BisoGenet: A new tool for gene network building, visualization and analysis

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Martin, Alexander ^a   Ochagavia, Maria E ^a   Rabasa, Laya C ^a   Miranda, Jamilet ^a   Fernandez de Cossio, Jorge ^a   Bringas, Ricardo ^a  

^a CENTER FOR GENETIC ENGINEERING AND BIOTECHNOLOGY   (Cuba)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL NETWORKS; CLIENT APPLICATIONS; FUNCTIONAL RELATIONSHIP; MULTI-TIER APPLICATIONS; PROTEIN-DNA INTERACTIONS; PROTEIN-PROTEIN INTERACTIONS; TOPOLOGICAL NETWORKS; VISUALIZATION AND ANALYSIS;

BIOINFORMATICS; DATA VISUALIZATION; GENES; PROTEINS; TOOLS; TOPOLOGY; VISUALIZATION; WEB SERVICES;

DATA INTEGRATION;

PROTEOME;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; COMPUTER SIMULATION; DATA BASE; FACTUAL DATABASE; GENE EXPRESSION PROFILING; METABOLISM; METHODOLOGY; PHYSIOLOGY; PROTEIN ANALYSIS; SIGNAL TRANSDUCTION;

ALGORITHMS; COMPUTER GRAPHICS; COMPUTER SIMULATION; DATABASE MANAGEMENT SYSTEMS; DATABASES, FACTUAL; GENE EXPRESSION PROFILING; MODELS, BIOLOGICAL; PROTEIN INTERACTION MAPPING; PROTEOME; SIGNAL TRANSDUCTION; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 77949504985     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-91     Document Type: Article

References (42)

