ArticleBMC plant biology2008
Development of a novel data mining tool to find cis-elements in rice gene promoter regions.
Article in BMC plant biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- Elucidating the role of brassinosteroid signaling genes and their promoters in Arabidopsis revealed regulatory mechanisms in plant development and responses to different abiotic stresses.BMC plant biology · 2025Article
- Transcript profiling of glutathione metabolizing genes reveals abiotic stress and glutathione-specific alteration inPhysiology and molecular biology of plants : an international journal of functional plant biology · 2022Article
- Genome-wide identification, evolution, and transcript profiling of Aldehyde dehydrogenase superfamily in potato during development stages and stress conditions.Scientific reports · 2021Article
- Transcriptome Analysis of Bread Wheat Genotype KRL3-4 Provides a New Insight Into Regulatory Mechanisms Associated With Sodicity (High pH) Tolerance.Frontiers in genetics · 2021Article
- Identification of stress defensive proteins in common wheat-Breeding science · 2020Article
- Diversity of cis-regulatory elements associated with auxin response in Arabidopsis thaliana.Journal of experimental botany · 2018Review
- Article
- Abscisic-acid-dependent basic leucine zipper (bZIP) transcription factors in plant abiotic stress.Protoplasma · 2017Review
- Transcriptional profiling of the leaves of near-isogenic rice lines with contrasting drought tolerance at the reproductive stage in response to water deficit.BMC genomics · 2015Article
- Global nucleosome positioning regulates salicylic acid mediated transcription in Arabidopsis thaliana.BMC plant biology · 2015Article
- NAC transcription factor family genes are differentially expressed in rice during infections with Rice dwarf virus, Rice black-streaked dwarf virus, Rice grassy stunt virus, Rice ragged stunt virus, and Rice transitory yellowing virus.Frontiers in plant science · 2015Article
- Heavy metals induce oxidative stress and genome-wide modulation in transcriptome of rice root.Functional & integrative genomics · 2014Article
- Comprehensive gene expression analysis of the NAC gene family under normal growth conditions, hormone treatment, and drought stress conditions in rice using near-isogenic lines (NILs) generated from crossing Aday Selection (drought tolerant) and IR64.Molecular genetics and genomics : MGG · 2012Article
- Comparative transcriptome analysis of AP2/EREBP gene family under normal and hormone treatments, and under two drought stresses in NILs setup by Aday Selection and IR64.Molecular genetics and genomics : MGG · 2012Article
- Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes.Nucleic acids research · 2011Article
- Transcriptomic and metabolomic shifts in rice roots in response to Cr (VI) stress.BMC genomics · 2010Article
- Mapping metabolic and transcript temporal switches during germination in rice highlights specific transcription factors and the role of RNA instability in the germination process.Plant physiology · 2009Article
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundInformation on more than 35 000 full-length Oryza sativa cDNAs, together with associated microarray gene expression data collected under various treatment conditions, has made it feasible to identify motifs that are conserved in gene promoters and may act as cis-regulatory elements with key roles under the various conditions.
resultsWe have developed a novel tool that searches for cis-element candidates in the upstream, downstream, or coding regions of differentially regulated genes. The tool first lists cis-element candidates by motif searching based on the supposition that if there are cis-elements playing important roles in the regulation of a given set of genes, they will be statistically overrepresented and will be conserved. Then it evaluates the likelihood scores of the listed candidate motifs by association rule analysis. This strategy depends on the idea that motifs overrepresented in the promoter region could play specific roles in the regulation of expression of these genes. The tool is designed so that any biological researchers can use it easily at the publicly accessible Internet site http://hpc.irri.cgiar.org/tool/nias/ces. We evaluated the accuracy and utility of the tool by using a dataset of auxin-inducible genes that have well-studied cis-elements. The test showed the effectiveness of the tool in identifying significant relationships between cis-element candidates and related sets of genes.
conclusionThe tool lists possible cis-element motifs corresponding to genes of interest, and it will contribute to the deeper understanding of gene regulatory mechanisms in plants.
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