External Links
Genomics
- AtPID (Arabidopsis thaliana Protein Interactome Database)
- http://www.megabionet.org/atpid/webfile/
- CocoaGenDB
- http://cocoagendb.cirad.fr/
- Genoscope
- http://www.genoscope.cns.fr/spip/Vitis-vinifera-e.html
- Gramene (A Resource for Comparative Grass Genomics)
- http://www.gramene.org/
- GreenPhylDB (A phylogenomic database for plant comparative genomics)
- http://www.greenphyl.org/cgi-bin/index.cgi
- KATANA (Kaszusa Arabidopsis thaliana Annotation Abstract)
- http://www.kazusa.or.jp/katana/
- Kazusa Full-length Tomato cDNA Database
- http://www.pgb.kazusa.or.jp/kaftom/
- Legume base
- http://www.shigen.nig.ac.jp/bean/lotusjaponicus/top/top.jsp
- MiBASE (Micro-Tom Database)
- http://www.kazusa.or.jp/jsol/microtom/indexj.html
- miyakogusa.jp
- http://www.kazusa.or.jp/lotus/
- Oryza Tag Line (OTL) database
- http://urgi.versailles.inra.fr/OryzaTagLine/
- Oryzabase
- http://www.shigen.nig.ac.jp/rice/oryzabaseV4/
- PAIR (Predicted Arabidopsis Interactome Resource)
- http://www.cls.zju.edu.cn/pair/
- PHYSCObase
- http://moss.nibb.ac.jp/
- PlantGDB (Plant Genome Database)
- http://www.plantgdb.org/
- RAP-DB (Rice Annotation Project Database)
- http://rapdb.dna.affrc.go.jp
- Saccharomyces Genome Deletion Project
- http://www-sequence.stanford.edu/group/yeast_deletion_project/
- Selaginella moellendorffii v1.0
- http://genome.jgi-psf.org/Selmo1/Selmo1.home.html
- SGN (Sol Genomics Network)
- http://solgenomics.net/
- Shanghai RAPESEED Database
- http://rapeseed.plantsignal.cn/welcome.do
- SIGnAL (Salk Institute Genomic Analysis Laboratory)
- http://signal.salk.edu/
- SoyBase
- http://soybase.org/
- Strawberry Server
- http://www.strawberrygenome.org/
- TAIR Homepage
- http://www.arabidopsis.org/
- Tree of LifeGenome ProjectsLogin Populus trichocarpa v1.1
- http://genome.jgi-psf.org/Poptr1_1/Poptr1_1.home.html
- UCSC Genome Bioinformatics
- http://www.genome.ucsc.edu/
Transcriptomics
- Agilent Design Files
- http://www.chem.agilent.com/cag/bsp/pp4_1.asp
- ArrayExpress
- http://www.ebi.ac.uk/microarray-as/ae/
- ATTED II (Arabidopsis thaliana trans-factor and cis-element prediction database)
- http://atted.jp
- AVT (AtGenExpress Visualization Tool)
- http://jsp.weigelworld.org/expviz/expviz.jsp
- Basic Search (Agilent Oligo Microarrays)
- http://www.chem.agilent.com/cag/bsp/ArrayInfo.asp
- CATdb (Complete Arabidopsis Transcriptome database)
- http://urgv.evry.inra.fr/CATdb
- CressExpress
- http://cressexpress.org/index.jsp
- Genevestigator
- http://www.genevestigator.ethz.ch/
- GEO (Gene Expression Omnibus)
- http://www.ncbi.nlm.nih.gov/geo/
- KAGIANA
- http://pmnedo.kazusa.or.jp/kagiana/indexjpn.html
- RiceXpro (Rice Expression Profile Database)
- http://ricexpro.dna.affrc.go.jp/
- Soybean Full-Length cDNA Database
- http://rsoy.psc.riken.jp/
- TFGD (Tomato Functional Genomics Database)
- http://ted.bti.cornell.edu/
Proteomics
- Arabidopsis Seed Proteome
- http://www.seed-proteome.com/
- CCDB (Cell Cycle Database)
- http://www.itb.cnr.it/cellcycle/
- Matrix Science
- http://www.matrixscience.com/home.html
- Plant Transcription Factor Databases
- http://planttfdb.cbi.pku.edu.cn/
- PlanTAP 3.0 (Plant Transcription Associated Proteins)
- http://plntfdb.bio.uni-potsdam.de/v3.0/
- PPDB (The Plant Proteome Database)
- http://ppdb.tc.cornell.edu
Organelles
- Arabidopsis Mitochondrial Protein Database
- http://www.plantenergy.uwa.edu.au/applications/ampdb/index.html
- AraPerox 1.2 (A Database of Putative Protein from Plant Peroxisomes)
- http://www3.uis.no/araperoxv1/
- Cell Wall Navigator
- http://bioweb.ucr.edu/Cellwall/index.pl
- CpBase (The Stramenopile Chloroplast Genomics Project)
- http://chloroplast.ocean.washington.edu
- ER-GolgiDB (A Database of Predicted ER and Golgi Localization Based on Sequence Homology)
- http://rostlab.org/services/ERGolgiDB/index.html
- eSLDB (Eukaryotic Subcellular Localization DataBase)
- http://gpcr2.biocomp.unibo.it/esldb/index.htm
- GolgiP
