Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy.

ABSTRACT: 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 genera

SUBMITTER: Jung KH 

PROVIDER: S-EPMC2556097 | biostudies-literature | 2008 Oct

REPOSITORIES: biostudies-literature