Links

	The Arabidopsis Information Resource (TAIR) provides resource for the scientific community working with A. thaliana, a widely used model plant. TAIR consists of a searchable relational database. The data can be viewed using our interactive MapViewer, and analyzed with our tools. In addition, pages on news, information on the Arabidopsis Genome Initiative (AGI), Arabidopsis lab protocols, and useful links are provided. Garcia-Hernandez et al. TAIR: a resource for integrated Arabidopsis data. Functional and Integrative Genomics 2002 2(6):239 pdf
	Arabidopsis thaliana microarray database and analysis toolbox (Gene Atlas, Gene Chronologer, Gene Correlator, Meta-Analyzer, Response Viewer, Digital Northern) - Free registration needed - The Genevestigator project was started in spring 2003 by Philip Zimmermann, Matthias Hirsch-Hoffmann and Lars Hennig by initially collecting data and information about all Affymetrix GeneChip® experiments from the Gruissem Laboratory at ETH Zurich. GENEVESTIGATOR. Arabidopsis Microarray Database and Analysis Toolbox, Zimmermann et al. - Plant Physiol. 136: 2621-2632. September 2004 pdf
	NCBI : National Center for Biotechnology Information
	GABI stands for the Genome Analysis of the plant BIological system (Germany) - GABI-Kat
	TIGR : The Institute for Genomic Research (US)
	MIPS : Munich Information center for Protein Sequences (Germany) - Its main focus is the genome oriented bioinformatics, in particular the systematic analysis of genome information including the development and application of bioinformatics methods in genome annotation, expression analysis and proteomics. MIPS supports and maintains a set of generic databases as well as the systematic comparative analysis of microbial, fungal, and plant genomes.
	SIGnAL : Salk Institute Genomic Analysis Laboratory (US)
	DRASTIC : Database Resource for Analysis of Signal Transduction In Cells (Scotland) - "Making sense of molecular data from host-pathogen interactions" - DRASTIC is a collaboration between the Scottish Crop Research Institute and the University of Abertay Dundee
	GARNet : Genomic Arabidopsis Resource Network (UK) - GARNet is intended to function as a platform for international Arabidopsis research and for research on other plant species. All GARNet services and resources are publicly available, and data created using the GARNet resources will be freely distributed via databases designed and held at NASC (AGR, NTP) and the JIC (ATIdb)
	RIKEN Genomic Science Center, Plant Functional Genomics Reseach Group (Suehiro, Tsurumi, Yokohama, Kanagawa), Japan - Activation tagging lines database, RARGE (RIKEN ARabidopsis Genome Encyclopedia) Full-length cDNAs, Ac/Ds Tranposon Insertion Lines...
	The miRNA Registry (Sanger Institute, UK) : provides miRNA gene hunters with unique names for novel miRNA genes prior to publication of results and contains a searchable database of published miRNAs
	ARAMEMNON (© Flügge Group, Botanisches Institut, Universität zu Köln, Germany) is a database about transmembrane (TM) proteins of thale cress (Arabidopsis thaliana) and rice (Oryza sativa). The database stores data about: genomic sequence and cDNA/protein sequence predictions location of the genomic sequence on BAC, several transmembrane region predictions in comparison, several signal peptide predictions in comparison, isospecic homologs ('paralogs') in list view and cluster view, mutually heterospecic homologs ('orthologs'), classification according to the Transporter Classification (TC) system, etc... ARAMEMNON, a Novel Database for Arabidopsis Integral Membrane Proteins Plant Physiol. 2003 Jan; 131(1): 16-26
	iHOP : information Hyperlinked Over Proteins - Search for a gene in MEDLINE, and you'll probably get a long list of abstracts, but the results won't show how your target relates to other genes. Adding this context is the goal of a site called iHOP, sponsored by the Spanish National Center of Biotechnology in Madrid. Type in the name of a gene, and the site maps the molecular interrelationships that abstracts reveal Nature (2004). [pdf]
	MPSS : Massively Parallel Signature Sequencing - MPSS and related technologies have been described in publications by Brenner et al. (Nature Biotechnol. [2000] 18:630-634, and PNAS [2000] 97:1665-1670). Like SAGE (Serial Analysis of Gene Expression), MPSS produces short sequence signatures produced from a defined position within an mRNA, and the relative abundance of these signatures in a given library represents a quantitative estimate of expression of that gene. The MPSS signatures are 17 bp in length, and can uniquely identify >95% of all genes in Arabidopsis. Brenner, S., Williams, S.R., Vermaas, E.H., Storck, T., Moon, K., McCollum, C., Mao, J.I., Luo, S., Kirchner, J.J., Eletr, S., DuBridge, R.B., Burcham, T., and Albrecht, G. (2000). In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs. Proc Natl Acad Sci USA 97, 1665-1670. [pdf]
	ASRP : Arabidopsis Small RNA Project - The Arabidopsis Small RNA Project seeks to characterize and functionally analyze the two major classes of endogenous small RNAs - microRNAs (miRNAs) and short-interferring RNAs (siRNAs). These RNAs function to regulate gene expression at the transcriptional and posttranscriptional levels, to guide modification of chromatin and to control developmental pathways. The specific aims of the project include : Discovery of new miRNAs and siRNAs, Functional analysis of miRNAs and siRNAs, Functional analysis of multidomain RNaseIII-like genes
	Arabidopsis Proteins from Plant Peroxisomes Database of Putative Arabidopsis Proteins from Plant Peroxisomes. Reumann S, Ma C, Lemke S, Babujee L. - Plant Physiol. 2004 Aug 27
	Essential Gene Functions in Arabidopsis Seed Development. This project studies genes that give a seed phenotype when disrupted by mutation. The database presents information on genes and mutants generated at Syngenta, from the Salk collection, from the Versailles collection of INRA/Genoplante, and numerous contributions from the community. Tzafrir I, Dickerman A, Brazhnik O, Nguyen Q, McElver J, Frye C, Patton D, Meinke D (2003). The Arabidopsis SeedGenes Project. Nucleic Acids Res. 31: 90-93
	STRING - Search Tool for the Retrieval of Interacting Genes/Proteins Database of known and predicted protein-protein interactions. The interactions include direct (physical) and indirect (functional) associations they are derived from four sources : Genomic Context, High-throughput Experiments, Coexpression, Previous Knowledge. von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA, Bork P. - STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D433-7.[pdf]
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