Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy.
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.
Jung
Ki-Hong
KH
Department of Plant Pathology, University of California Davis, Davis, California, United States of America.
Dardick
Christopher
C
Bartley
Laura E
LE
Cao
Peijian
P
Phetsom
Jirapa
J
Canlas
Patrick
P
Seo
Young-Su
YS
Shultz
Michael
M
Ouyang
Shu
S
Yuan
Qiaoping
Q
Frank
Bryan C
BC
Ly
Eugene
E
Zheng
Li
L
Jia
Yi
Y
Hsia
An-Ping
AP
An
Kyungsook
K
Chou
Hui-Hsien
HH
Rocke
David
D
Lee
Geun Cheol
GC
Schnable
Patrick S
PS
An
Gynheung
G
Buell
C Robin
CR
Ronald
Pamela C
PC
D016000:Cluster Analysis; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D018745:Genome, Plant; D008027:Light; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis / Q000191:economics / Q000379:methods*; D012275:Oryza / Q000235:genetics* / Q000502:physiology / Q000528:radiation effects*; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D015203:Reproducibility of Results; D014158:Transcription, Genetic / Q000528:radiation effects
D010940:Plant Proteins