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PhylomeDB

http://phylomedb.bioinfo.cipf.es/

Description :
Experimentally validated and predicted serine phosphorylation sites in Arabidopsis thaliana

AtPID

http://atpid.biosino.org/

Description :
Arabidopsis thaliana Protein Interactome Database

PhosPhAt

http://phosphat.mpimp-golm.mpg.de/app.html

Description :
Arabidopsis Protein Phosphorylation Site Database

Arabidopsis Hormone Database

http://ahd.cbi.pku.edu.cn/

Description :
Plant hormones are small organic molecules that influence almost every aspect of plant growth and development. Genetic and molecular studies have revealed a large number of genes that are involved in responses to numerous plant hormones, including auxin, gibberellin, cytokinin, abscisic acid, ethylene, jasmonic acid, salicylic acid, and brassinosteroid (1). Here, we develop an Arabidopsis hormone database (AHD), which aims to provide a systematic and comprehensive view of genes participating in plant hormonal regulation, as well as morphological phenotypes controlled by plant hormones. Based on data from mutant studies, transgenic analysis and gene ontology annotation, we have identified a total of 1,026 genes in the Arabidopsis genome that participate in plant hormone functions. Meanwhile, a phenotype ontology is developed to precisely describe myriad hormone-regulated morphological processes with standardized vocabularies. A web interface (http://ahd.cbi.pku.edu.cn) allows users to get rapid access to information about these hormone-related genes, including sequences, functional category, mutant information, phenotypic description, microarray data, and linked publications.

Aknowledgement :
This work was supported by NSFC30625003, ED20060047 and 111 project(to H.G.). We thank Qiyao Li for web decoration, Fengying An and Qiong Zhao for helpful discussion.

References :
1. Alonso, J.M. and Ecker, J.R. (2006) Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis. Nat Rev Genet, 7, 524-536.

ASRP - Arabidopsis Small RNA Project

http://asrp.cgrb.oregonstate.edu/

Description :
Arabidopsis thaliana small RNA project

CATdb

http://urgv.evry.inra.fr/CATdb

Description :
Arabidopsis transcriptome data

GABI-Kat

http://www.gabi-kat.de/

Description :
Insertional mutagenesis approaches, especially by T-DNA, play important roles in gene function studies of the model plant Arabidopsis thaliana. GABI-Kat SimpleSearch is a Flanking Sequence Tag (FST)-based database for T-DNA insertion mutants generated by the GABI-Kat project. Currently the database contains more than 108,000 mapped FSTs from about 64,000 lines which cover 64 percent of all annotated A. thaliana protein-coding genes. The web interface allows to search for relevant insertions by gene code, keyword, line identifier, GenBank accession number of the FST, and also by BLAST. A graphic display of the genome region around the gene or the FST location assists users to select insertion lines of their interests. About 3,800 insertions were confirmed in the offspring of the plant from which the original FST was generated, and the seeds of these lines are available from the Nottingham Arabidopsis Stock Centre. The database now also contains additional information such as segregation data, gene-specific primers and confirmation sequences. This information not only helps users to evaluate the usefulness of the mutant lines, but also covers a big part of the molecular characterization of the insertion alleles.

Aknowledgement :
GABI-Kat was supported by the Federal Ministry of Education and Research (BMBF) in the context of the German plant genomics program GABI (grant no. 0312273).

References :
1. Li, Y., Rosso, M.G., Strizhov, N., Viehoever, P. and Weisshaar, B. (2003) GABI-Kat SimpleSearch: a flanking sequence tag (FST) database for the identification of T-DNA insertion mutants in Arabidopsis thaliana. Bioinformatics, 19, 1441-1442.

GreenPhylDB

http://greenphyl.cirad.fr/

Description :
Comparative genomics of rice and Arabidopsis thaliana

Brassica BASC

http://hornbill.cspp.latrobe.edu.au/cgi-binpub/brassica/index.pl

Description :
The BASC system provides tools for the integrated mining and browsing of genetic, genomic and phenotypic data. This public resource hosts information on Brassica species supporting the Multinational Brassica Genome Sequencing Project, and is based upon five distinct modules, ESTDB, Microarray, MarkerQTL, CMap and EnsEMBL. ESTDB hosts expressed gene sequences and related annotation derived from comparison with GenBank, UniRef, and the genome sequence of Arabidopsis. The Microarray module hosts gene expression information related to genes annotated within ESTDB. MarkerQTL is the most complex module and integrates information on genetic markers, maps, individuals, genotypes and traits. Two further modules include an Arabidopsis EnsEMBL genome viewer and the CMap comparative genetic map viewer for the visualisation and integration of genetic and genomic data. The database is accessible at http://bioinformatics.pbcbasc.latrobe.edu.au

Aknowledgement :
We are grateful to Professor Yong Pyo Lim, Chungnam National University, Korea, for the provision of BAC end sequence data for Brassica rapa.

Gramene

http://www.gramene.org/ Gramene is a curated, open-source, data resource for comparative genome analysis in the grasses. Our goal is to facilitate the study of cross-species homology relationships using information derived from public projects involved in genomic and EST sequencing, protein structure and function analysis, genetic and physical mapping, interpretation of biochemical pathways, gene and QTL localization and descriptions of phenotypic characters and mutations.

The Arabidopsis Information Resource (TAIR)

http://www.arabidopsis.org/

Description :
Comprehensive resource for the scientific community working with Arabidopsis thaliana.

Arabidopsis Ensembl

http://atensembl.arabidopsis.info/

Description :
Access to the Arabidopsis thaliana genome through the Ensembl user interface. There are two independent assemblies available, one from TIGR and one from MIPS. Includes the collection of NASC insertion mutants.

Interolog/Regulog Database

http://interolog.gersteinlab.org/

Description :
Database of protein orthologs that interact (interologs) and proteins with conserved regulatory relationships across species (regulogs). Contains data for C. elegans, Drosophila, Arabidopsis, and Yeast.

SUBA

http://www.suba.bcs.uwa.edu.au/

Description :
The Arabidopsis Subcellular Database (SUBA, http://www.suba.bcs.uwa.edu.au) is maintained by the ARC Centre of Excellence in Plant Energy Biology at The University of Western Australia. The database contains publicly available protein subcellular localisation data from a variety of sources from the model plant Arabidopsis. The database can be relationally interrogated through a purpose built web interface that enables powerful SQL queries to be formulated against the datasets. Localisation information include data from chimeric fluorescent fusion protein studies, large scale proteomic analyses of subcellular compartments, literature and homology information (Gene Ontology annotations, Swiss-Prot and gene descriptors) and pre-computed bioinformatic prediction of localisation by 10 software packages. These data provide non-redundant subcellular localisation information on approximately 7000 Arabidopsis proteins and bioinformatic localisation information for all ~30,000 proteins in the database.

Arabidopsis Mitochondrial Protein Database

http://www.plantenergy.uwa.edu.au/applications/ampdb/index.html

Description :
Experimentally identified mitochondrial proteins in Arabidopsis

References :
1. Heazlewood JL, Tonti-Filippini JS, Gout A, Day DA, Whelan J and Millar AH (2004) Experimental analysis of the Arabidopsis mitochondrial proteome highlights signalling and regulatory components, provides assessment of targeting prediction programs and points to plant specific mitochondrial proteins. Plant Cell 16: 241-256.

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