A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization

BioData Mining

Volumn 5, Issue 1, 2012, Pages

  Tuikkala, Johannes ^a   Vähämaa, Heidi ^a   Salmela, Pekka ^a   Nevalainen, Olli S ^a   Aittokallio, Tero ^a,b  

^a UNIVERSITY OF TURKU   (Finland)

^b UNIVERSITY OF HELSINKI   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; COMPARATIVE STUDY; COMPUTER PROGRAM; CYTOSCAPE SOFTWARE; DATA BASE; DRAWING; GENE INTERACTION; HUMAN; MULTILEVEL LAYOUT; NONHUMAN; PHYSICAL INTERACTION; PHYSICAL PHENOMENA; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE;

EID: 84858739028     PISSN: None     EISSN: 17560381     Source Type: Journal    
DOI: 10.1186/1756-0381-5-2     Document Type: Article

References (72)

1. Network biology: understanding the cell's functional organization. Barabási AL, Oltvai ZN, Nat Rev Genet 2004 5 101 113 10.1038/nrg1272 14735121 (Pubitemid 38160277)
2. Scale-free networks in cell biology. Albert R, J Cell Sci 2005 118 4947 4957 10.1242/jcs.02714 16254242 (Pubitemid 41672427)
3. Graph-based methods for analysing networks in cell biology. Aittokallio T, Schwikowski B, Brief Bioinform 2006 7 243 255 10.1093/bib/bbl022 16880171 (Pubitemid 44404874)
4. Tools for visually exploring biological network. Suderman M, Hallett M, Bioinformatics 2007 23 2651 2659 10.1093/bioinformatics/btm401 17720984 (Pubitemid 350048327)
5. A survey of visualization tools for biological network analysis. Pavlopoulos GA, Wegener AL, Schneider R, BioData Mining 2008 1 12 10.1186/1756-0381-1-12 19040716
6. How to visually interpret biological data using networks. Merico D, Gfeller D, Bader GD, Nat Biotechnol 2009 27 921 924 10.1038/nbt.1567 19816451
7. A decade of systems biology. Chuang HY, Hofree M, Ideker T, Annu Rev Cell Dev Biol 2010 26 721 744 10.1146/annurev-cellbio-100109-104122 20604711
8. Using graph theory to analyze biological networks. Pavlopoulos GA, Secrier M, Moschopoulos CN, Soldatos TG, Kossida S, Aerts J, Schneider R, Bagos PG, BioData Mining 2011 4 10 10.1186/1756-0381-4-10 21527005
9. Schreiber F, Vis Methods Mol Biol 2008 453 441 450 10.1007/978-1-60327- 429-6-23
10. Visualization of omics data for systems biology. Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin AC, Nat Methods 2010 7 3 Suppl 56 S68 20195258
11. Layout search of a gene regulatory network for 3-D visualization. Hosoyama N, Nasimul N, Iba H, Genome Inform 2003 14 103 113
12. An efficient grid layout for biological networks utilizing various biological attributes. Kojima K, Nagasaki M, Jeong E, Kato M, Miyano S, BMC Bioinforma 2007 8 76 10.1186/1471-2105-8-76 (Pubitemid 46443806)
13. The Pathways Tools cellular overview diagram and Omics Viewer. Paley SM, Karp PD, Nucleic Acids Res 2006 34 3771 3778 10.1093/nar/gkl334 16893960 (Pubitemid 44400426)
14. Arcadia: a visualization tool for metabolic pathways. Villéger AC, Pettifer SR, Kell DB, Bioinformatics 2010 26 1470 1471 10.1093/bioinformatics/ btq154 20453003
15. OptFlux: an open-source software platform for in silico metabolic engineering. Rocha I, Maia P, Evangelista P, Vilaca P, Soares S, Pinto JP, Nielsen J, Patil KR, Ferreira EC, Rocha M, BMC Syst Biol 2010 4 45 10.1186/1752-0509-4-45 20403172
16. Improved layout of phylogenetic networks. Gambette P, Huson DH, IEEE/ACM Trans Comput Biol Bioinform 2008 5 472 479 18670049
17. FragViz: visualization of fragmented networks. Stajdohar M, Mramor M, Zupan B, Demar J, BMC Bioinforma 2010 11 475 10.1186/1471-2105-11-475
