Adaptation of the MapMan ontology to biotic stress responses: Application in solanaceous species

Plant Methods

Volumn 3, Issue 1, 2007, Pages

  Rotter, Ana ^a   Usadel, Björn ^b   Baebler, Spela ^a   Stitt, Mark ^b   Gruden, Kristina ^a,c  

^a NATIONAL INSTITUTE OF BIOLOGY   (Slovenia)

^b MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

^c JO EF STEFAN INSTITUTE   (Slovenia)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; SOLANUM TUBEROSUM;

EID: 35348892233     PISSN: None     EISSN: 17464811     Source Type: Journal    
DOI: 10.1186/1746-4811-3-10     Document Type: Article

References (33)

1. MapMan homepage [http://gabi.rzpd.de/projects/MapMan]
2. Cavalieri D, De Filippo C: Bioinformatic methods for integrating whole-genome expression results into cellular networks. Drug Discov Today 2005, 10:727-734.
3. Tokimatsu T, Sakurai N, Suzuki H, Ohta H, Nishitani K, Koyama T, Umezawa T, Misawa N, Saito K, Shibata D: KaPPA-View. A Web-Based Analysis Tool for Integration of Transcript and Metabolite Data on Plant Metabolic Pathway Maps. Plant Physiol 2005, 138:1289-1300.
4. Junker BH, Klukas C, Schreiber F: VANTED: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics 2006, 7:109.
5. Usadel B, Nagel A, Thimm O, Redestig H, Blaesing OE, Palacios-Rojas N, Selbig J, Hannemann J, Conceição Piques M, Steinhauser D, Scheine 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 Physiol 2005, 138:1195-1204.
6. Thimm O, Biasing O, Gibon Y, Nagel A, Meyer S, Krüger P, Selbig J, Müller LA, Rhee SY, Stitt M: MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 2004, 37:914-939.
7. Urbanczyk-Wochniak E, Usadel B, Thimm O, Nunes-Nesi A, Carrari F, Davy M, Biasing O, Kowalczyk M, Weicht D, Polinceusz A, Meyer S, Stitt M, Fernie AR: Conversion of MapMan to allow the analysis of transcript data from Solanaceous species: effects of genetic and environmental alterations in energy metabolism in the leaf. Plant Mol Biol 2006, 60:773-792.
8. Potato gene index [http://compbio.dfci.harvard.edu/tgi/cgi-bin/ tgi/gimain,pl?gudb=potato]
9. Ronning CM, Stegalkina SS, Ascenzi RA, Bougri O, Hart AL, Utterbach TR, Vanaken SE, Riedmuller SB, White JA, Cho J, Pertea GM, Lee Y, Karamycheva S, Sultana R, Tsai J, Quackenbush J, Griffiths HM, Restrepo S, Smart CD, Fry WE, Van Der Hoeven R, Tanksley S, Zhang P, Jin H, Yamamoto ML, Baker BJ, Buell CR: Comparative analyses of potato expressed sequence tag libraries. Plant Physiol 2003, 131:419-429.
10. Usadel B, Nagel A, Steinhauser D, Gibon Y, Biasing O, Redestig H, Sreenivasulu N, Krall L, Hannah MA, Poree F, Fernie AR, Stitt M: PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments. BMC Bioinformatics 2006, 7:535.
11. Senthil G, Liu H, Puram VG, Clark A, Stromberg A, Goodin MM: Specific and common changes in Nicotiana benthamiana gene expression in response to infection by enveloped viruses. Journal of Genetical Virology 2005, 86:2615-2625.
12. Rensink WA, Iobst S, Hart A, Stegalkina S, Liu J, Buell CR: Gene expression profiling of potato responses to cold, heat, and salt stress. Functional and Integrative Genomics 2005, 5:201-207.
13. Samuel MA, Hall H, Krzyrnowska M, Drzewiecka K, Hennig J, Ellis BE: SIPK signaling controls multiple components of harpin-induced cell death in tobacco. Plant J 2005, 42:406-416.
14. Fernie AR, Willmitzer L: Molecular and biochemical triggers of potato tuber development. Plant Physiol 2001, 127:1459-1465.
15. Mosolov W, Valueva TA: Proteinase inhibitors and their function in plants: A review. Applied Biochemistry and Microbiology 2005, 41:227-246.
16. Devoto A, Muskett PR, Shirasu K: Role of ubiquitination in the regulation of plant defence against pathogens. Curr Opin Plant Biol 2003 6:307-311.
17. Whitham SA, Yang C, Goodin MM: Global impact: elucidating plant responses to viral infection. Mol Plant Microbe Interact 2006, 19:1207-1215.
18. Singh K, Foley RC, Oñate Sánchez L: Transcription factors in plant defense and stress responses. Curr Opin Plant Biol 2002, 5:430-436.
19. Matton DP, Brisson N: Cloning, expression, and sequence conservation of pathogenesis-related gene transcripts of potato. Molecular Plant-Microbe Interactions 1989, 2:325-331.
20. Hasegawa Y, Seki M, Mochizuki Y, Heida N, Hirosawa K, Okamoto N, Sakurai T, Satou M, Akiyama K, Iida K, Lee K, Kanaya S, Demura T, Shinozaki K, Konagaya A, Toyoda T: A flexible representation of omic knowledge for thorough analysis of microarray data. Plant Methods 2006, 2:5.
21. Schmidt DD, Voelckel C, Hartl M, Schmidt S, Baldwin IT: Specificity in Ecological Interactions. Attack from the Same Lepidopteran Herbivore Results in Species-Specific Transcriptional Responses in Two Solanaceous Host Plants. Plant Physiol 2005, 138:1763-1773.
22. Potato experiments deposited at TIGR [ftp://ftp.tigr.org/pub/ data/]
23. Smyth GK: Limma: linear models for microarray data New York: Springer; 2005:397-420.
24. Marathe R, Guan Z, Anandalakshmi R, Zhao H, Dinesh-Kumar S: Study of Arabidopsis thaliana resistome in response to cucumber mosaic virus infection using whole genome microarray. Plant Molecular Biology 2004, 55:501-520.
25. Pageman: a tool for gene representation analysis [http://mapman.mpimp-golm.mpg.de/general/ora/ora.shtml]
26. Tellstrom V, Usadel B, Thimm O, Stitt M, Kuster H, Niehaus K: The Lipopolysaccharide of Sinorhizobium meliloti Suppresses Defense-Associated Gene Expression in Cell Cultures of the Host Plant Medicago truncatula. Plant Physiol 2007, 143:825-837.
27. TAIR 6 genome release [ftp://ftp.arabidopsis.org/home/tair/ Genes/TAIR6genomerelease/]
28. PFAM protein domain information [http://www.sanger.ac.uk/ Software/Pfam/]
29. SMART protein domain information [http://smart.embl-heidelberg. de/]
30. R Development Core Team: R: A Language and Environment for Statistical Computing 2007 [http://www.R-project.org]. R Foundation for Statistical Computing, Vienna, Austria [ISBN 3-900051-07-0].
31. Cleveland WS: Robust locally weighted regression and smoothing scatterplots. Journal of the American Statistical Association 1979, 74:829-836.
32. Huber W, von Heydebreck A, Sultmann H, Poustka A, Vingron M: Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 2002, 18:S96-104.
33. Gruden K, Kuipers AGJ, Gunčar G, Slapar N, Štrukelj B, Jongsma MA: Molecular basis of Colorado potato beetle adaptation to potato plant defence at the level of digestive cysteine proteinases, Insect biochem mol biol 2004, 34:365-375.