prediction of pharmacological and xenobiotic responses to drugs based on time course gene expression profiles. PLoS ONE 4(12):e8126. doi:10.1371/journal.pone.0008126
20. Huang T, Shi XH, Wang P, He Z, Feng KY, Hu L, Kong X, Li YX, Cai YD, Chou KC (2010a) Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks. PLoS One 5(6):e10972. doi:10.1371/journal.pone.0010972
21. Huang T, Wang P, Ye ZQ, Xu H, He Z, Feng KY, Hu L, Cui W, Wang K, Dong X, Xie L, Kong X, Cai YD, Li Y (2010b) Prediction of deleterious non-synonymous SNPs based on protein interaction network and hybrid properties. PLoS One 5(7):e11900. doi:10.1371/journal.pone.0011900
22. Kawashima S, Kanehisa M (2000) Aaindex: amino acid index database. Nucleic Acids Res 28(1):374 pii:gkd029 (Pubitemid 30047811)
23. Kirkpatrick DS, Denison C, Gygi SP (2005) Weighing in on ubiquitin: the expanding role of mass-spectrometry-based proteomics. Nat Cell Biol 7(8):750-757 (Pubitemid 41079043)
24. Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22(13):1658-1659. doi:10.1093/bioinformatics/btl158 (Pubitemid 43985301)
25. Li S, Liu B, Cai Y, Li Y (2007) Predicting protein n-glycosylation by combining functional domain and secretion information. J Biomol Struct Dyn 25(1):49-54 (Pubitemid 47124366)
26. Li H, Xing X, Ding G, Li Q, Wang C, Xie L, Zeng R, Li Y (2009) Sysptm: a systematic resource for proteomic research on posttranslational modifications. Mol Cell Proteomics 8(8):1839-1849. doi:10.1074/mcp.M900030-MCP200
27. Lin DH, Sterling H, Wang Z, Babilonia E, Yang B, Dong K, Hebert SC, Giebisch G, Wang WH (2005) Romk1 channel activity is regulated by monoubiquitination. Proc Natl Acad Sci USA 102(12):4306-4311 (Pubitemid 40397107)
28. Nonaka T, Iwatsubo T, Hasegawa M (2005) Ubiquitination of alphasynuclein. Biochemistry 44(1):361-368
29. Peng H, Long F, Ding C (2005a) Feature selection based on mutual information: criteria of max-dependency, max-relevance, and minredundancy. IEEETrans PatternAnalMach Intell 27(8):1226-1238 (Pubitemid 41245053)
30. Peng H, Long F, Ding C (2005b) Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy. IEEE Trans Pattern Anal Mach Intell 27(8): 1226-1238. doi:10.1109/TPAMI.2005.159 (Pubitemid 41245053)
31. Peng K, Radivojac P, Vucetic S, Dunker AK, Obradovic Z (2006) Length-dependent prediction of protein intrinsic disorder. BMC Bioinform 7:208. doi:10.1186/1471-2105-7-208
32. Pickart CM (2001) Mechanisms underlying ubiquitination. Annu Rev Biochem 70:503-533 (Pubitemid 32663902)
33. Qian Z, Cai YD, Li Y (2006) A novel computational method to predict transcription factor DNA binding preference. Biochem Biophys Res Commun 348(3):1034-1037 (Pubitemid 44233519)
34. Qiu P, Gentles AJ, Plevritis SK (2009) Fast calculation of pairwise mutual information for gene regulatory network reconstruction. Comput Methods Programs Biomed 94(2):177-180. doi:10.1016/ j.cmpb.2008.11.003
35. Radivojac P, Vacic V, Haynes C, Cocklin RR, Mohan A, Heyen JW, Goebl MG, Iakoucheva LM (2010) Identification, analysis, and prediction of protein ubiquitination sites. Proteins 78(2):365-380. doi:10.1002/prot.22555
36. Reinstein E, Ciechanover A (2006) Narrative review: protein degradation and human diseases: the ubiquitin connection. Ann Intern Med 145(9):676-684 (Pubitemid 46768844)
37. Rubinstein ND, Mayrose I, Pupko T (2009) A machine-learning approach for predicting B cell epitopes. Mol Immunol 46(5): 840-847. doi:10.1016/j.molimm. 2008.09.009
38. Saghatelian A, Cravatt BF (2005) Assignment of protein function in the postgenomic era. Nat Chem Biol 1(3):130-142
39. Schulman BA, Carrano AC, Jeffrey PD, Bowen Z, Kinnucan ER, Finnin MS, Elledge SJ, Harper JW, Pagano M, Pavletich NP (2000) Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex. Nature 408(6810):381-386
40. Sickmeier M, Hamilton JA, LeGall T, Vacic V, Cortese MS, Tantos A, Szabo B, Tompa P, Chen J, Uversky VN, Obradovic Z, Dunker AK (2007) Disprot: the database of disordered proteins. Nucleic Acids Res 35(Database issue):D786-D793. doi:10.1093/ nar/gkl893 (Pubitemid 46056310)
41. Sun L, Chen ZJ (2004) The novel functions of ubiquitination in signaling. Curr Opin Cell Biol 16(2):119-126 (Pubitemid 38757287)
42. Tung CW, Ho SY (2008) Computational identification of ubiquitylation sites from protein sequences. BMC Bioinform 9:310. doi: 10.1186/1471-2105-9-310
43. Welchman RL, Gordon C, Mayer RJ (2005) Ubiquitin and ubiquitinlike proteins as multifunctional signals. Nat Rev Mol Cell Biol 6(8):599-609 (Pubitemid 41081264)
44. Wu G, Xu G, Schulman BA, Jeffrey PD, Harper JW, Pavletich NP (2003) Structure of a beta-trcp1-skp1-beta-catenin complex: destruction motif binding and lysine specificity of the scf(betatrcp1) ubiquitin ligase. Mol Cell 11(6):1445-1456 (Pubitemid 36776532)
45. Zheng N, Wang P, Jeffrey PD, Pavletich NP (2000) Structure of a c-cbl-ubch7 complex: ring domain function in ubiquitin-protein ligases. Cell 102(4):533-539
46. Zheng N, Schulman BA, Song L, Miller JJ, Jeffrey PD,Wang P, Chu C, Koepp DM, Elledge SJ, Pagano M, Conaway RC, Conaway JW, Harper JW, Pavletich NP (2002) Structure of the cul1-rbx1-skp1-f boxskp2 scf ubiquitin ligase complex. Nature 416(6882):703-709 (Pubitemid 34429140)