18. LucidDraw: efficiently visualizing complex biochemical networks within MATLAB. He S, Mei J, Shi G, Wang Z, Li W, BMC Bioinforma 2010 11 31 10.1186/1471-2105-11-31
19. FNV: Light-weight Flash-based network and pathway viewer. Dannenfelser R, Lachmann A, Szenk M, Ma'ayan A, Bioinformatics 2011 27 1181 1182 10.1093/bioinformatics/btr098 21349871
20. Integration of biological networks and gene expression data using Cytoscape. Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD, Nat Protoc 2007 2 2366 2382 10.1038/nprot.2007.324 17947979
21. 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 2498 2504 10.1101/gr.1239303 14597658 (Pubitemid 37428274)
22. An algorithm for drawing general undirected graphs. Kamada T, Kawai S, Inf Process Lett 1989 31 7 15 10.1016/0020-0190(89)90102-6
23. Graph drawing by force-directed placement. Fruchterman TM, Reingold EM, Software Pract Exper 1991 21 1129 1164 10.1002/spe.4380211102
24. From molecular to modular cell biology. Hartwell LH, Hopfield JJ, Leibler S, Murray AW, Nature 1999 402 6761 Suppl 47 C52 10591225
25. Quantitative genetic interactions reveal biological modularity. Beltrao P, Cagney G, Krogan NJ, Cell 2010 141 739 745 10.1016/j.cell.2010.05.019 20510918
26. Dynamic modularity in protein interaction networks predicts breast cancer outcome. Taylor IW, Linding R, Warde-Farley D, Liu Y, Pesquita C, Faria D, Bull S, Pawson T, Morris Q, Wrana JL, Nat Biotechnol 2009 27 199 204 10.1038/nbt.1522 19182785
27. Protein networks as logic functions in development and cancer. Dutkowski J, Ideker T, PLoS Comput Biol 2011 7 1002180 10.1371/journal.pcbi.1002180 21980275
28. Systematic mapping of genetic interaction networks. Dixon SJ, Costanzo M, Baryshnikova A, Andrews B, Boone C, Annu Rev Genet 2009 43 601 625 10.1146/annurev.genet.39.073003.114751 19712041
29. Protein complexes are central in the yeast genetic landscape. Michaut M, Baryshnikova A, Costanzo M, Myers CL, Andrews BJ, Boone C, Bader GD, PLoS Comput Biol 2011 7 1001092 10.1371/journal.pcbi.1001092 21390331
30. A multilevel algorithm for force-directed graph-drawing. Walshaw C, J Graph Algorithms Appl 2003 7 253 285 (Pubitemid 39064694)
31. A multilevel graph layout algorithm for Cytoscape bioinformatics software platform. Salmela P, Nevalainen OS, Aittokallio T, Turku Centre for Computer Science Turku 2008 http://tucs.fi:8080/publications/insight.php?id=tSaAiNe08a Technical Report 861
32. Indexing metric spaces with M-tree. Ciaccia P, Patella M, Rabitti F, Zezula P, Proc Quinto Convegno Nazionale SEBD Verona 1997 1 20
33. Accelerating GLA with an M-Tree. Luoma O, Tuikkala J, Nevalainen O, World Academy of Science, Engineering and Technology 2005 Volume 4 196 199
34. Multilevel Layout Project. http://code.google.com/p/multilevellayout/
35. Biological Evaluation Project. http://code.google.com/p/ externalvalidator/
36. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Lord PW, Stevens RD, Brass A, Goble CA, Bioinformatics 2003 19 1275 1283 10.1093/bioinformatics/btg153 12835272 (Pubitemid 36850221)
37. Semantic similarity in biomedical ontologies. Pesquita C, Faria D, Falcão AO, Lord P, Couto FM, PLoS Comput Biol 2009 5 1000443 10.1371/journal.pcbi.1000443 19649320
38. Improving missing value estimation in microarray data with gene ontology. Tuikkala J, Elo L, Nevalainen OS, Aittokallio T, Bioinformatics 2006 22 566 572 10.1093/bioinformatics/btk019 16377613 (Pubitemid 43372817)
