Refinement of Light-Responsive Transcript Lists Using Rice Oligonucleotide Arrays: Evaluation of Gene-Redundancy
| Autor: | Patrick E. Canlas, Hui-Hsien Chou, Chris Dardick, Michael A. Shultz, Geun Cheol Lee, Young Su Seo, Eugene Ly, Jirapa Phetsom, Peijian Cao, Yi Jia, Bryan C. Frank, Qiaoping Yuan, Patrick S. Schnable, Li Zheng, Laura E. Bartley, Pamela C. Ronald, David M. Rocke, Kyungsook An, Shu Ouyang, An-Ping Hsia, Gynheung An, Ki-Hong Jung, C. Robin Buell |
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| Jazyk: | angličtina |
| Rok vydání: | 2008 |
| Předmět: |
0106 biological sciences
Candidate gene Light Transcription Genetic Gene redundancy lcsh:Medicine Plant Biology Biology 01 natural sciences Genome Genetics and Genomics/Plant Genetics and Gene Expression 03 medical and health sciences Plant Biology/Plant Genetics and Gene Expression Cluster Analysis lcsh:Science 030304 developmental biology Oligonucleotide Array Sequence Analysis Plant Proteins 2. Zero hunger Genetics Expressed Sequence Tags 0303 health sciences Expressed sequence tag Multidisciplinary Gene Expression Profiling lcsh:R Life Sciences food and beverages Reproducibility of Results Oryza Genome project Gene expression profiling Multigene Family lcsh:Q DNA microarray Functional genomics Genome Plant 010606 plant biology & botany Research Article |
| Zdroj: | PLoS ONE PLoS ONE, Vol 3, Iss 10, p e3337 (2008) Jung, Ki-Hong; Dardick, Christopher; Bartley, Laura E; Cao, Peijian; Phetsom, Jirapa; Canlas, Patrick; et al.(2008). Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy.. PloS one, 3(10), e3337-e33e3337. UC Davis: Retrieved from: http://www.escholarship.org/uc/item/9z16z49z |
| ISSN: | 1932-6203 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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