PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences

By Magali Lescot, P. Déhais, Gert Thijs, Kathleen Marchal, Yves Moreau, Y. Van de Peer, Pierre Rouzé, Stephane Rombauts. Nucleic Acids Res., 2002

6,551 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/d364903a626ad70e6ce057209d9b7e004dafd4be

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Citations in the corpus

Genome-wide identification and characterization of the aquaporin gene family in Sorghum bicolor (L.) (2015, methodology): “The sequences were analyzed by different bioinformatics programs, including PlantPAN (Chang et al., 2008), PLACE (Higo et al., 1999), and PlantCARE (Lescot et al., 2002), and the available literature.”
ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis (2006, background): “It could enforce the estimation of regulatory scheme of the target genes deduced from the limited amount of experimentally determined cis elements, which are stored in cis -element databases (14,15).”
Isoprene emission from plants: why and how. (2007, methodology): “The sequences of these regions (2000 nucleotides upstream of the start codon) were found on the P. trichocarpa genome website (http://genome.jgi-psf.org/ Poptr1_1/Poptr1_1.home.html) and analysed with PLACE (Higo et al., 1999) and PlantCARE (Lescot et al., 2002), which search DNA sequences for trans”
Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa. (2010, background): “be/webtools/plantcare/html/) in order to reveal further precise promoter motifs and the relationship between a drought-induced miRNA, its target gene, and the relevant promoter (Lescot et al., 2002).”
Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, neutral): “Metal concentrations were measured by using inductively coupled plasma optical emission spectrometry SPS3000 (Seiko, Tokyo, Japan).”
Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. (2008, methodology): “Fourteen stress-inducible miRNAs were detected, and our results were further confirmed by detecting their expression patterns and analyzing the cis-elements in their promoter sequences.”
The evolution of transcriptional regulation in eukaryotes. (2003, background): “In the former category are programs that use databases of known binding site matrices to scan a sequence for potential binding sites (e.g., TRANSFAC: Wingender et al. 2001; EPD: Praz et al. 2002; PlantCARE: Lescot et al. 2002; SCPD: Zhu and Zhang 1999).”
A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed Genes (2001, positive): “The automated upstream sequence retrieval of INCLUSive (Thijs et al. , 2002) was used to (cid:142) nd the upstream sequences of the genes in each of the selected clusters.”