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

BackgroundThe results of transcriptome microarray analysis are usually presented as a list of differentially expressed genes. As these lists can be long, it is hard to interpret the desired experimental treatment effect on the physiology of analysed tissue, e.g. via selected metabolic or other pathways. For some organisms, gene ontologies and data visualization software have been implemented to overcome this problem, whereas for others, software adaptation is yet to be done.ResultsWe present the classification of tentative potato contigs from the potato gene index (StGI) available from Dana-Farber Cancer Institute (DFCI) into the MapMan ontology to enable the application of the MapMan family of tools to potato microarrays. Special attention has been focused on mapping genes that could not be annotated based on similarity to Arabidopsis genes alone, thus possibly representing genes unique for potato. 97 such genes were classified into functional BINs (i.e. functional classes) after manual annotation. A new pathway, focusing on biotic stress responses, has been added and can be used for all other organisms for which mappings have been done. The BIN representation on the potato 10 k cDNA microarray, in comparison with all putative potato gene sequences, has been tested. The functionality of the prepared potato mapping was validated with experimental data on plant response to viral infection. In total 43,408 unigenes were mapped into 35 corresponding BINs.ConclusionThe potato mappings can be used to visualize up-to-date, publicly available, expressed sequence tags (ESTs) and other sequences from GenBank, in combination with metabolic pathways. Further expert work on potato annotations will be needed with the ongoing EST and genome sequencing of potato. The current MapMan application for potato is directly applicable for analysis of data obtained on potato 10 k cDNA microarray by TIGR (The Institute for Genomic Research) but can also be used by researchers working on other potato gene sets. The potato mapping file and the stress mapping diagram are available from the MapMan website [1].

[1]  W. Cleveland.  Robust Locally Weighted Regression and Smoothing Scatterplots , 1979 .

[2]  N. Brisson,et al.  Cloning, expression, and sequence conservation of pathogenesis-related gene transcripts of potato. , 1989, Molecular plant-microbe interactions : MPMI.

[3]  Molecular and biochemical triggers of potato tuber development. , 2001, Plant physiology.

[4]  Karam B. Singh,et al.  Transcription factors in plant defense and stress responses. , 2002, Current opinion in plant biology.

[5]  Martin Vingron,et al.  Variance stabilization applied to microarray data calibration and to the quantification of differential expression , 2002, ISMB.

[6]  G. Pertea,et al.  Comparative Analyses of Potato Expressed Sequence Tag Libraries1 , 2003, Plant Physiology.

[7]  Ken Shirasu,et al.  Role of ubiquitination in the regulation of plant defence against pathogens. , 2003, Current opinion in plant biology.

[8]  S. Rhee,et al.  MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. , 2004, The Plant journal : for cell and molecular biology.

[9]  Hongyu Zhao,et al.  Study of Arabidopsis thalianaresistome in response to cucumber mosaic virus infection using whole genome microarray , 2004, Plant Molecular Biology.

[10]  K. Gruden,et al.  Molecular basis of Colorado potato beetle adaptation to potato plant defence at the level of digestive cysteine proteinases. , 2004, Insect biochemistry and molecular biology.

[11]  F. Carrari,et al.  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 , 2006, Plant Molecular Biology.

[12]  Hideyuki Suzuki,et al.  KaPPA-View. A Web-Based Analysis Tool for Integration of Transcript and Metabolite Data on Plant Metabolic Pathway Maps1[w] , 2005, Plant Physiology.

[13]  D. Cavalieri,et al.  Bioinformatic methods for integrating whole-genome expression results into cellular networks. , 2005, Drug discovery today.

[14]  Gordon K. Smyth,et al.  limma: Linear Models for Microarray Data , 2005 .

[15]  I. Baldwin,et al.  Specificity in Ecological Interactions. Attack from the Same Lepidopteran Herbivore Results in Species-Specific Transcriptional Responses in Two Solanaceous Host Plants1[w] , 2005, Plant Physiology.

[16]  A. Stromberg,et al.  Specific and common changes in Nicotiana benthamiana gene expression in response to infection by enveloped viruses. , 2005, The Journal of general virology.

[17]  Masakazu Satou,et al.  A flexible representation of omic knowledge for thorough analysis of microarray data , 2006, Plant Methods.

[18]  B. Ellis,et al.  SIPK signaling controls multiple components of harpin-induced cell death in tobacco. , 2005, The Plant journal : for cell and molecular biology.

[19]  Jia Liu,et al.  Gene expression profiling of potato responses to cold, heat, and salt stress , 2005, Functional & Integrative Genomics.

[20]  Joachim Selbig,et al.  Extension of the Visualization Tool MapMan to Allow Statistical Analysis of Arrays, Display of Coresponding Genes, and Comparison with Known Responses1 , 2005, Plant Physiology.

[21]  Falk Schreiber,et al.  VANTED: A system for advanced data analysis and visualization in the context of biological networks , 2006, BMC Bioinformatics.

[22]  T. A. Valueva,et al.  Proteinase inhibitors and their function in plants: A review , 2005, Applied Biochemistry and Microbiology.

[23]  Yves Gibon,et al.  PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments , 2006, BMC Bioinformatics.

[24]  S. Whitham,et al.  Global impact: elucidating plant responses to viral infection. , 2006, Molecular plant-microbe interactions : MPMI.

[25]  B. Usadel,et al.  The Lipopolysaccharide of Sinorhizobium meliloti Suppresses Defense-Associated Gene Expression in Cell Cultures of the Host Plant Medicago truncatula1[W][OA] , 2006, Plant Physiology.