39. Exploring genetic interactions and networks with yeast. Boone C, Bussey H, Andrews BJ, Nat Rev Genet 2007 8 437 449 10.1038/nrg2085 17510664 (Pubitemid 46789246)
40. Integrating physical and genetic maps: from genomes to interaction networks. Beyer A, Bandyopadhyay S, Ideker T, Nat Rev Genet 2007 8 699 710 10.1038/nrg2144 17703239 (Pubitemid 47281988)
41. CCSB Interactome Database. http://interactome.dfci.harvard.edu/S- cerevisiae/index.php
42. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y, Proc Natl Acad Sci USA 2001 98 4277 4278 10.1073/pnas.091096398 11296274 (Pubitemid 32294963)
43. High-quality binary protein interaction map of the yeast interactome network. Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, Sahalie J, Hirozane- Kishikawa T, Gebreab F, Li N, Simonis N, Hao T, Rual JF, Dricot A, Vazquez A, Murray RR, Simon C, Tardivo L, Tam S, Svrzikapa N, Fan C, de Smet AS, Motyl A, Hudson ME, Park J, Xin X, Cusick ME, Moore T, Boone C, Snyder M, Roth FP, Barabási AL, Tavernier J, Hill DE, Vidal M, Science 2008 322 104 110 10.1126/science.1158684 18719252
44. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM, Nature 2000 403 623 627 10.1038/35001009 10688190 (Pubitemid 30103994)
45. Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Collins SR, Kemmeren P, Zhao XC, Greenblatt JF, Spencer F, Holstege FC, Weissman JS, Krogan NJ, Mol Cell Proteomics 2007 6 439 450 17200106 (Pubitemid 46554539)
46. 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, Dümpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, Hudak M, Michon AM, Schelder M, Schirle M, Remor M, Rudi T, Hooper S, Bauer A, Bouwmeester T, Casari G, Drewes G, Neubauer G, Rick JM, Kuster B, Bork P, Russell RB, Superti-Furga G, Nature 2006 440 631 636 10.1038/nature04532 16429126
47. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrín-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Mandy HY, Lam MHY, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF, Nature 2006 440 637 643 10.1038/nature04670 16554755
48. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hon GC, Myers CL, Parsons A, Friesen H, Oughtred R, Tong A, Stark C, Ho Y, Botstein D, Andrews B, Boone C, Troyanskya OG, Ideker T, Dolinski K, Batada NN, Tyers M, J Biol 2006 5 11 10.1186/jbiol36 16762047
49. Comparative assessment of large-scale data sets of protein-protein interactions. von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P, Nature 2002 417 399 403 12000970 (Pubitemid 34563526)
50. A network of protein-protein interactions in yeast. Schwikowski B, Uetz P, Fields S, Nat Biotechnol 2000 18 1257 1261 10.1038/82360 11101803
51. The Krogan Lab Interactome Database. http://interactome-cmp.ucsf.edu/
52. The Boone Lab DRYGIN Database. http://drygin.ccbr.utoronto.ca/
53. Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Schuldiner M, Collins SR, Thompson NJ, Denic V, Bhamidipati A, Punna T, Ihmels J, Andrews B, Boone C, Greenblatt JF, Weissman JS, Krogan NJ, Cell 2005 123 507 519 10.1016/j.cell.2005.08.031 16269340 (Pubitemid 41546679)
54. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Collins SR, Miller KM, Maas NL, Roguev A, Fillingham J, Chu CS, Schuldiner M, Gebbia M, Recht J, Shales M, Ding H, Xu H, Han J, Ingvarsdottir K, Cheng B, Andrews B, Boone C, Berger SL, Hieter P, Zhang Z, Brown GW, Ingles CJ, Emili A, Allis CD, Toczyski DP, Weissman JS, Greenblatt JF, Krogan NJ, Nature 2007 446 806 810 10.1038/nature05649 17314980 (Pubitemid 46582025)
