ArticleFunctional & integrative genomics2007
Differentiation of the two rice subspecies indica and japonica: a Gene Ontology perspective.
Article in Functional & integrative genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
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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.
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Who cites it
6 citing papers in PubMed, 10 citations in OpenAlex.
- Heat stress impact on rice reproductive processes: challenges and new approaches.Frontiers in genome editing · 2026Review
- Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism.Nature genetics · 2014Article
- Article
- Genome-wide identification and analysis of Japonica and Indica cultivar-preferred transcripts in rice using 983 Affymetrix array data.Rice (New York, N.Y.) · 2013Article
- Article
- Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy.PloS one · 2008Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Cultivated rice (Oryza sativa) is comprised of two subspecies: japonica and indica. Polymorphism levels between putative homologues were determined for genes whose japonica homologue had been classified into functional categories using the Gene Ontology (GO) system. Genes were partitioned into below-average and above-average polymorphism groups, and then the set of genes having each GO term was checked for the randomness of its distribution into these polymorphism groups using a series of False Discovery Rate (FDR) tests. The robustness of the conclusions was enhanced by employing different cutoff values and sequence samplings in the FDR tests. Significant nonrandom polymorphism distributions were found for protein-coding sequences in many GO categories. In contrast, a random distribution for nearly all GO terms was seen with intron sequences. These results were extended by measuring the nonsynonymous to synonymous codon usage ratio (dN/dS) using a permutation test, which showed that some above-average polymorphism GO categories also had a high proportion of genes with a dN/dS ratio greater than one, suggesting positive selection on these GO categories during indica-japonica differentiation. An analysis of predominant gene names in the significant GO categories divided them into four functional classes: production of defense-related compounds, cell wall, cell signaling, and transcription factors.
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Registered trials
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