SVD-phy: Improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles

Bioinformatics

Volumn 32, Issue 7, 2016, Pages 1085-1087

  Franceschini, Andrea ^a,b   Lin, Jianyi ^c   Von Mering, Christian ^a,b   Jensen, Lars Juhl ^d  

^a UNIVERSITY OF ZURICH   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^c UNIVERSITY OF MILAN   (Italy)

^d University of Copenhagen   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ALGORITHM; MOLECULAR EVOLUTION; PHYLOGENY; SOFTWARE;

ALGORITHMS; EVOLUTION, MOLECULAR; PHYLOGENY; PROTEINS; SOFTWARE;

EID: 84964432671     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv696     Document Type: Article

References (16)

1. Arnold,R. et al. (2014) SIMAP-the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage. Nucleic Acids Res., 42, D279-D284.
2. Cheng,Y. and Perocchi,F. (2015) ProtPhylo: identification of protein-phenotype and protein-protein functional associations via phylogenetic profiling. Nucleic Acids Res., 43, W160-W168.
3. Croft,D. et al. (2014) The Reactome pathway knowledgebase. Nucleic Acids Res., 42, D472-D477.
4. Date,S. V. and Marcotte,E. M. (2003) Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat. Biotechnol., 21, 1055-1062.
5. Dimitrieva,S. and Bucher,P. (2012) Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements. Bioinformatics, 28, i395-i401.
6. Enault,F. et al. (2003) Annotation of bacterial genomes using improved phylogenomic profiles. Bioinformatics, 19, i105-i107.
7. Kanehisa,M. et al. (2014) Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res., 42, D199-D205.
8. Keseler,I. M. et al. (2013) EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res., 41, D605-D612.
9. Li,Y. et al. (2014) Expansion of biological pathways based on evolutionary inference. Cell, 158, 213-225.
10. Ott,A. et al. (2012) NAPP: the Nucleic Acid Phylogenetic Profile Database. Nucleic Acids Res., 40, D205-D209.
11. Pellegrini,M. et al. (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. U. S. A., 96, 4285-4288.
12. Psomopoulos,F. E. et al. (2013) Detection of genomic idiosyncrasies using fuzzy phylogenetic profiles. PLoS One, 8, e52854.
13. S. kunca,N. and Dessimoz,C. (2015) Phylogenetic profiling: how much input data is enough. PLos One, 10, e0114701
14. Szklarczyk,D. et al. (2015) STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res., 43, D447-D452.
15. Tabach,Y. et al. (2013a) Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence. Nature, 493, 694-698.
16. Tabach,Y. et al. (2013b) Human disease locus discovery and mapping to molecular pathways through phylogenetic profiling. Mol. Syst. Biol., 9, 692.