A visualization of 3D proteome universe: Mapping of a proteome ensemble into 3D space based on the protein-structure composition

Molecular Phylogenetics and Evolution

Volumn 61, Issue 2, 2011, Pages 484-494

  Aita, Takuyo ^a   Nishigaki, Koichi ^a  

^a SAITAMA UNIVERSITY   (Japan)

Author keywords

Biodiversity; Biosystematics; Comparative genomics; Dimensionality reduction; Metagenomics; Metaproteomics

Indexed keywords

PROTEOME;

ARTICLE; CHEMICAL STRUCTURE; METHODOLOGY; PRINCIPAL COMPONENT ANALYSIS; PROTEIN CONFORMATION; PROTEOMICS;

MODELS, MOLECULAR; PRINCIPAL COMPONENT ANALYSIS; PROTEIN CONFORMATION; PROTEOME; PROTEOMICS;

AVES;

EID: 80052782415     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2011.06.020     Document Type: Article

References (35)

1. Abe T., Kanaya S., Kinouchi M., Ichiba Y., Kozuki T., Ikemura T. Informatics for unveiling hidden genome signatures. Genome Res. 2003, 13(4):693-702.
2. Borg I., Groenen P.J.F. Modern Multidimensional Scaling: Theory and Applications 2005, Springer.
3. Caetano-Anolles G., Caetano-Anolles D. An evolutionarily structured universe of protein architecture. Genome Res. 2003, 13(7):1563-1571.
4. Fukami-Kobayashi K., Minezaki Y., Tateno Y., Nishikawa K. A tree of life based on protein domain organizations. Mol. Biol. Evol. 2007, 24(5):1181-1189.
5. Fukuchi S., Homma K., Sakamoto S., Sugawara H., Tateno Y., Gojobori T., Nishikawa K. The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions. Nucleic Acids Res. 2009, 37(Database issue):D333-D337.
6. Gerstein M. Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census. Proteins 1998, 33(4):518-534.
7. Hamada M., Mituyama T., Asai K. Large scale similarity search for locally stable secondary structures among RNA sequences. IPSJ Trans. Bioinform. 2009, 2:36-46.
8. Hou J., Sims G.E., Zhang C., Kim S.H. A global representation of the protein fold space. Proc. Natl. Acad. Sci. USA 2002, 100(5):2386-2390.
9. Jolliffe I.T. Principal Component Analysis 2002, Springer, NY.
10. Kanaya S., Kinouchi M., Abe T., Kudo Y., Yamada Y., Nishi T., Mori H., Ikemura T. Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM): characterization of horizontally transferred genes with emphasis on the E. coli O157 genome. Gene 2001, 276(1-2):89-99.
11. Kawabata T., Fukuchi S., Homma K., Ota M., Araki J., Ito T., Ichiyoshi N., Nishikawa K. GTOP: a database of protein structures predicted from genome sequences. Nucleic Acids Res. 2002, 30(1):294-298.
12. Kohonen T. Self-organizing Maps 2000, Springer.
13. Li J.X. Visualization of high-dimensional data with relational perspective map. Inform. Visual. 2004, 3:49-59.
14. Li M., Badger J.H., Chen X., Kwong S., Kearney P., Zhang H. An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics 2001, 17(2):149-154.
15. Lin J., Gerstein M. Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels. Genome Res. 2000, 10(6):808-818.
16. Murzin AG., Brenner SE., Hubbard T., Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 1995, 247(4):536-540.
17. Nacher J.C., Hayashida M., Akutsu T. Protein domain networks: scale-free mixing of positive and negative exponents. Physica A 2006, 367:538-552.
18. Nacher J.C., Hayashida M., Akutsu T. The role of internal duplication in the evolution of multi-domain proteins. BioSystems 2010, 101:127-135.
19. Nishigaki, K. 2006. Genomu to seibutsu (Genome and organism). In: Sinka, Jouhou, Katachi (Evolution, information and form); Husimi, Y., Nishigaki, K., (Eds.), Baihuukan, 2006, pp. 114-129 (in Japanese).
20. Nishio, H., Altaf-Ul-Amin, Md., Kurokawa, K., Minato, K., Kanaya, S., 2005. Spherical SOM with arbitrary number of neurons and measure of suitability. In: Proc. WSOM 2005, pp. 323-330.
21. Randic M., Zupan J., Novic M. On 3-D graphical representation of proteomics maps and their numerical characterization. J. Chem. Inf. Comput. Sci. 2001, 41(5):1339-1344.
22. Rao P.K., Li Q. Principal component analysis of proteome dynamics in iron-starved mycobacterium tuberculosis. J. Proteomics Bioinform. 2009, 2:19-31.
23. Ritter H. Self-organizing maps on non-euclidean spaces. Kohonen Maps 1999, 95-110. Elsevier, New York. E. Oja, S. Kaski (Eds.).
24. Sammon J.W. A nonlinear mapping for data structure analysis. IEEE Trans. Comput. 1969, C-18:401-409.
25. Sasaki N.V., Sato N. Elucidating genome structure evolution by analysis of isoapostatic gene clusters using statistics of variance of gene distances. Genome Biol. Evol. 2009, 2010:1-12.
26. Standley D.M., Kinjo A.R., Kinoshita K., Nakamura H. Protein structure databases with new web services for structural biology and biomedical research. Brief Bioinform. 2008, 9(4):276-285.
27. Stuart G.W., Moffet K., Leader J.J. A comprehensive vertebrate phylogeny using vector representations of protein sequences from whole genomes. Mol. Biol. Evol. 2002, 19(4):554-562.
28. Taguchi Y.H., Oono Y. Relational patterns of gene expression via non-metric multidimensional scaling analysis. Bioinformatics 2005, 21(6):730-740.
29. Winstanley H.F., Abeln S., Deane C.M. How old is your fold ?. Bioinformatics 2005, 21(Suppl. 1):i449-i458.
30. Woese C.R. Bacterial evolution. Microbiol. Rev. 1987, 51(2):221-271.
31. Wolf Y.I., Brenner S.E., Bash P.A., Koonin E.V. Distribution of protein folds in the three superkingdoms of life. Genome Res. 1999, 9(1):17-26.
32. Yamada, T., Saito, K., Ueda, N. Cross-entropy directed embedding of network data. In: Proceedings of the Twentieth International Conference on Machine LearningC, pp. 832-839C2003.
33. Yang S., Doolittle RF., Bourne P.E. Phylogeny determined by protein domain content. Proc. Natl. Acad. Sci. USA 2005, 102(2):373-378.
34. Yin H. ViSOM - a novel method for multivariate data projection and structure visualization. IEEE Trans. Neural Netw. 2002, 13(1):237-243.
35. Yu ZG., Zhan XW., Han GS., Wang RW., Anh V., Chu K.H. Proper distance metrics for phylogenetic analysis using complete genomes without sequence alignment. Int. J. Mol. Sci. 2010, 11(3):1141-1154.