55. The genetic landscape of a cell. Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, et al. Science 2010 327 425 431 10.1126/science.1180823 20093466
56. A hierarchical O(N log N) force-calculation algorithm. Barnes J, Hut P, Nature 1986 324 446 449 10.1038/324446a0
57. Cytoscape website. http://www.cytoscape.org
58. Quantitative maps of genetic interactions in yeast: Comparative evaluation and integrative analysis. Lindén RO, Eronen VP, Aittokallio T, BMC Syst Biol 2011 5 45 10.1186/1752-0509-5-45 21435228
59. Characterizing genetic interactions in human disease association studies using statistical epistasis networks. Hu T, Sinnott-Armstrong NA, Kiralis JW, Andrew AS, Karagas MR, Moore JH, BMC Bioinforma 2011 12 364 10.1186/1471-2105- 12-364
60. Human Protein Reference Database-2009 update. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A, Nucleic Acids Res 2009 37 767 D772
61. Module finding approaches for protein interaction networks. Aittokallio T, Biological Data Mining in Protein Interaction Networks Hershey: IGI Global, Li XL, Ng SK, 2009 335 353 Medical Information Science Series
62. An automated method for finding molecular complexes in large protein interaction networks. Bader GD, Hogue CW, BMC Bioinforma 2003 4 2 10.1186/1471-2105-4-2 (Pubitemid 38751268)
63. Graphle: interactive exploration of large, dense graphs. Huttenhower C, Mehmood SO, Troyanskaya OG, BMC Bioinforma 2009 10 417 10.1186/1471-2105-10-417
64. GenePro: a Cytoscape plug-in for advanced visualization and analysis of interaction networks. Vlasblom J, Wu S, Pu S, Superina M, Liu G, Orsi C, Wodak SJ, Bioinformatics 2006 22 2178 2179 10.1093/bioinformatics/btl356 16921162 (Pubitemid 44390917)
65. GLay: community structure analysis of biological networks. Su G, Kuchinsky A, Morris JH, States DJ, Meng F, Bioinformatics 2010 26 3135 3137 10.1093/bioinformatics/btq596 21123224
66. GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. Garcia O, Saveanu C, Cline M, Fromont-Racine M, Jacquier A, Schwikowski B, Aittokallio T, Bioinformatics 2007 23 394 396 10.1093/bioinformatics/btl605 17127678 (Pubitemid 46323170)
67. A generic algorithm for layout of biological networks. Schreiber F, Dwyer T, Marriott K, Wybrow M, BMC Bioinforma 2009 10 375 10.1186/1471-2105-10-375
68. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pagès F, Trajanoski Z, Galon J, Bioinformatics 2009 25 1091 1093 10.1093/bioinformatics/btp101 19237447
69. MetNetGE: interactive views of biological networks and ontologies. Jia M, Choi SY, Reiners D, Wurtele ES, Dickerson JA, BMC Bioinforma 2010 11 469 10.1186/1471-2105-11-469
70. Using the clustered circular layout as an informative method for visualizing protein-protein interaction networks. Fung DC, Wilkins MR, Hart D, Hong SH, Proteomics 2010 10 2723 2727 10.1002/pmic.201000046 20480505
71. Interactive, multiscale navigation of large and complicated biological networks. Praneenararat T, Takagi T, Iwasaki W, Bioinformatics 2011 27 1121 1127 10.1093/bioinformatics/btr083 21349867
72. NAViGaTOR: Network Analysis, Visualization and Graphing Toronto. Brown KR, Otasek D, Ali M, McGuffin MJ, Xie W, Devani B, Toch IL, Jurisica I, Bioinformatics 2009 25 3327 3329 10.1093/bioinformatics/btp595 19837718