Complex phylogenetic profiling reveals fundamental genotype-phenotype associations

Computational Biology and Chemistry

Volumn 32, Issue 6, 2008, Pages 412-416

  Antonov, Alexey V ^a   Mewes, Hans W ^a,b  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

Comparative genomics; Genotype phenotype associations; Phylogenetic profiling

Indexed keywords

GLYCOPROTEINS;

BACTERIAL; BIOCHEMICAL PATHWAYS; COMPARATIVE GENOMICS; COMPUTATIONAL TECHNIQUES; GENOTYPE-PHENOTYPE ASSOCIATIONS; IT IDENTIFIES; LOGIC ANALYSES; LOGIC RELATIONSHIPS; PHYLOGENETIC PROFILES; PHYLOGENETIC PROFILING;

PROTEINS;

OXYGEN;

ARTICLE; BACILLUS SUBTILIS; BACTERIAL GENE; GENE EXPRESSION PROFILING; GENETICS; GENOTYPE; METABOLISM; PHENOTYPE; PHYLOGENY;

BACILLUS SUBTILIS; GENE EXPRESSION PROFILING; GENES, BACTERIAL; GENOTYPE; OXYGEN; PHENOTYPE; PHYLOGENY;

BACTERIA (MICROORGANISMS);

EID: 54149103270     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2008.07.003     Document Type: Article

References (20)

1. Antonov A.V., and Mewes H.W. BIOREL: the benchmark resource to estimate the relevance of the gene networks. FEBS Lett. 580 3 (2006) 844-848
2. Antonov A.V., and Mewes H.W. Complex functionality of gene groups identified from high-throughput data. J. Mol. Biol. 363 1 (2006) 289-296
3. Antonov A.V., Tetko I.V., and Mewes H.W. A systematic approach to infer biological relevance and biases of gene network structures. Nucleic Acids Res. 34 1 (2006) e6
4. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Harris M.A., Hill D.P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J.C., Richardson J.E., Ringwald M., Rubin G.M., and Sherlock G. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat. Genet. 25 1 (2000) 25-29
5. Bowers P.M., Cokus S.J., Eisenberg D., and Yeates T.O. Use of logic relationships to decipher protein network organization. Science 306 5705 (2004) 2246-2249
6. Bowers P.M., O'Connor B.D., Cokus S.J., Sprinzak E., Yeates T.O., and Eisenberg D. Utilizing logical relationships in genomic data to decipher cellular processes. FEBS J. 272 20 (2005) 5110-5118
7. Draghici S., Khatri P., Martins R.P., Ostermeier G.C., and Krawetz S.A. Global functional profiling of gene expression. Genomics 81 2 (2003) 98-104
8. Huynen M., Dandekar T., and Bork P. Differential genome analysis applied to the species-specific features of Helicobacter pylori. FEBS Lett. 426 1 (1998) 1-5
9. Jim K., Parmar K., Singh M., and Tavazoie S. A cross-genomic approach for systematic mapping of phenotypic traits to genes. Genome Res. 14 1 (2004) 109-115
10. Khatri P., Bhavsar P., Bawa G., and Draghici S. Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments. Nucleic Acids Res. 32 Web Server issue (2004) W449-W456
11. Khatri P., and Draghici S. Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 21 18 (2005) 3587-3595
12. Levesque M., Shasha D., Kim W., Surette M.G., and Benfey P.N. Trait-to-gene: a computational method for predicting the function of uncharacterized genes. Curr. Biol. 13 2 (2003) 129-133
13. Makarova K.S., Wolf Y.I., and Koonin E.V. Potential genomic determinants of hyperthermophily. Trends Genet. 19 4 (2003) 172-176
14. Marcotte E.M., Pellegrini M., Thompson M.J., Yeates T.O., and Eisenberg D. A combined algorithm for genome-wide prediction of protein function. Nature 402 6757 (1999) 83-86
15. Mewes H.W., Amid C., Arnold R., Frishman D., Guldener U., Mannhaupt G., Munsterkotter M., Pagel P., Strack N., Stumpflen V., Warfsmann J., and Ruepp A. MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res. 32 Database issue (2004) D41-D44
16. Pellegrini M., Marcotte E.M., Thompson M.J., Eisenberg D., and Yeates T.O. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. U.S.A. 96 8 (1999) 4285-4288
17. Ruepp A., Zollner A., Maier D., Albermann K., Hani J., Mokrejs M., Tetko I., Guldener U., Mannhaupt G., Munsterkotter M., and Mewes H.W. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res. 32 18 (2004) 5539-5545
18. Slonim N., Elemento O., and Tavazoie S. Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks. Mol. Syst. Biol. 2 (2006) 2006
19. von M.C., Jensen L.J., Kuhn M., Chaffron S., Doerks T., Kruger B., Snel B., and Bork P. STRING 7-recent developments in the integration and prediction of protein interactions. Nucleic Acids Res. 35 Database issue (2007) D358-D362
20. Westfall P.H., Zaykin D.V., and Young S.S. Multiple tests for genetic effects in association studies. Methods Mol. Biol. 184 (2002) 143-168