Vanted: A system for advanced data analysis and visualization in the context of biological networks

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Junker, Björn H ^a   Klukas, Christian ^a   Schreiber, Falk ^a  

^a LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATICALLY GENERATED; BIOCHEMICAL EXPERIMENTS; BIOINFORMATICS TOOLS; CLASSIFICATION HIERARCHIES; DEVELOPMENTAL STAGE; HIGH-THROUGHPUT METHOD; METABOLITE PROFILING; VISUALIZATION AND ANALYSIS;

BIOINFORMATICS; BIOMOLECULES; JAVA PROGRAMMING LANGUAGE; METABOLISM; METABOLITES; RESEARCH; TOOLS; VISUALIZATION;

DATA VISUALIZATION;

ARTICLE; BIOCHEMISTRY; COMPUTER PROGRAM; COMPUTER SYSTEM; CORRELATION ANALYSIS; DATA ANALYSIS; DATA BASE; DEVELOPMENTAL STAGE; ENZYME ACTIVITY; GENE EXPRESSION; METABOLITE; NONHUMAN; PLANT GENETICS; STATISTICAL ANALYSIS; ALGORITHM; BIOLOGICAL MODEL; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER SIMULATION; METABOLISM; PHYSIOLOGY; SIGNAL TRANSDUCTION; SOFTWARE;

TRANSCRIPTION FACTOR;

ALGORITHMS; COMPUTER GRAPHICS; COMPUTER SIMULATION; MODELS, BIOLOGICAL; SIGNAL TRANSDUCTION; SOFTWARE; TRANSCRIPTION FACTORS; USER-COMPUTER INTERFACE;

EID: 33645241830     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-109     Document Type: Article

References (50)

