PathFinder: reconstruction and dynamic visualization of metabolic pathways

Goesmann A, Haubrock M, Meyer F, Kalinowski J, Giegerich R (2002)
BIOINFORMATICS 18(1): 124-129.

Download
Es wurde kein Volltext hochgeladen. Nur Publikationsnachweis!
Zeitschriftenaufsatz | Veröffentlicht | Englisch
Abstract / Bemerkung
Motivation: Beyond methods for a gene-wise annotation and analysis of sequenced genomes new automated methods for functional analysis on a higher level are needed. The identification of realized metabolic pathways provides valuable information on gene expression and regulation. Detection of incomplete pathways helps to improve a constantly evolving genome annotation or discover alternative biochemical pathways. To utilize automated genome analysis on the level of metabolic pathways new methods for the dynamic representation and visualization of pathways are needed. Results: PathFinder is a tool for the dynamic visualization of metabolic pathways based on annotation data. Pathways are represented as directed acyclic graphs, graph layout algorithms accomplish the dynamic drawing and visualization of the metabolic maps. A more detailed analysis of the input data on the level of biochemical pathways helps to identify genes and detect improper parts of annotations. As an Relational Database Management System (RDBMS) based internet application PathFinder reads a list of EC-numbers or a given annotation in EMBL- or Genbank-format and dynamically generates pathway graphs.
Erscheinungsjahr
Zeitschriftentitel
BIOINFORMATICS
Band
18
Ausgabe
1
Seite(n)
124-129
ISSN
eISSN
PUB-ID

Zitieren

Goesmann A, Haubrock M, Meyer F, Kalinowski J, Giegerich R. PathFinder: reconstruction and dynamic visualization of metabolic pathways. BIOINFORMATICS. 2002;18(1):124-129.
Goesmann, A., Haubrock, M., Meyer, F., Kalinowski, J., & Giegerich, R. (2002). PathFinder: reconstruction and dynamic visualization of metabolic pathways. BIOINFORMATICS, 18(1), 124-129. doi:10.1093/bioinformatics/18.1.124
Goesmann, A., Haubrock, M., Meyer, F., Kalinowski, J., and Giegerich, R. (2002). PathFinder: reconstruction and dynamic visualization of metabolic pathways. BIOINFORMATICS 18, 124-129.
Goesmann, A., et al., 2002. PathFinder: reconstruction and dynamic visualization of metabolic pathways. BIOINFORMATICS, 18(1), p 124-129.
A. Goesmann, et al., “PathFinder: reconstruction and dynamic visualization of metabolic pathways”, BIOINFORMATICS, vol. 18, 2002, pp. 124-129.
Goesmann, A., Haubrock, M., Meyer, F., Kalinowski, J., Giegerich, R.: PathFinder: reconstruction and dynamic visualization of metabolic pathways. BIOINFORMATICS. 18, 124-129 (2002).
Goesmann, Alexander, Haubrock, Martin, Meyer, Folker, Kalinowski, Jörn, and Giegerich, Robert. “PathFinder: reconstruction and dynamic visualization of metabolic pathways”. BIOINFORMATICS 18.1 (2002): 124-129.

27 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Identification of metabolic pathways using pathfinding approaches: a systematic review.
Abd Algfoor Z, Shahrizal Sunar M, Abdullah A, Kolivand H., Brief Funct Genomics 16(2), 2017
PMID: 26969656
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases.
Kumar A, Suthers PF, Maranas CD., BMC Bioinformatics 13(), 2012
PMID: 22233419
Multi-membership gene regulation in pathway based microarray analysis.
Pavlidis SP, Payne AM, Swift SM., Algorithms Mol Biol 6(), 2011
PMID: 21939531
Reconstruction of biochemical networks in microorganisms.
Feist AM, Herrgård MJ, Thiele I, Reed JL, Palsson BØ., Nat Rev Microbiol 7(2), 2009
PMID: 19116616
SYSTOMONAS--an integrated database for systems biology analysis of Pseudomonas.
Choi C, Münch R, Leupold S, Klein J, Siegel I, Thielen B, Benkert B, Kucklick M, Schobert M, Barthelmes J, Ebeling C, Haddad I, Scheer M, Grote A, Hiller K, Bunk B, Schreiber K, Retter I, Schomburg D, Jahn D., Nucleic Acids Res 35(database issue), 2007
PMID: 17202169
Mining pathway signatures from microarray data and relevant biological knowledge.
Panteris E, Swift S, Payne A, Liu X., J Biomed Inform 40(6), 2007
PMID: 17395545
BiologicalNetworks: visualization and analysis tool for systems biology.
Baitaluk M, Sedova M, Ray A, Gupta A., Nucleic Acids Res 34(web server issue), 2006
PMID: 16845051
VitaPad: visualization tools for the analysis of pathway data.
Holford M, Li N, Nadkarni P, Zhao H., Bioinformatics 21(8), 2005
PMID: 15564306
A grid layout algorithm for automatic drawing of biochemical networks.
Li W, Kurata H., Bioinformatics 21(9), 2005
PMID: 15677705
PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways.
Mlecnik B, Scheideler M, Hackl H, Hartler J, Sanchez-Cabo F, Trajanoski Z., Nucleic Acids Res 33(web server issue), 2005
PMID: 15980551
A graphic tool for curating molecular interaction networks from the literature.
Lee C, Park J, Park JC., Comput Biol Med 35(7), 2005
PMID: 15809096
Symbolic inference of xenobiotic metabolism.
McShan DC, Updadhayaya M, Shah I., Pac Symp Biocomput (), 2004
PMID: 14992532
PathAligner: metabolic pathway retrieval and alignment.
Chen M, Hofestädt R., Appl Bioinformatics 3(4), 2004
PMID: 15702955
LGL: creating a map of protein function with an algorithm for visualizing very large biological networks.
Adai AT, Date SV, Wieland S, Marcotte EM., J Mol Biol 340(1), 2004
PMID: 15184029
Web-based information retrieval system for the prediction of metabolic pathways.
Chen M, Hofestädt R., IEEE Trans Nanobioscience 3(3), 2004
PMID: 15473071
Information Visualization Techniques in Bioinformatics during the Postgenomic Era.
Tao Y, Liu Y, Friedman C, Lussier YA., Drug Discov Today Biosilico 2(6), 2004
PMID: 20976032
GenDB--an open source genome annotation system for prokaryote genomes.
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Pühler A., Nucleic Acids Res 31(8), 2003
PMID: 12682369
PathMiner: predicting metabolic pathways by heuristic search.
McShan DC, Rao S, Shah I., Bioinformatics 19(13), 2003
PMID: 12967966
Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology.
Goesmann A, Linke B, Rupp O, Krause L, Bartels D, Dondrup M, McHardy AC, Wilke A, Pühler A, Meyer F., J Biotechnol 106(2-3), 2003
PMID: 14651858
Metabolic database systems for the analysis of genome-wide function.
Tsoka S, Ouzounis CA., Biotechnol Bioeng 84(7), 2003
PMID: 14708115

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 11836220
PubMed | Europe PMC

Suchen in

Google Scholar