Medusa: A tool for exploring and clustering biological networks

BMC Research Notes

Volumn 4, Issue , 2011, Pages

  Pavlopoulos, Georgios A ^a,b   Hooper, Sean D ^c   Sifrim, Alejandro ^a   Schneider, Reinhard ^b,d   Aerts, Jan ^a  

^a UNIVERSITY OF LEUVEN   (Belgium)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^c UPPSALA UNIVERSITY   (Sweden)

^d UNIVERSITY OF LUXEMBOURG   (Luxembourg)

Author keywords

biological networks; clustering analysis; Data integration; graph; visualization

Indexed keywords

EID: 80053463904     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-4-384     Document Type: Article

References (28)

1. Using graph theory to analyze biological networks. Pavlopoulos GA, Secrier M, Moschopoulos CN, Soldatos TG, Kossida S, Aerts J, Schneider R, Bagos PG, BioData Min 2011 4 1 10 10.1186/1756-0381-4-10 21527005
2. A survey of visualization tools for biological network analysis. Pavlopoulos GA, Wegener AL, Schneider R, BioData Min 2008 1 12 10.1186/1756-0381-1-12 19040716
3. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T, Genome Res 2003 13 11 2498 2504 10.1101/gr.1239303 14597658 (Pubitemid 37428274)
4. Cytoscape Web: an interactive web-based network browser. Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD, Bioinformatics 2010 26 18 2347 2348 10.1093/bioinformatics/btq430 20656902
5. Osprey: a network visualization system. Breitkreutz BJ, Stark C, Tyers M, Genome Biol 2003 4 3 22 10.1186/gb-2003-4-3-r22 12620107
6. Graph-based analysis and visualization of experimental results with ONDEX. Kohler J, Baumbach J, Taubert J, Specht M, Skusa A, Ruegg A, Rawlings C, Verrier P, Philippi S, Bioinformatics 2006 22 11 1383 1390 10.1093/ bioinformatics/btl081 16533819 (Pubitemid 43985275)
7. Medusa: a simple tool for interaction graph analysis. Hooper SD, Bork P, Bioinformatics 2005 21 24 4432 4433 10.1093/bioinformatics/bti696 16188923 (Pubitemid 41782941)
8. Arena3D: visualization of biological networks in 3D. Pavlopoulos GA, O'Donoghue SI, Satagopam VP, Soldatos TG, Pafilis E, Schneider R, BMC Syst Biol 2008 2 104 10.1186/1752-0509-2-104 19040715
9. Pajek-Program for Large Network Analysis. Batagelj V, Mrvar A, Connections 1998 21 47 57
10. BioLayout(Java): versatile network visualisation of structural and functional relationships. Goldovsky L, Cases I, Enright AJ, Ouzounis CA, Appl Bioinformatics 2005 4 1 71 74 10.2165/00822942-200504010-00009 16000016 (Pubitemid 41043904)
11. ClusterMaker. http://www.rbvi.ucsf.edu/cytoscape/cluster/clusterMaker. html
12. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Maere S, Heymans K, Kuiper M, Bioinformatics 2005 21 16 3448 3449 10.1093/bioinformatics/bti551 15972284 (Pubitemid 41222459)
13. Arena3D: visualization of biological networks in 3D. Pavlopoulos GA, Seán IOD, Venkata PS, Soldatos T, Pafilis E, Schneider R, BMC Syst Biol 2008 2
14. Graph Drawing by Force-Directed Placement. Fruchterman TMJ, Reingold EM, Software, Practice and Experience 1991 21 1129 1164 10.1002/spe.4380211102
15. Distance Geometry and Molecular Conformation. Crippen GM, Havel TF, New York: Wiley 1988
16. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Nat Genet 2000 25 1 25 29 10.1038/75556 10802651 (Pubitemid 30257031)
17. Clustering by passing messages between data points. Frey BJ, Dueck D, Science 2007 315 5814 972 976 10.1126/science.1136800 17218491 (Pubitemid 46281181)
18. Kmeans Some Methods for classification and Analysis of Multivariate Observations. MacQueen JB, 5-th Berkeley Symposium on Mathematical Statistics and Probability Berkeley University of California Press 1967 281 297
19. Spectral clustering of protein sequences. Paccanaro A, Casbon JA, Saqi MA, Nucleic Acids Res 2006 34 5 1571 1580 10.1093/nar/gkj515 16547200
20. Proteome survey reveals modularity of the yeast cell machinery. Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dumpelfeld B, et al. Nature 2006 440 7084 631 636 10.1038/nature04532 16429126
21. An enhanced Markov clustering method for detecting protein complexes. Moschopoulos CN, Pavlopoulos GA, Likothanassis SD, Kossida S, 8st IEEE International Conference on Bioinformatics and Bioengineering: 8-10 October 2008, 2008; Athens, Greece
22. jClust: a clustering and visualization toolbox. Pavlopoulos GA, Moschopoulos CN, Hooper SD, Schneider R, Kossida S, Bioinformatics 2009 25 15 1994 1996 10.1093/bioinformatics/btp330 19454618
23. GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques. Satagopam VP, Theodoropoulou MC, Stampolakis CK, Pavlopoulos GA, Papandreou NC, Bagos PG, Schneider R, Hamodrakas SJ, Database (Oxford) 2010 2010 aq019
24. STRING 7-recent developments in the integration and prediction of protein interactions. von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Krüger B, Snel B, Bork P, Nucleic Acids Res 2006 35 D358-62
25. Integration of phenotypic metadata and protein similarity in Archaea using a spectral bipartitioning approach. Hooper SD, Anderson IJ, Pati A, Dalevi D, Mavromatis K, Kyrpides NC, Nucleic Acids Res 2009 37 7 2096 2104 10.1093/nar/gkp075 19223325
26. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, et al. Bioinformatics 2003 19 4 524 531 10.1093/bioinformatics/btg015 12611808 (Pubitemid 36336519)
27. The HUPO PSI's molecular interaction format - a community standard for the representation of protein interaction data. Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, et al. Nat Biotechnol 2004 22 2 177 183 10.1038/nbt926 14755292 (Pubitemid 38160532)
28. Processing. http://processing.org/