1. Maglott D, Ostell J, Pruitt KD, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 2005, 33:D54-D58. 10.1093/nar/gki031, 539985, 15608257.
2. Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, et al. Ensembl 2008. Nucl Acids Res 2008, 36:D707-D714. 10.1093/nar/gkm988, 2238821, 18000006.
3. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D. The Database of Interacting Proteins: 2004 update. Nucleic Acids Res 2004, (32 Database):D449-D451. 10.1093/nar/gkh086, 308820, 14681454.
4. Alfarano C, Andrade CE, Anthony K, Bahroos N, Bajec M, Bantoft K, et al. The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res 2005, 33:D418-D424. 10.1093/nar/gki051, 540005, 15608229.
5. Mishra GR, Suresh M, Kumaran K, Kannabiran N, Suresh S, Bala P, et al. Human protein reference database--2006 update. Nucleic Acids Res 2006, (34 Database):D411-D414. 10.1093/nar/gkj141, 1347503, 16381900.
6. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. BioGRID: a general repository for interaction datasets. Nucleic Acids Res 2006, (34 Database):D535-D539. 10.1093/nar/gkj109, 1347471, 16381927.
7. Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, Cesareni G. MINT: a Molecular INTeraction database. FEBS Lett 2002, 513:135-140. 10.1016/S0014-5793(01)03293-8, 11911893.
8. Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, et al. IntAct - Open Source Resource for Molecular Interaction Data. Nucleic Acids Res 2007, 35:D561-D565. 10.1093/nar/gkl958, 1751531, 17145710.
9. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, et al. KEGG for linking genomes to life and the environment. Nucl Acids Res 2008, 36:D480-D484. 10.1093/nar/gkm882, 18077471, 2238879.
10. Vastrik I, D'Eustachio P, Schmidt E, Joshi-Tope G, Gopinath G, Croft D, et al. Reactome: a knowledge base of biologic pathways and processes. Genome Biol 2007, 8:R39. 10.1186/gb-2007-8-3-r39, 1868929, 17367534.
11. Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, et al. The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucl Acids Res 2008, 36:D623-D631. 10.1093/nar/gkm900, 17965431, 2238876.
12. Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T, et al. PID: the Pathway Interaction Database. Nucl Acids Res 2009, 37:D674-D679. 10.1093/nar/gkn653, 2686461, 18832364.
13. Klamts S, Haus UU, Theis F. Hypergraphs and Cellular Networks. Plos Computational Biology 2009, 5:e1000385. 10.1371/journal.pcbi.1000385, 2673028, 19478865.
14. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-2504. 10.1101/gr.1239303, 403769, 14597658.
15. Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, et al. The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucl Acids Res 2008, 36:D623-D631. 10.1093/nar/gkm900, 2238876, 17965431.
16. Hu Z, Mellor J, Wu J, DeLisi C. VisANT: data-integrating visual framework for biological networks and modules. Nucleic Acids Res 2005, 33:W352-W357. 10.1093/nar/gki431, 1160192, 15980487.
17. Breitkreutz BJ, Stark C, Tyers M. Osprey: a network visualization system. Genome Biol 2003, 4:R22. 10.1186/gb-2003-4-3-r22, 153462, 12620107.
18. Baitaluk M, Sedova M, Ray A, Gupta A. BiologicalNetworks: visualization and analysis tool for systems biology. Nucleic Acids Res 2006, 34:W466-W471. 10.1093/nar/gkl308, 1538788, 16845051.
19. Pavlopoulos GA, Wegener AL, Schneider R. A survey of visualization tools for biological network analysis. BioData Min 2009, 1.
20. Suderman M, Hallett M. Tools for visually exploring biological networks. Bioinformatics 2007, 23:2651-2659. 10.1093/bioinformatics/btm401, 17720984.
21. Cytoscape plugins. , http://www.cytoscape.org/plugins/index.php
22. Pathway Commons. , http://www.pathwaycommons.org/
23. Intact. , http://www.ebi.ac.uk/intact/
24. Cytoscape Plugin for MiMI. , http://mimiplugin.ncibi.org/index.html
25. Hernandez-Toro J, Prieto C, De Las Rivas J. APID2NET: unified interactome graphic analyzer. Bioinformatics 2007, 23:2495-2497. 10.1093/bioinformatics/btm373, 17644818.
26. Zinovyev A, Viara E, Calzone L, Barillot E. BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. Bioinformatics 2008, 24:876-877. 10.1093/bioinformatics/btm553, 18024474.
27. Funahashi A, Tanimura N, Morohashi M, Kitano H. CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. BIOSILICO 2003, 1:159-162.
28. Xu Q, Modrek B, Lee C. Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. Nucleic Acids Res 2009, 30:3754-3766. 10.1093/nar/gkf492.
29. Wang GS, Cooper TA. Splicing in disease: disruption of the splicing code and the decoding machinery. Nat Rev Genet 2007, 8:749-761. 10.1038/nrg2164, 17726481.
30. NCBI Mapview. , http://www.ncbi.nlm.nih.gov/mapview
31. Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, et al. The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res 2006, (34 Database):D187-D191. 10.1093/nar/gkj161, 1347523, 16381842.
32. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29. 10.1038/75556, 10802651.
33. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, et al. KEGG for linking genomes to life and the environment. Nucl Acids Res 2008, 36:D480-D484. 10.1093/nar/gkm882, 2238879, 18077471.
34. McKusick VA. Mendelian Inheritance in Man. A Catalog of Human Genes and Genetic Disorders. 2009, Baltimore: Johns Hopkins University Press.
35. Pontius JU, Wagner L, Schuler GD. UniGene: a unified view of the transcriptome. The NCBI Handbook 2009, 1-12. Bethesda (MD): National Center for Biotechnology Information.
36. Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2007, 35:D61-D65. 10.1093/nar/gkl842, 1716718, 17130148.
37. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths JS, et al. The Pfam protein families database. Nucleic Acids Res 2004, 32:D138-D141. 10.1093/nar/gkh121, 308855, 14681378.
38. PubMed. , http://www.ncbi.nlm.nih.gov/Pubmed/
39. JUNG: Java Universal Network/Graph Framework. , http://jung.sourceforge.net/
40. JFreeChart. , http://www.jfree.org/jfreechart/
41. CERN colt project. , http://acs.lbl.gov/~hoschek/colt/
42. Wang GS, Cooper TA. Splicing in disease: disruption of the splicing code and the decoding machinery. Nat Rev Genet 2007, 8:749-761. 10.1038/nrg2164, 17726481.