BiologicalNetworks: Visualization and Analysis Tool for Systems Biology

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2006 Jul 18

PMID 16845051

Citations 31

Authors

Michael Baitaluk

Mayya Sedova

Animesh Ray

Amarnath Gupta

Affiliations

Soon will be listed here.

Abstract

Systems level investigation of genomic scale information requires the development of truly integrated databases dealing with heterogeneous data, which can be queried for simple properties of genes or other database objects as well as for complex network level properties, for the analysis and modelling of complex biological processes. Towards that goal, we recently constructed PathSys, a data integration platform for systems biology, which provides dynamic integration over a diverse set of databases [Baitaluk et al. (2006) BMC Bioinformatics 7, 55]. Here we describe a server, BiologicalNetworks, which provides visualization, analysis services and an information management framework over PathSys. The server allows easy retrieval, construction and visualization of complex biological networks, including genome-scale integrated networks of protein-protein, protein-DNA and genetic interactions. Most importantly, BiologicalNetworks addresses the need for systematic presentation and analysis of high-throughput expression data by mapping and analysis of expression profiles of genes or proteins simultaneously on to regulatory, metabolic and cellular networks. BiologicalNetworks Server is available at http://brak.sdsc.edu/pub/BiologicalNetworks.

Citing Articles

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Zhang Y, Li H, Guo H, Li B, Zhao Z, Wang P Front Pharmacol. 2020; 10:1383.

PMID: 31920636 PMC: 6920098. DOI: 10.3389/fphar.2019.01383.

BioNetApp: An interactive visual data analysis platform for molecular expressions.

Roumani A, Madkour A, Ouzzani M, McGrew T, Omran E, Zhang X PLoS One. 2019; 14(2):e0211277.

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Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.

Pavlopoulos G, Malliarakis D, Papanikolaou N, Theodosiou T, Enright A, Iliopoulos I Gigascience. 2015; 4:38.

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Wang L, Liu J, Li Y, Li B, Zhang Y, Jing Z BMC Syst Biol. 2015; 9:11.

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References

Goesmann A, Haubrock M, Meyer F, Kalinowski J, Giegerich R . PathFinder: reconstruction and dynamic visualization of metabolic pathways. Bioinformatics. 2002; 18(1):124-9. DOI: 10.1093/bioinformatics/18.1.124. View

Schacherer F, Choi C, Gotze U, Krull M, Pistor S, Wingender E . The TRANSPATH signal transduction database: a knowledge base on signal transduction networks. Bioinformatics. 2001; 17(11):1053-7. DOI: 10.1093/bioinformatics/17.11.1053. View

Hucka M, Finney A, Sauro H, Bolouri H, Doyle J, Kitano H . The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003; 19(4):524-31. DOI: 10.1093/bioinformatics/btg015. View

Breitkreutz B, Stark C, Tyers M . Osprey: a network visualization system. Genome Biol. 2003; 4(3):R22. PMC: 153462. DOI: 10.1186/gb-2003-4-3-r22. View

Krishnamurthy L, Nadeau J, Ozsoyoglu G, Ozsoyoglu M, Schaeffer G, Tasan M . Pathways database system: an integrated system for biological pathways. Bioinformatics. 2003; 19(8):930-7. DOI: 10.1093/bioinformatics/btg113. View

Nikitin A, Egorov S, Daraselia N, Mazo I . Pathway studio--the analysis and navigation of molecular networks. Bioinformatics. 2003; 19(16):2155-7. DOI: 10.1093/bioinformatics/btg290. View

Shannon P, Markiel A, Ozier O, Baliga N, Wang J, Ramage D . Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003; 13(11):2498-504. PMC: 403769. DOI: 10.1101/gr.1239303. View

Harris M, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R . The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2003; 32(Database issue):D258-61. PMC: 308770. DOI: 10.1093/nar/gkh036. View

Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A . The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol. 2004; 22(2):177-83. DOI: 10.1038/nbt926. View

10.

Pan D, Sun N, Cheung K, Guan Z, Ma L, Holford M . PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis. BMC Bioinformatics. 2003; 4:56. PMC: 302111. DOI: 10.1186/1471-2105-4-56. View

11.

Hu Z, Mellor J, Wu J, DeLisi C . VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinformatics. 2004; 5:17. PMC: 368431. DOI: 10.1186/1471-2105-5-17. View

12.

Chung H, Kim M, Park C, Kim J, Kim J . ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics. Nucleic Acids Res. 2004; 32(Web Server issue):W460-4. PMC: 441614. DOI: 10.1093/nar/gkh476. View

13.

Chen K, Calzone L, Csikasz-Nagy A, Cross F, Novak B, Tyson J . Integrative analysis of cell cycle control in budding yeast. Mol Biol Cell. 2004; 15(8):3841-62. PMC: 491841. DOI: 10.1091/mbc.e03-11-0794. View

14.

Pandey R, Guru R, Mount D . Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data. Bioinformatics. 2004; 20(13):2156-8. DOI: 10.1093/bioinformatics/bth215. View

15.

Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M . KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 1998; 27(1):29-34. PMC: 148090. DOI: 10.1093/nar/27.1.29. View

16.

Hu Z, Mellor J, Wu J, Yamada T, Holloway D, DeLisi C . VisANT: data-integrating visual framework for biological networks and modules. Nucleic Acids Res. 2005; 33(Web Server issue):W352-7. PMC: 1160192. DOI: 10.1093/nar/gki431. View

17.

Mlecnik B, Scheideler M, Hackl H, Hartler J, Sanchez-Cabo F, Trajanoski Z . PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways. Nucleic Acids Res. 2005; 33(Web Server issue):W633-7. PMC: 1160152. DOI: 10.1093/nar/gki391. View

18.

Baitaluk M, Qian X, Godbole S, Raval A, Ray A, Gupta A . PathSys: integrating molecular interaction graphs for systems biology. BMC Bioinformatics. 2006; 7:55. PMC: 1409799. DOI: 10.1186/1471-2105-7-55. View

19.

Ball C, Jin H, Sherlock G, Weng S, Matese J, Andrada R . Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2000; 29(1):80-1. PMC: 29796. DOI: 10.1093/nar/29.1.80. View

20.

Bader G, Donaldson I, Wolting C, Ouellette B, Pawson T, Hogue C . BIND--The Biomolecular Interaction Network Database. Nucleic Acids Res. 2000; 29(1):242-5. PMC: 29820. DOI: 10.1093/nar/29.1.242. View