ArticlePlant physiology2006
Large-scale cis-element detection by analysis of correlated expression and sequence conservation between Arabidopsis and Brassica oleracea.
Article in Plant physiology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants.Plant communications · 2023Review
- An expanded role for the transcription factorFrontiers in plant science · 2022Article
- Conserved Function of ACYL-ACYL CARRIER PROTEIN DESATURASE 5 on Seed Oil and Oleic Acid Biosynthesis betweenFrontiers in plant science · 2017Article
- PoplarGene: poplar gene network and resource for mining functional information for genes from woody plants.Scientific reports · 2016Article
- Isolation, structural analysis, and expression characteristics of the maize TIFY gene family.Molecular genetics and genomics : MGG · 2015Article
- Characterization and identification of cis-regulatory elements in Arabidopsis based on single-nucleotide polymorphism information.Plant physiology · 2014Article
- An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions.Nature genetics · 2013Article
- Plant core environmental stress response genes are systemically coordinated during abiotic stresses.International journal of molecular sciences · 2013Article
- Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes.Nucleic acids research · 2011Article
- A mutation degree model for the identification of transcriptional regulatory elements.BMC bioinformatics · 2011Article
- Gene coexpression clusters and putative regulatory elements underlying seed storage reserve accumulation in Arabidopsis.BMC genomics · 2011Article
- Article
- Correlation Network Analysis reveals a sequential reorganization of metabolic and transcriptional states during germination and gene-metabolite relationships in developing seedlings of Arabidopsis.BMC systems biology · 2010Article
- A composite transcriptional signature differentiates responses towards closely related herbicides in Arabidopsis thaliana and Brassica napus.Plant molecular biology · 2010Article
- Article
- Sequence, expression divergence, and complementation of homologous ALCATRAZ loci in Brassica napus.Planta · 2009Article
- Discovery of cis-elements between sorghum and rice using co-expression and evolutionary conservation.BMC genomics · 2009Article
- Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks.Plant physiology · 2009Article
- Sequence analysis and functional characterization of the promoter of the Picea glauca Cinnamyl Alcohol Dehydrogenase gene in transgenic white spruce plants.Plant cell reports · 2009Article
- Genome-wide targeted prediction of ABA responsive genes in rice based on over-represented cis-motif in co-expressed genes.Plant molecular biology · 2009Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The rapidly increasing amount of plant genomic sequences allows for the detection of cis-elements through comparative methods. In addition, large-scale gene expression data for Arabidopsis (Arabidopsis thaliana) have recently become available. Coexpression and evolutionarily conserved sequences are criteria widely used to identify shared cis-regulatory elements. In our study, we employ an integrated approach to combine two sources of information, coexpression and sequence conservation. Best-candidate orthologous promoter sequences were identified by a bidirectional best blast hit strategy in genome survey sequences from Brassica oleracea. The analysis of 779 microarrays from 81 different experiments provided detailed expression information for Arabidopsis genes coexpressed in multiple tissues and under various conditions and developmental stages. We discovered candidate transcription factor binding sites in 64% of the Arabidopsis genes analyzed. Among them, we detected experimentally verified binding sites and showed strong enrichment of shared cis-elements within functionally related genes. This study demonstrates the value of partially shotgun sequenced genomes and their combinatorial use with functional genomics data to address complex questions in comparative genomics.
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