ProdoNet:: identification and visualization of prokaryotic gene regulatory and metabolic networks

被引：11

作者：

Klein, Johannes ^{[1
]}

Leupold, Stefan ^{[1
]}

Muench, Richard ^{[1
]}

Pommerenke, Claudia ^{[1
,2
]}

Johl, Thorsten ^{[2
]}

Kaerst, Uwe ^{[2
]}

Jaensch, Lothar ^{[2
]}

Jahn, Dieter ^{[1
]}

Retter, Ida ^{[1
]}

机构：

[1] Tech Univ Carolo Wilhelmina Braunschweig, Inst Microbiol, D-38106 Braunschweig, Germany

[2] Helmholtz Ctr Infect Res, Dept Cell Biol, D-38124 Braunschweig, Germany

来源：

NUCLEIC ACIDS RESEARCH | 2008年 / 36卷

关键词：

D O I：

10.1093/nar/gkn217

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：

ProdoNet is a web-based application for the mapping of prokaryotic genes and the corresponding proteins to common gene regulatory and metabolic networks. For a given list of genes, the system detects shared operons, identifies co-expressed genes and deduces joint regulators. In addition, the contribution to shared metabolic pathways becomes visible on KEGG maps. Furthermore, the co-occurrence of genes of interest in gene expression profiles can be added to the visualization of the global network. In this way, ProdoNet provides the basis for functional genomics approaches and for the interpretation of transcriptomics and proteomics data. As an example, we present an investigation of an experimental membrane subproteome analysis of Pseudomonas aeruginosa with ProdoNet. The ProdoNet dataset on transcriptional regulation is based on the PRODORIC Prokaryotic Database of Gene Regulation and the Virtual Footprint tool. ProdoNet is accessible at http://www.prodonet.tu-bs.de.

引用

页码：W460 / W464

页数：5

共 24 条

[1] The ENZYME database in 2000 [J].

Bairoch, A .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :304-305

[2] The Universal Protein Resource (UniProt) [J].

Bairoch, Amos ;

Bougueleret, Lydie ;

Altairac, Severine ;

Amendolia, Valeria ;

Auchincloss, Andrea ;

Puy, Ghislaine Argoud ;

Axelsen, Kristian ;

Baratin, Delphine ;

Blatter, Marie-Claude ;

Boeckmann, Brigitte ;

Bollondi, Laurent ;

Boutet, Emmanuel ;

Quintaje, Silvia Braconi ;

Breuza, Lionel ;

Bridge, Alan ;

Saux, Virginie Bulliard-Le ;

decastro, Edouard ;

Ciampina, Luciane ;

Coral, Danielle ;

Coudert, Elisabeth ;

Cusin, Isabelle ;

David, Fabrice ;

Delbard, Gwennaelle ;

Dornevil, Dolnide ;

Duek-Roggli, Paula ;

Duvaud, Severine ;

Estreicher, Anne ;

Famiglietti, Livia ;

Farriol-Mathis, Nathalie ;

Ferro, Serenella ;

Feuermann, Marc ;

Gasteiger, Elisabeth ;

Gateau, Alain ;

Gehant, Sebastian ;

Gerritsen, Vivienne ;

Gos, Arnaud ;

Gruaz-Gumowski, Nadine ;

Hinz, Ursula ;

Hulo, Chantal ;

Hulo, Nicolas ;

Innocenti, Alessandro ;

James, Janet ;

Jain, Eric ;

Jimenez, Silvia ;

Jungo, Florence ;

Junker, Vivien ;

Keller, Guillaume ;

Lachaize, Corinne ;

Lane-Guermonprez, Lydie ;

Langendijk-Genevaux, Petra .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D190-D195

[3]

BAUMBACH J, 2007, BMC BIOINFORMATICS, V429, P4

[4]

Caspi R, 2008, NUCLEIC ACIDS RES, V36, pD623, DOI [10.1093/nar/gkm900, 10.1093/nar/gkt1103]

[5] Integration of biological networks and gene expression data using Cytoscape [J].

Cline, Melissa S. ;

Smoot, Michael ;

Cerami, Ethan ;

Kuchinsky, Allan ;

Landys, Nerius ;

Workman, Chris ;

Christmas, Rowan ;

Avila-Campilo, Iliana ;

Creech, Michael ;

Gross, Benjamin ;

Hanspers, Kristina ;

Isserlin, Ruth ;

Kelley, Ryan ;

Killcoyne, Sarah ;

Lotia, Samad ;

Maere, Steven ;

Morris, John ;

Ono, Keiichiro ;

Pavlovic, Vuk ;

Pico, Alexander R. ;

Vailaya, Aditya ;

Wang, Peng-Liang ;

Adler, Annette ;

Conklin, Bruce R. ;

Hood, Leroy ;

Kuiper, Martin ;

Sander, Chris ;

Schmulevich, Ilya ;

Schwikowski, Benno ;

Warner, Guy J. ;

Ideker, Trey ;

Bader, Gary D. .

NATURE PROTOCOLS, 2007, 2 (10) :2366-2382

[6] VIS-O-BAC:: exploratory visualization of functional genome studies from bacteria [J].

Dieterich, G ;

Kärst, U ;

Wehland, J ;

Jänsch, L .

BIOINFORMATICS, 2006, 22 (05) :630-631

[7] RegulonDB (version 6.0):: gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation [J].

Gama-Castro, Socorro ;

Jimenez-Jacinto, Veronica ;

Peralta-Gil, Martin ;

Santos-Zavaleta, Alberto ;

Penaloza-Spinola, Monica I. ;

Contreras-Moreira, Bruno ;

Segura-Salazar, Juan ;

Muniz-Rascado, Luis ;

Martinez-Flores, Irma ;

Salgado, Heladia ;

Bonavides-Martinez, Cesar ;

Abreu-Goodger, Cei ;

Rodriguez-Penagos, Carlos ;

Miranda-Rios, Juan ;

Morett, Enrique ;

Merino, Enrique ;

Huerta, Araceli M. ;

Trevino-Quintanilla, Luis ;

Collado-Vides, Julio .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D120-D124

[8] Tractor_DB (version 2.0):: a database of regulatory interactions in gamma-proteobacterial genomes [J].

Gonzalez Perez, Abel ;

Espinosa Angarica, Vladimir ;

Vasconcelos, Ana Tereza R. ;

Collado-Vides, Julio .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D132-D136

[9]

Heer Jeffrey., 2005, Proceedings of the SIGCHI Conference on Hu- man Factors in Computing Systems (CHI), P421, DOI DOI 10.1145/1054972.1055031

[10] KEGG for linking genomes to life and the environment [J].

Kanehisa, Minoru ;

Araki, Michihiro ;

Goto, Susumu ;

Hattori, Masahiro ;

Hirakawa, Mika ;

Itoh, Masumi ;

Katayama, Toshiaki ;

Kawashima, Shuichi ;

Okuda, Shujiro ;

Tokimatsu, Toshiaki ;

Yamanishi, Yoshihiro .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D480-D484

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