ArticlePloS one2008
Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy.
Article in PloS one, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
61 citing papers in PubMed, 2 syntheses or guidelines pooled it, 108 citations in OpenAlex.
- A Systematic View Exploring the Role of Chloroplasts in Plant Abiotic Stress Responses.BioMed research international · 2019Pooled it
- Meta-analysis of the expression profiles of the Arabidopsis ESCRT machinery.Plant signaling & behavior · 2011Pooled it
- A Systemic View of Carbohydrate Metabolism in Rice to Facilitate Productivity.Plants (Basel, Switzerland) · 2021Article
- Rice Senescence-Induced Receptor-Like Kinase (International journal of molecular sciences · 2019Article
- Genome-Wide Transcriptome Analysis of Rice Seedlings after Seed Dressing withInternational journal of molecular sciences · 2019Article
- Expression Divergence as an Evolutionary Alternative Mechanism Adopted by Two Rice Subspecies Against Rice Blast Infection.Rice (New York, N.Y.) · 2019Article
- Genome-wide analyses of late pollen-preferred genes conserved in various rice cultivars and functional identification of a gene involved in the key processes of late pollen development.Rice (New York, N.Y.) · 2018Article
- Mapping the microRNA Expression Profiles in Glyoxalase Over-expressing Salinity Tolerant Rice.Current genomics · 2018Article
- Molecular bases for differential aging programs between flag and second leaves during grain-filling in rice.Scientific reports · 2017Article
- Crosstalk between diurnal rhythm and water stress reveals an altered primary carbon flux into soluble sugars in drought-treated rice leaves.Scientific reports · 2017Article
- Genome-Wide Identification and Analysis of Genes, Conserved betweenFrontiers in plant science · 2017Article
- OsPhyB-Mediating Novel Regulatory Pathway for Drought Tolerance in Rice Root Identified by a Global RNA-Seq Transcriptome Analysis of Rice Genes in Response to Water Deficiencies.Frontiers in plant science · 2017Article
- Article
- Thermodynamically optimal whole-genome tiling microarray design and validation.BMC research notes · 2016Article
- Ocimum sanctum leaf extract induces drought stress tolerance in rice.Plant signaling & behavior · 2016Article
- Dose-dependent response of Trichoderma harzianum in improving drought tolerance in rice genotypes.Planta · 2016Article
- Global epigenomic analysis indicates that epialleles contribute to Allele-specific expression via Allele-specific histone modifications in hybrid rice.BMC genomics · 2015Article
- Rational Design of High-Number dsDNA Fragments Based on Thermodynamics for the Construction of Full-Length Genes in a Single Reaction.PloS one · 2015Article
- Article
- Evaluation of rice promoters conferring pollen-specific expression in a heterologous system, Arabidopsis.Plant reproduction · 2014Article
1 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
23 authors at 6 institutions in 2 countries.
Funding
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.