APID: Agile Protein Interaction DataAnalyzer

被引：156

作者：

Prieto, Carlos ^{[1
]}

Rivas, Javier De Las ^{[1
]}

机构：

[1] CSIC, Bioinformat & Funct Genom Res Grp, CIC, USAL,Canc Res Ctr, E-37007 Salamanca, Spain

来源：

NUCLEIC ACIDS RESEARCH | 2006年 / 34卷

关键词：

D O I：

10.1093/nar/gkl128

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Agile Protein Interaction DataAnalyzer (APID) is an interactive bioinformatics web tool developed to integrate and analyze in a unified and comparative platform main currently known information about protein-protein interactions demonstrated by specific small-scale or large-scale experimental methods. At present, the application includes information coming from five main source databases enclosing an unified sever to explore > 35 000 different proteins and 111 000 different proven interactions. The web includes search tools to query and browse upon the data, allowing selection of the interaction pairs based in calculated parameters that weight and qualify the reliability of each given protein interaction. Such parameters are for the 'proteins': connectivity, cluster coefficient, Gene Ontology ( GO) functional environment, GO environment enrichment; and for the 'interactions': number of methods, GO overlapping, iPfam domain-domain interaction. APID also includes a graphic interactive tool to visualize selected sub-networks and to navigate on them or along the whole interaction network. The application is available open access at http://bioinfow.dep.usal.es/apid/.

引用

页码：W298 / W302

页数：5

共 20 条

[1] The Biomolecular Interaction Network Database and related tools 2005 update [J].

Alfarano, C ;

Andrade, CE ;

Anthony, K ;

Bahroos, N ;

Bajec, M ;

Bantoft, K ;

Betel, D ;

Bobechko, B ;

Boutilier, K ;

Burgess, E ;

Buzadzija, K ;

Cavero, R ;

D'Abreo, C ;

Donaldson, I ;

Dorairajoo, D ;

Dumontier, MJ ;

Dumontier, MR ;

Earles, V ;

Farrall, R ;

Feldman, H ;

Garderman, E ;

Gong, Y ;

Gonzaga, R ;

Grytsan, V ;

Gryz, E ;

Gu, V ;

Haldorsen, E ;

Halupa, A ;

Haw, R ;

Hrvojic, A ;

Hurrell, L ;

Isserlin, R ;

Jack, F ;

Juma, F ;

Khan, A ;

Kon, T ;

Konopinsky, S ;

Le, V ;

Lee, E ;

Ling, S ;

Magidin, M ;

Moniakis, J ;

Montojo, J ;

Moore, S ;

Muskat, B ;

Ng, I ;

Paraiso, JP ;

Parker, B ;

Pintilie, G ;

Pirone, R .

NUCLEIC ACIDS RESEARCH, 2005, 33 :D418-D424

[2] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[3] Analyzing yeast protein-protein interaction data obtained from different sources [J].

Bader, GD ;

Hogue, CWV .

NATURE BIOTECHNOLOGY, 2002, 20 (10) :991-997

[4] Gaining confidence in high-throughput protein interaction networks [J].

Bader, JS ;

Chaudhuri, A ;

Rothberg, JM ;

Chant, J .

NATURE BIOTECHNOLOGY, 2004, 22 (01) :78-85

[5] Greedily building protein networks with confidence [J].

Bader, JS .

BIOINFORMATICS, 2003, 19 (15) :1869-1874

[6] The universal protein resource (UniProt) [J].

Bairoch, A ;

Apweiler, R ;

Wu, CH ;

Barker, WC ;

Boeckmann, B ;

Ferro, S ;

Gasteiger, E ;

Huang, HZ ;

Lopez, R ;

Magrane, M ;

Martin, MJ ;

Natale, DA ;

O'Donovan, C ;

Redaschi, N ;

Yeh, LSL .

NUCLEIC ACIDS RESEARCH, 2005, 33 :D154-D159

[7]

Cockburn A., 2002, AGILE SOFTWARE DEV, V177

[8] Interactome data and databases: different types of protein interaction [J].

De Las Rivas, J ;

de Luis, A .

COMPARATIVE AND FUNCTIONAL GENOMICS, 2004, 5 (02) :173-178

[9] Protein interactions - Two methods for assessment of the reliability of high throughput observations [J].

Deane, CM ;

Salwinski, L ;

Xenarios, I ;

Eisenberg, D .

MOLECULAR & CELLULAR PROTEOMICS, 2002, 1 (05) :349-356

[10] IntAct: an open source molecular interaction database [J].

Hermjakob, H ;

Montecchi-Palazzi, L ;

Lewington, C ;

Mudali, S ;

Kerrien, S ;

Orchard, S ;

Vingron, M ;

Roechert, B ;

Roepstorff, P ;

Valencia, A ;

Margalit, H ;

Armstrong, J ;

Bairoch, A ;

Cesareni, G ;

Sherman, D ;

Apweller, R .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D452-D455

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