Protein function prediction using the Protein Link EXplorer (PLEX)

被引：27

作者：

Date, SV

Marcotte, EM

机构：

[1] Univ Texas, Inst Mol & Cellular Biol, Ctr Syst & Synthet Biol, Austin, TX 78712 USA

[2] Univ Texas, Dept Chem & Biochem, Austin, TX 78712 USA

来源：

BIOINFORMATICS | 2005年 / 21卷 / 10期

关键词：

D O I：

10.1093/bioinformatics/bti313

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

We introduce the Protein Link EXplorer (PLEX), a web-based environment that allows the construction of a phylogenetic profile for any given amino acid sequence, and its comparison with profiles of similar to 350 000 predicted genes from 89 genomes, as a means of interactively identifying functionally linked genes and predicting protein function. PLEX can be searched iteratively and also enables searches for chromosomal gene neighbors and Rosetta Stone linkages. PLEX search results are accompanied by quantitative estimates of linkage confidence, enabling users to take advantage of coinheritance, operon and gene fusion-based methods for inferring gene function and reconstructing cellular systems and pathways.

引用

收藏

页码：2558 / 2559

页数：2

相关论文

共 10 条

[1] Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages [J].

Date, SV ;

Marcotte, EM .

NATURE BIOTECHNOLOGY, 2003, 21 (09) :1055-1062

[2] Protein interaction maps for complete genomes based on gene fusion events [J].

Enright, AJ ;

Iliopoulos, I ;

Kyrpides, NC ;

Ouzounis, CA .

NATURE, 1999, 402 (6757) :86-90

[3] Genome sequence of the human malaria parasite Plasmodium falciparum [J].

Gardner, MJ ;

Hall, N ;

Fung, E ;

White, O ;

Berriman, M ;

Hyman, RW ;

Carlton, JM ;

Pain, A ;

Nelson, KE ;

Bowman, S ;

Paulsen, IT ;

James, K ;

Eisen, JA ;

Rutherford, K ;

Salzberg, SL ;

Craig, A ;

Kyes, S ;

Chan, MS ;

Nene, V ;

Shallom, SJ ;

Suh, B ;

Peterson, J ;

Angiuoli, S ;

Pertea, M ;

Allen, J ;

Selengut, J ;

Haft, D ;

Mather, MW ;

Vaidya, AB ;

Martin, DMA ;

Fairlamb, AH ;

Fraunholz, MJ ;

Roos, DS ;

Ralph, SA ;

McFadden, GI ;

Cummings, LM ;

Subramanian, GM ;

Mungall, C ;

Venter, JC ;

Carucci, DJ ;

Hoffman, SL ;

Newbold, C ;

Davis, RW ;

Fraser, CM ;

Barrell, B .

NATURE, 2002, 419 (6906) :498-511

[4] Differential genome analysis applied to the species-specific features of Helicobacter pylori [J].

Huynen, M ;

Dandekar, T ;

Bork, P .

FEBS LETTERS, 1998, 426 (01) :1-5

[5]

MARCOTTE CJV, 2002, APPL BIOINFORMATICS, V1, P37

[6] Detecting protein function and protein-protein interactions from genome sequences [J].

Marcotte, EM ;

Pellegrini, M ;

Ng, HL ;

Rice, DW ;

Yeates, TO ;

Eisenberg, D .

SCIENCE, 1999, 285 (5428) :751-753

[7] Predictome: a database of putative functional links between proteins [J].

Mellor, JC ;

Yanai, I ;

Clodfelter, KH ;

Mintseris, J ;

DeLisi, C .

NUCLEIC ACIDS RESEARCH, 2002, 30 (01) :306-309

[8] Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles [J].

Pellegrini, M ;

Marcotte, EM ;

Thompson, MJ ;

Eisenberg, D ;

Yeates, TO .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1999, 96 (08) :4285-4288

[9] Operons in Escherichia coli:: Genomic analyses and predictions [J].

Salgado, H ;

Moreno-Hagelsieb, G ;

Smith, TF ;

Collado-Vides, J .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (12) :6652-6657

[10] STRING: a database of predicted functional associations between proteins [J].

von Mering, C ;

Huynen, M ;

Jaeggi, D ;

Schmidt, S ;

Bork, P ;

Snel, B .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :258-261