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

Keywords

Biology, In silico, Database, Computational biology, Regulatory sequence

References

• Analysis of the genome sequence of the flowering plant Arabidopsis thalianaArabidopsis Genome Initiative — 2000
• PlantCARE, a plant cis-acting regulatory element databaseStéphane Rombauts, Patrice Déhais, Marc Van Montagu — 1999
• Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.Charles E. Lawrence, Stephen F. Altschul, Mark S. Boguski — 1993
• MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data.Kerstin Quandt, Kornelie Frech, Holger Karas — 1995
• A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed GenesGert Thijs, Kathleen Marchal, Magali Lescot — 2001
• Promoter Analysis of Co-regulated Genes in the Yeast GenomeMichael Q. Zhang — 1999
• INCLUSive: INtegrated Clustering, Upstream sequence retrieval and motif SamplingGert Thijs, Yves Moreau, Frank De Smet — 2002
• TRANSFAC: an integrated system for gene expression regulationEdgar Wingender — 2000
• Gibbs motif sampling: Detection of bacterial outer membrane protein repeatsAndrew F. Neuwald, Jun S. Liu, Charles E. Lawrence — 1995

Cited by

• Molecular and mutational analysis of a wheat thaumatin-like xylanase inhibitor (TLXI)Sigrid Rombouts — 2007
• Sl-ERF2, a tomato ethylene response factor involved in ethylene response and seed germination.Julien Pirrello, Fabiola Jaimes‐Miranda, M. Teresa Sánchez-Ballesta — 2006
• ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in ArabidopsisMary Thompson — 2006
• Synthetic promoters: genetic control through cis engineering.Haruo Shirane — 2007
• Molecular cloning and characterization of the yew gene encoding squalene synthase from Taxus cuspidata.Manuela Bosch Príncep, Inmaculada Domínguez Fabián — 2007
• Evidence that the BONZAI1/COPINE1 protein is a calcium- and pathogen-responsive defense suppressorCatherine Léglu, Stephen J. Milner — 2008
• Isolation and phylogenetic footprinting analysis of the 5'-regulatory region of the floral homeotic gene OrcPI from Orchis italica (Orchidaceae).V. G. Lagutin, E. Lepa — 2010
• LOX genes in blast fungus (Magnaporthe grisea) resistance in riceSoma S. Marla, Vinay Kumar Singh — 2012
• The cis-acting CTTC-P1BS module is indicative for gene function of LjVTI12, a Qb-SNARE protein gene that is required for arbuscule formation in Lotus japonicus.Беспалов Николай Николаевич, Голембиовский Юрий Мичиславович, Ильин Михаил Владимирович — 2013
• The wheat HMW-glutenin 1Dy10 gene promoter controls endosperm expression in Brachypodium distachyonRoger Thilmony, Mara Guttman, Jeanie Lin — 2013
• GhPSY, a phytoene synthase gene, is related to the red plant phenotype in upland cotton (Gossypium hirsutum L.)雄一 石川, 範人 藤田 — 2014
• Characterization of Mannitol-2-Dehydrogenase in Saccharina japonica: Evidence for a New Polyol-Specific Long-Chain Dehydrogenases/ReductaseJean Pierre Wickersheimer — 2014
• Glyma11g13220, a homolog of the vernalization pathway gene VERNALIZATION 1 from soybean [Glycine max (L.) Merr.], promotes flowering in Arabidopsis thalianaPhilippe Fargues — 2015
• Genome-wide identification and expression profiling of the copper transporter gene family in Populus trichocarpa.Kayleigh R. Mayer — 2015
• A comparative gene analysis with rice identified orthologous group II HKT genes and their association with Na+ concentration in bread wheatMartin Große-Hüttmann, Christian L. Roth, Josef Schmid — 2016
• Evolutionary Expansion of WRKY Gene Family in Banana and Its Expression Profile during the Infection of Root Lesion Nematode, Pratylenchus coffeaeUlrich Winter — 2016
• Genome-Wide Analysis Suggests the Relaxed Purifying Selection Affect the Evolution of WOX Genes in Pyrus bretschneideri, Prunus persica, Prunus mume, and Fragaria vescaHong Ryul Kim, Deok‐Woo Kim — 2017
• The Tyrosyl-DNA Phosphodiesterase 1β (Tdp1β) Gene Discloses an Early Response to Abiotic StressesMario Pisani — 2017
• Molecular characterization of the genome-wide BOR transporter gene family and genetic analysis of BnaC04.BOR1;1c in Brassica napusFelix Winata, Stefanus Januar, Erik Wijaya — 2018
• Genome-Wide Identification and Expression Profiling of the TCP Family Genes in Spike and Grain Development of Wheat (Triticum aestivum L.)Чучалин Александр Иванович — 2018

Related papers

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• Identification of sparsely distributed clusters of cis-regulatory elements in sets of co-expressed genes.Gabriel Kreiman — 2004
• Genomic approaches to finding cis-regulatory modules in animalsRoss C. Hardison, James Taylor — 2012
• Computational approaches to finding and analyzing cis-regulatory elements.C. Titus Brown — 2008
• A relational database system for the maintenance and verification of the Los Alamos sequence libraryMinoru Kanehisa, James W. Fickett, Walter B. Goad — 1984
• Synthetic and genomic regulatory elements reveal aspects of cis regulatory grammar in Mouse Embryonic Stem CellsDana King, Brett Maricque, Barak A. Cohen — 2018
• Modular cis‐regulatory logic of yellow gene expression in silkmoth larvaeTakao Suzuki, Shigeyuki Koshikawa, Isao Kobayashi — 2019