Refinement of Light-Responsive Transcript Lists Using Rice Oligonucleotide Arrays: Evaluation of Gene-Redundancy

• Published in: PloS one Vol. 3; no. 10; p. e3337
• Main Authors: Jung, Ki-Hong, Dardick, Christopher, Bartley, Laura E, Cao, Peijian, Phetsom, Jirapa, Canlas, Patrick, Seo, Young-Su, Shultz, Michael, Ouyang, Shu, Yuan, Qiaoping, Frank, Bryan C, Ly, Eugene, Zheng, Li, Jia, Yi, Hsia, An-Ping, An, Kyungsook, Chou, Hui-Hsien, Rocke, David, Lee, Geun Cheol, Schnable, Patrick S, An, Gynheung, Buell, C. Robin, Ronald, Pamela C, Grebe, Markus
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 06.10.2008; Public Library of Science (PLoS)
• Subjects: Algorithms; Analysis; Anatomy; Annotations; Arabidopsis; Artificial chromosomes; biochemical pathways; Bioinformatics; Chlamydomonas reinhardtii; Cluster Analysis; Crop diseases; Data processing; Deoxyribonucleic acid; Design; DNA; DNA microarrays; Expressed Sequence Tags; Flowers & plants; Gene expression; Gene Expression Profiling; Genes; Genetics and Genomics/Plant Genetics and Gene Expression; Genome, Plant; Genomes; Genomics; Hypotheses; Kinases; Laboratories; leaves; Light; Lists; microarray technology; Multigene Family; Oligonucleotide Array Sequence Analysis - economics; Oligonucleotide Array Sequence Analysis - methods; Oligonucleotides; Oryza - genetics; Oryza - physiology; Oryza - radiation effects; Oryza sativa; Photorespiration; Plant Biology; Plant Biology/Plant Genetics and Gene Expression; Plant pathology; Plant Proteins - genetics; Plant Proteins - metabolism; Plant tissues; Polymerase chain reaction; prediction; Proteins; Redundancy; Reproducibility of Results; reverse transcriptase polymerase chain reaction; Reverse transcription; Rice; Studies; Transcription (Genetics); Transcription, Genetic - radiation effects; transcriptomics; Trends; Iowa; California; United States > US; Maryland
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0003337

Studies of gene function are often hampered by gene-redundancy, especially in organisms with large genomes such as rice (Oryza sativa). We present an approach for using transcriptomics data to focus functional studies and address redundancy. To this end, we have constructed and validated an inexpensive and publicly available rice oligonucleotide near-whole genome array, called the rice NSF45K array. We generated expression profiles for light- vs. dark-grown rice leaf tissue and validated the biological significance of the data by analyzing sources of variation and confirming expression trends with reverse transcription polymerase chain reaction. We examined trends in the data by evaluating enrichment of gene ontology terms at multiple false discovery rate thresholds. To compare data generated with the NSF45K array with published results, we developed publicly available, web-based tools (www.ricearray.org). The Oligo and EST Anatomy Viewer enables visualization of EST-based expression profiling data for all genes on the array. The Rice Multi-platform Microarray Search Tool facilitates comparison of gene expression profiles across multiple rice microarray platforms. Finally, we incorporated gene expression and biochemical pathway data to reduce the number of candidate gene products putatively participating in the eight steps of the photorespiration pathway from 52 to 10, based on expression levels of putatively functionally redundant genes. We confirmed the efficacy of this method to cope with redundancy by correctly predicting participation in photorespiration of a gene with five paralogs. Applying these methods will accelerate rice functional genomics.