FORG3D: Force-directed 3D graph editor for visualization of integrated genome scale data

BMC Systems Biology

Volumn 3, Issue , 2009, Pages

  Paananen, Jussi ^a   Wong, Garry ^a  

^a UNIVERSITY OF EASTERN FINLAND   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

CAENORHABDITIS ELEGANS;

ANIMAL; ARTICLE; BIOLOGY; CAENORHABDITIS ELEGANS; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; COMPUTER SIMULATION; GENE REGULATORY NETWORK; GENETICS; GENOMICS; METHODOLOGY; PARKINSON DISEASE;

ANIMALS; CAENORHABDITIS ELEGANS; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; COMPUTER SIMULATION; GENE REGULATORY NETWORKS; GENOMICS; PARKINSON DISEASE; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 62149111135     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-3-26     Document Type: Article

References (31)

1. Djebbari A Quackenbush J Seeded Bayesian Networks: Constructing genetic networks from microarray data BMC Syst Biol 2008, 2:57. 2474592 18601736 10.1186/1752-0509-2-57
2. Goni J Esteban FJ de Mendizabal NV Sepulcre J Ardanza-Trevijano S Agirrezabal I Villoslada P A computational analysis of protein-protein interaction networks in neurodegenerative diseases BMC Syst Biol 2008, 2:52. 2443111 18570646 10.1186/1752-0509-2-52
3. Gunsalus KC Ge H Schetter AJ Goldberg DS Han JD Hao T Berriz GF Bertin N Huang J Chuang LS et al Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis Nature 2005, 436:861-865. 10.1038/nature03876 16094371
4. Piano F Gunsalus KC Hill DE Vidal M C. elegans network biology: A beginning WormBook 2006:1-20. 18050437
5. Ruths D Nakhleh L Ram PT Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle BMC Syst Biol 2008, 2:76. 2527501 18713463 10.1186/1752-0509-2-76
6. Zhang S Zhang XS Chen L Biomolecular network querying: A promising approach in systems biology BMC Syst Biol 2008, 2:5. 2245906 18205908 10.1186/1752-0509-2-5
7. Hartwell LH Hopfield JJ Leibler S Murray AW From molecular to modular cell biology Nature 1999, 402:C47-52. 10.1038/35011540 10591225
8. Li S Armstrong CM Bertin N Ge H Milstein S Boxem M Vidalain PO Han JD Chesneau A Hao T et al A map of the interactome network of the metazoan C. elegans Science 2004, 303:540-543. 1698949 14704431 10.1126/ science.1091403
9. Byrne AB Weirauch MT Wong V Koeva M Dixon SJ Stuart JM Roy PJ A global analysis of genetic interactions in Caenorhabditis elegans J Biol 2007, 6:8. 2373897 17897480 10.1186/jbiol58
10. Fire A Xu S Montgomery MK Kostas SA Driver SE Mello CC Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans Nature 1998, 391:806-811. 10.1038/35888 9486653
11. Lehner B Crombie C Tischler J Fortunato A Fraser AG Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathways Nat Genet 2006, 38:896-903. 10.1038/ng1844 16845399
12. Jansen R Greenbaum D Gerstein M Relating whole-genome expression data with protein-protein interactions Genome Res 2002, 12:37-46. 155252 11779829 10.1101/gr.205602
13. Garcia O Saveanu C Cline M Fromont-Racine M Jacquier A Schwikowski B Aittokallio T GOlorize: A Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring Bioinformatics 2007, 23:394-396. 10.1093/bioinformatics/btl605 17127678
14. Shannon P Markiel A Ozier O Baliga NS Wang JT Ramage D Amin N Schwikowski B Ideker T Cytoscape: A software environment for integrated models of biomolecular interaction networks Genome Res 2003, 13:2498-2504. 403769 14597658 10.1101/gr.1239303
15. Butcher JC Numerical methods for ordinary differential equations Hoboken, NJ: J. Wiley; 2003.
16. Becker MY Rojas I A graph layout algorithm for drawing metabolic pathways Bioinformatics 2001, 17:461-467. 10.1093/bioinformatics/ 17.5.461 11331241
17. Enright AJ Ouzounis CA BioLayout - an automatic graph layout algorithm for similarity visualization Bioinformatics 2001, 17:853-854. 10.1093/ bioinformatics/17.9.853 11590107
18. Lakso M Vartiainen S Moilanen AM Sirvio J Thomas JH Nass R Blakely RD Wong G Dopaminergic neuronal loss and motor deficits in Caenorhabditis elegans overexpressing human alpha-synuclein J Neurochem 2003, 86:165-172. 10.1046/j.1471-4159.2003.01809.x 12807436
19. Vartiainen S Pehkonen P Lakso M Nass R Wong G Identification of gene expression changes in transgenic C. elegans overexpressing human alpha-synuclein Neurobiol Dis 2006, 22:477-486. 10.1016/ j.nbd.2005.12.021 16626960
20. Rogers A Antoshechkin I Bieri T Blasiar D Bastiani C Canaran P Chan J Chen WJ Davis P Fernandes J et al WormBase 2007 Nucleic Acids Res 2008, 36:D612-617. 2238927 17991679 10.1093/nar/gkm975
21. Kenyon C Chang J Gensch E Rudner A Tabtiang R A C. elegans mutant that lives twice as long as wild type Nature 1993, 366:461-464. 10.1038/ 366461a0 8247153
22. Lee I Lehner B Crombie C Wong W Fraser AG Marcotte EM A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans Nat Genet 2008, 40:181-188. 10.1038/ng.2007.70 18223650
23. Paananen J Storvik M Wong G CROPPER: A metagene creator resource for cross-platform and cross-species compendium studies BMC Bioinformatics 2006, 7:418. 1592126 16995941 10.1186/1471-2105-7-418
24. Breitkreutz BJ Stark C Tyers M Osprey: A network visualization system Genome Biol 2003, 4:R22. 153462 12620107 10.1186/gb-2003-4-3-r22
25. Dogrusoz U Erson EZ Giral E Demir E Babur O Cetintas A Colak R PATIKAweb: A Web interface for analyzing biological pathways through advanced querying and visualization Bioinformatics 2006, 22:374-375. 10.1093/bioinformatics/bti776 16287939
26. Hu Z Snitkin ES DeLisi C VisANT: An integrative framework for networks in systems biology Brief Bioinform 2008, 9:317-325. 10.1093/bib/bbn020 18463131
27. NAViGaTOR 1.2 http://ophid.utoronto.ca/navigator
28. Mutzel P Jünger M Leipert S Graph drawing: 9th international symposium, GD 2001 Vienna, Austria, September 23-26, 2001: Revised papers Berlin; New York: Springer; 2002.
29. Ju BH Park B Park JH Han K Visualization and analysis of protein interactions Bioinformatics 2003, 19:317-318. 10.1093/bioinformatics/ 19.2.317 12538268
30. Ho E Webber R Wilkins MR Interactive three-dimensional visualization and contextual analysis of protein interaction networks J Proteome Res 2008, 7:104-112. 10.1021/pr070274m 18020406
31. Freeman TC Goldovsky L Brosch M van Dongen S Maziere P Grocock RJ Freilich S Thornton J Enright AJ Construction, visualisation, and clustering of transcription networks from microarray expression data PLoS Comput Biol 2007, 3:2032-2042. 2041979 17967053 10.1371/ journal.pcbi.0030206