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

Jung KH, Dardick C, Bartley LE, Cao P, Phetsom J, Canlas P, Seo YS, Shultz M, Ouyang S, Yuan Q, Frank BC, Ly E, Zheng L, Jia Y, Hsia AP, An K, Chou HH, Rocke D, Lee GC, Schnable PS, An G, Buell CR, Ronald PC - PLoS ONE (2008)

Bottom Line: To compare data generated with the NSF45K array with published results, we developed publicly available, web-based tools (www.ricearray.org).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.Applying these methods will accelerate rice functional genomics.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Pathology, University of California Davis, Davis, California, United States of America.

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 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.

Show MeSH
Plant GOSlim enrichment analysis of light-induced transcripts.(A) Enrichment or depletion among light-induced transcripts of selected cellular component GOSlim terms. (B) Enrichment or depletion among light-induced transcripts of selected biological process GOSlim terms. Enrichment and depletion values were generated for transcript lists determine with four FDR cutoff-values, ≤10−6 (black bars), ≤10−4 (dark grey bars), ≤0.01 (light grey bars), and ≤0.05 (open bars). Shown are selected enriched GOSlim terms with a hypergeometric p-value<0.05 at FDR≤10−6 and most other FDRs examined (left panel), less consistently enriched GOSlim terms with a hypergeometric p-value>0.05 at FDR≤10−6 (middle panel), and depleted GOSlim terms with a hypergeometric p-value<0.05 at FDR≤10−6 and most other FDRs examined (right panel). The y-axis indicates the GOSlim fold- enrichment or depletion. GO enrichment values are calculated as the observed number of transcripts for a particular term divided by the expected number of transcripts and GO depletion values are the inverse of GO enrichment values. A GO enrichment value >1 means that the analyzed term occurs more frequently than expected in a gene list at a selected FDR than it would in a random list with the same number of genes. GO enrichment data for all other GOSlim terms are available in Table S6. The symbol (∞) indicates that the denominator for generating the GO depletion values was zero.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2556097&req=5

pone-0003337-g002: Plant GOSlim enrichment analysis of light-induced transcripts.(A) Enrichment or depletion among light-induced transcripts of selected cellular component GOSlim terms. (B) Enrichment or depletion among light-induced transcripts of selected biological process GOSlim terms. Enrichment and depletion values were generated for transcript lists determine with four FDR cutoff-values, ≤10−6 (black bars), ≤10−4 (dark grey bars), ≤0.01 (light grey bars), and ≤0.05 (open bars). Shown are selected enriched GOSlim terms with a hypergeometric p-value<0.05 at FDR≤10−6 and most other FDRs examined (left panel), less consistently enriched GOSlim terms with a hypergeometric p-value>0.05 at FDR≤10−6 (middle panel), and depleted GOSlim terms with a hypergeometric p-value<0.05 at FDR≤10−6 and most other FDRs examined (right panel). The y-axis indicates the GOSlim fold- enrichment or depletion. GO enrichment values are calculated as the observed number of transcripts for a particular term divided by the expected number of transcripts and GO depletion values are the inverse of GO enrichment values. A GO enrichment value >1 means that the analyzed term occurs more frequently than expected in a gene list at a selected FDR than it would in a random list with the same number of genes. GO enrichment data for all other GOSlim terms are available in Table S6. The symbol (∞) indicates that the denominator for generating the GO depletion values was zero.

Mentions: Here, we report construction and validation of a 43,311 oligo rice gene array based on 45,116 gene models from the 61,420 total target sequences present in TIGR rice annotation release 3 [30]. Because this array was supported by the National Science Foundation and is based on 45,116 gene models, it is called the NSF45K array. To validate the functional utility of the NSF45K array, we conducted experiments to identify candidate genes involved in light responses. We hybridized RNAs from four rice varieties exposed to light and dark treatments to the array. With the data resulting from these experiments, we employed five methods to verify the usefulness of the NSF45K array (Table 1), including analyzing the sources of variation, GO-term enrichment in lists of light- and dark-induced genes, and comparing the data with rice EST and other microarray data. We then assessed functional redundancy with an approach for integrating expression data with pathway information by analyzing available gene expression profiles from multiple array platforms. For the project, we developed publicly available web-based tools for analysis of gene expression based on rice ESTs and data from other array platforms. These methods and tools will allow users to more accurately refine their candidate gene lists to improve the efficiency of functional testing, greatly accelerating rice gene discovery.