1. Roessner U, Luedemann A, Brust D, Fiehn O, Linke T, Willmitzer L, Fernie AR: Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. Plant Cell 2001, 13:11-29.
2. Fiehn O, Kopka J, Dormann P, Altmann T, Trethewey RN, Willmitzer L: Metabolite profiling for plant functional genomics. Nature Biotechnology 2000, 18:1157-1161.
3. De Risi JL, Iyer VR, Brown PO: Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 1997, 278:680-686.
4. Celis JE, Kruhoffer M, Gromova I, Frederiksen C, Ostergaard M, Thykjaer T, Gromov P, Yu JS, Palsdottir H, Magnusson N, Orntoft TF: Gene expression profiling: monitoring transcription and translation products using DNA microarrays and proteomics. FEBS Letters 2000, 480:2-16.
5. Gibon Y, Blaesing OE, Hannemann J, Carillo P, Hohne M, Hendriks JHM, Palacios N, Cross J, Selbig J, Stitt M: A robot-based platform to measure multiple enzyme activities in Arabidopsis using a set of cycling assays: Comparison of changes of enzyme activities and transcript levels during diurnal cycles and in prolonged darkness. Plant Cell 2004, 16:3304-3325.
6. Kanehisa M, Goto S: KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research 2000, 28:27-30.
7. Demir E, Babur O, Dogrusöz U, Gürsoy A, Nisanci G, Çetin Atalay R, Ozturk M: PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways. Bioinformatics 2002, 18:996-1003.
8. Sirava M, Schäfer T, Eiglsperger M, Kaufmann M, Kohlbacher O, Bornberg-Bauer E, Lenhof H: BioMiner -modeling, analyzing, and visualizing biochemical pathways and networks. Bioinformatics 2002, 18:S219-S230.
9. Lüdemann A, Weicht D, Seibig J, Kopka J: PaVESy: pathway visualization and editing system. Bioinformatics 2004, 20:2841-2844.
10. Shannon P, Markiel A, Ozier O, Baliga N, Wang J, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 2003, 13:2498-2504.
11. Usadel B, Nagel A, Thimm O, Redestig H, Blaesing OE, Palacios-Rojas N, Selbig J, Hannemann J, Piques MC, Steinhauser D, Scheible WR, Gibon Y, Morcuende R, Weicht D, Meyer S, Stitt M: Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of coresponding genes, and comparison with known responses. Plant Physiology 2005, 138:1195-1204.
12. Tokimatsu T, Sakurai N, Suzuki H, Ohta, H, Nishitani K, Koyama T, Umezawa T, Misawa N, Saito K, Shibatanenell D: KaPPA-View. A web-based analysis tool for integration of transcript and metabolite data on plant metabolic pathway maps. Plant Physiology 2005, 138:1289-1300.
13. Mlecnik B, Scheideler M, Hackl H, Hartler J, Sanchez-Cabo F, Trajanoski Z: Pathway Explorer: web service for visualizing high-throughput expression data on biological pathways. Nucleic Acids Research 2005, 33:W633-W637.
14. Krieger CJ, Zhang P, Müller LA, Wang A, Paley S, Arnaud M, Pick J, Rhee SY, Karp PD: MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Research 2004, 32:438-442.
15. Müller LA, Zhang P, Rhee SY: AraCyc: A Biochemical Pathway Database for Arabidopsis. Plant Physiology 2003, 132:453-460.
16. Borisjuk L, Hajirezaei MR, Klukas C, Rolletschek H, Schreilber F: Integrating data from biological experiments into metabolic networks with the DBE information system. In Silica Biology 2005, 5:93-102.
17. Bachmaier C, Brandenburg FJ, Forster M, Raitner M, Holleis P: Gravisto: Graph Visualization Toolkit. in Proceedings of the 12th International Symposium on Graph Drawing of LNCS Volume 3383. Springer 2004:502-503.
18. BeanShell: Lightweight Scripting for Java [http://www.beanshell.org]
19. JRuby: A Ruby interpreter written in pure Java [http://jruby.sourceforge.net]
20. Gilbert D, Morgner T: JFreeChart, a free Java class library for generating charts. [http://www.jfree.org/jfreechart].
21. Commons-Math: The Jakarta Mathematics Library [http://jakarta.apache.org/ commons/math]
22. Sachs L: Applied Statistics 2nd edition. Springer 1984.
23. Gottwald W: Statistik für Anwender Wiley-VCH; 2000.
24. Kohonen T: The Self-Organizing Map. Proceedings of the IEEE 1990, 78:1464-1480.
25. Himsolt M: Graphlet: Design and Implementation of a Graph Editor. Software - Practice and Experience 2000, 30:1303-1324.
26. Finney A, Hucka M: Systems Biology Markup Language: Level 2 and beyond. Biochemical Society Transactions 2003, 31:1472-1473.
27. Dwyer T, Marriott K, Stuckey P: Fast node overlap removal. In Proceedings of the 13th International Symposium on Graph Drawing, LNCS Springer 2005. to appear
28. Batagelj V, Mrvar A. Pajek - analysis and visualization of large networks. In Graph Drawing Software Edited by: Jünger M, Mutzel P. Springer; 2004:77-103.
29. Goto S, Okuno Y, Hattori M, Nishioka T, Kanehisa M: LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Research 2002, 30:402-404.
30. Bairoch A: The ENZYME database in 2000. Nucleic Acids Research 2000, 28:304-305.
31. Kasturi J, Acharya R, Ramanathan M: An information theoretic approach for analyzing temporal patterns of gene expression. Bioinformatics 2003, 19:449-458.
32. Geigenberger P: Regulation of sucrose to starch conversion in growing potato tubers. Journal of Experimental Botany 2003, 54:457-465.
33. Junker BH, Wuttke R, Tiessen A, Geigenberger P, Sonnewald U, Wilimitzer IL, Fernie AR: Temporally regulated expression of a yeast invertase in potato tubers allows dissection of the complex metabolic phenotype obtained following its constitutive expression. Plant Molecular Biology 2004, 56:91-110.
34. Trethewey R, Geigenberger P, Riedel K, Hajirezai MR, Sonnewald U, Stitt M, Riesmeier J, Willmitzer L Combined expression of glucokinase and invertase in potato tubers leads to a dramatic reduction in starch accumulation and a stimulation of glycolysis. Plant Journal 1998, 15:109-118.
35. Weckwerth W: Metabolomics in systems biology. Annual Reviews in Plant Biology 2003, 54:669-689.
36. James M, Denyer K, Myers A: Starch synthesis in the cereal endosperm. Current Opinion in Plant Biology 2003, 6:215-222.
37. Rolletschek H, Weschke W, Weber H, Wobus U, Boriskuk L: Energy state and its control on seed development: starch accumulation is associated with high ATP and steep oxygen gradients within barley grains. Journal of Experimental Botany 2004, 55:1351-1359.
38. Sreenivasulu N, Altschmied L, Radchuk V, Gubatz S, Wobus U, Weschke W: Transcript profiles and deduced changes of metabolic pathways in maternal and filial tissues of developing barley grains. Plant Journal 2004, 37:539-553.
39. Hu Z, Mellor J, Wu J, DeLisi C: VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinformatics 2004, 5:17.
40. Breitkreutz BJ, Stark C, Tyers M: Osprey: a network visualization system. Genome Biology 2003, 4:R22.
41. Fruchterman T, Reingold E: Graph drawing by force-directed placement. Software - Practice and Experience 1991, 21:1129-1164.
42. Sugiyama K, Tagawa S, Toda M: Methods for visual understanding of hierarchical system structures. IEEE Transactions on Systems, Man and Cybernetics 1981, 11:109-125.
43. Wurtele E, Li J, Diao L, Zhang H, Foster C, Fatland B, Dickerson J, A B, Brown A, Cox Z, Cook D, Lee EK Hofmann H: MetNet: software to build and model the biogenetic lattice of Arabidopsis. Comparative and Functional Genomics 2003, 4:239-245.
44. Hanisch D, Sohier F, Zimmer R: ToPNet - an application for interactive analysis of expression data and biological networks. Bioinformatics 2004, 20:1470-1471.
45. Pan D, Sun N, Cheung KH, Guan Z, Ma L, Holford M, Deng X, Zhao H: PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis. BMC Bioinformatics 2003, 4:56.
46. Holford M, Li N, Nadkarni P, Zhao H: VitaPad: visualization tools for the analysis of pathway data. Bioinformatics 2005, 21:1596-1602.
47. Grosu P, Townsend J, Hartl D, Cavalieri D: Pathway Processor a tool for integrating whole-genome expression results into metabolic networks. Genome Research 2002, 12:1121-1126.
48. Bergmann S, Ihmels J, Barkai N: Similarities and differences in genome-wide expression data of six organisms. PLoS Biology 2004, 2:85-93.
49. Lisso J, Steinhauser D, Altmann T, Kopka J, Müssig C: Identification of brassinosteroid-related genes by means of transcript coresponse analysis. Nucleic Acids Research 2005, 33:2685-2696.
50. Weckwerth W, Loureiro ME, Wenzel K, Fiehn O: Differential metabolic networks unravel the effects of silent plant phenotypes. Proceedings of the National Academy of Sciences USA 2004, 101:7809-7814.