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

Jung KH, Dardick C, Bartley LE, Cao P, Phetsom J, Canlas P, Seo YS, Shultz M, Ouyang S, Yuan Q, Frank BC, Ly E, Zheng L, Jia Y, Hsia AP, An K, Chou HH, Rocke D, Lee GC, Schnable PS, An G, Buell CR, Ronald PC - PLoS ONE (2008)

Plant GOSlim enrichment analysis of light-induced transcripts.(A) Enrichment or depletion among light-induced transcripts of selected cellular component GOSlim terms. (B) Enrichment or depletion among light-induced transcripts of selected biological process GOSlim terms. Enrichment and depletion values were generated for transcript lists determine with four FDR cutoff-values, ≤10−6 (black bars), ≤10−4 (dark grey bars), ≤0.01 (light grey bars), and ≤0.05 (open bars). Shown are selected enriched GOSlim terms with a hypergeometric p-value<0.05 at FDR≤10−6 and most other FDRs examined (left panel), less consistently enriched GOSlim terms with a hypergeometric p-value>0.05 at FDR≤10−6 (middle panel), and depleted GOSlim terms with a hypergeometric p-value<0.05 at FDR≤10−6 and most other FDRs examined (right panel). The y-axis indicates the GOSlim fold- enrichment or depletion. GO enrichment values are calculated as the observed number of transcripts for a particular term divided by the expected number of transcripts and GO depletion values are the inverse of GO enrichment values. A GO enrichment value >1 means that the analyzed term occurs more frequently than expected in a gene list at a selected FDR than it would in a random list with the same number of genes. GO enrichment data for all other GOSlim terms are available in Table S6. The symbol (∞) indicates that the denominator for generating the GO depletion values was zero.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2556097&req=5

pone-0003337-g002: Plant GOSlim enrichment analysis of light-induced transcripts.(A) Enrichment or depletion among light-induced transcripts of selected cellular component GOSlim terms. (B) Enrichment or depletion among light-induced transcripts of selected biological process GOSlim terms. Enrichment and depletion values were generated for transcript lists determine with four FDR cutoff-values, ≤10−6 (black bars), ≤10−4 (dark grey bars), ≤0.01 (light grey bars), and ≤0.05 (open bars). Shown are selected enriched GOSlim terms with a hypergeometric p-value<0.05 at FDR≤10−6 and most other FDRs examined (left panel), less consistently enriched GOSlim terms with a hypergeometric p-value>0.05 at FDR≤10−6 (middle panel), and depleted GOSlim terms with a hypergeometric p-value<0.05 at FDR≤10−6 and most other FDRs examined (right panel). The y-axis indicates the GOSlim fold- enrichment or depletion. GO enrichment values are calculated as the observed number of transcripts for a particular term divided by the expected number of transcripts and GO depletion values are the inverse of GO enrichment values. A GO enrichment value >1 means that the analyzed term occurs more frequently than expected in a gene list at a selected FDR than it would in a random list with the same number of genes. GO enrichment data for all other GOSlim terms are available in Table S6. The symbol (∞) indicates that the denominator for generating the GO depletion values was zero.
Mentions: Here, we report construction and validation of a 43,311 oligo rice gene array based on 45,116 gene models from the 61,420 total target sequences present in TIGR rice annotation release 3 [30]. Because this array was supported by the National Science Foundation and is based on 45,116 gene models, it is called the NSF45K array. To validate the functional utility of the NSF45K array, we conducted experiments to identify candidate genes involved in light responses. We hybridized RNAs from four rice varieties exposed to light and dark treatments to the array. With the data resulting from these experiments, we employed five methods to verify the usefulness of the NSF45K array (Table 1), including analyzing the sources of variation, GO-term enrichment in lists of light- and dark-induced genes, and comparing the data with rice EST and other microarray data. We then assessed functional redundancy with an approach for integrating expression data with pathway information by analyzing available gene expression profiles from multiple array platforms. For the project, we developed publicly available web-based tools for analysis of gene expression based on rice ESTs and data from other array platforms. These methods and tools will allow users to more accurately refine their candidate gene lists to improve the efficiency of functional testing, greatly accelerating rice gene discovery.

Bottom Line: To compare data generated with the NSF45K array with published results, we developed publicly available, web-based tools (www.ricearray.org).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.Applying these methods will accelerate rice functional genomics.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Pathology, University of California Davis, Davis, California, United States of America.

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 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.

Show MeSH