- http://csbl1.bmb.uga.edu/GolgiP/
- LocDB (Protein Localization Database for Human and Arabidopsis)
- http://www.rostlab.org/services/locDB/
- Organelle Genome Resources
- http://www.ncbi.nlm.nih.gov/genomes/ORGANELLES/organelles.html
- PeroxisomeDB 2.0
- http://www.peroxisomedb.org/
- PPMdb (A plant plasma membrane database)
- http://bioinformatics.psb.ugent.be/publications/abstract/PPMdb:-a-plant-plasma-membrane-database.--169
- SUBA II (The Subcellular Proteomic Database)
- http://suba2.plantenergy.uwa.edu.au/index.php
- The Arabidopsis Mitochondrial Proteome Project
- http://www.genetik.uni-hannover.de/arabidopsis.html
Images
- AtNoPDB (Arabidopsis Nucleolar Protein Database)
- http://bioinf.scri.sari.ac.uk/cgi-bin/atnopdb/home
- FTFLP (Fluorescent Tagging of Full-length Proteins)
- http://gfp.stanford.edu/
- GFP Database in JOHN INNES CENTRE
- http://data.jic.bbsrc.ac.uk/cgi-bin/gfp/
- GFP Localisome Database
- http://www.psb.ugent.be/papers/cellbiol/
- ImageBank
- http://imagebank.org.uk
- LIPS (Live Images of Plant Stomata)
- http://hasezawa.ib.k.u-tokyo.ac.jp/lips/index.html
- Plant Cell Dynamics
- http://deepgreen.stanford.edu/
- Plants Database
- http://plants.usda.gov/
- Protist Information Server
- http://protist.i.hosei.ac.jp/
- RAPID (RIKEN Arabidopsis Phenome Information Database)
- http://rarge.gsc.riken.jp/phenome/
- The Illuminated Plant Cell
- http://www.illuminatedcell.com/
Analytical Tools
- BioImage Suite
- http://bioimagesuite.yale.edu/index.aspx
- Bisque (Bio-Image Semantic Query User Environment)
- http://www.bioimage.ucsb.edu/
- CellProfiler
- http://www.cellprofiler.org/index.htm
- CellTracker
- http://dbkgroup.org/celltracker/index.php
- Cold Spring Harbor Protocols
- http://cshprotocols.cshlp.org/
- iCluster
- http://icluster.imb.uq.edu.au/
- ImageJ
- http://rsb.info.nih.gov/ij/
- ImageSurfer
- http://imagesurfer.cs.unc.edu/
- MSI (Molecular Sciences Institute)
- http://www.molsci.org/about/index.html
- OME (Open Microscopy Environment)
- http://www.openmicroscopy.org/site
- ParaView
- http://www.paraview.org/
- SCMD (Saccharomyces Cerevisiae Morphological Database)
- http://scmd.gi.k.u-tokyo.ac.jp/datamine/
- TGI database (The Gene Index Project)
- http://compbio.dfci.harvard.edu/tgi/
- The MayaVi Data Visualizer
- http://mayavi.sourceforge.net/
- μManager
- http://valelab.ucsf.edu/~MM/MMwiki/
Others
- AGRIS (The Arabidopsis Gene Regulatory Information Server)
- http://arabidopsis.med.ohio-state.edu/
- Autophagy Database
- http://tp-apg.genes.nig.ac.jp/autophagy/
- DrugBank
- http://www.drugbank.ca/
- EWDB (European Wheat Database)
- http://genbank.vurv.cz/ewdb/default.htm
- FioreDB (Database for Flower Bio-engineering by CRES-T)
- http://www.cres-t.org/fiore/public_db/index.shtml
- GCP Comparative Stress Gene Catalog
- http://dayhoff.generationcp.org:8080/DayhoffWeb2/
- Gene Ontology
- http://www.geneontology.org/
- KaPPA-View4 (Kazusa Plant Pathway Viewer)
- http://kpv.kazusa.or.jp/kpv4/
- KNApSAcK (A Comprehensive Species-Metabolite Relationship Database)
- http://kanaya.naist.jp/KNApSAcK/
- Lipid bank
- http://lipidbank.jp/
- Metabolome.JP
- http://www.metabolome.jp/
- PathoPlant
- http://www.pathoplant.de/
- PhosPhAt 3.0 (The Arabidopsis Protein Phosphorylation Site Database)
- http://phosphat.mpimp-golm.mpg.de/
- Plant Ontology Consortium
- http://www.plantontology.org/
- PlnTFDB 3.0 (Plant Transcription Factor Database)
- http://plntfdb.bio.uni-potsdam.de/v3.0/
- PmiRKB (Plant microRNA Knowledge Base)
- http://bis.zju.edu.cn/pmirkb/
- ppdb 2.1 (plantpromoterdb 2.1)
- http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/index.cgi
- PRIMe (Platform for RIKEN Metabolomics)
- http://prime.psc.riken.jp/
- RNA Editing Web Site
- http://dna.kdna.ucla.edu/rna/index.aspx
- TarBase V.5c (a manually curated collection of experimentally supported microRNA targets)
- http://diana.cslab.ece.ntua.gr/tarbase/
- TOBFAC (The database of tobacco transcription factors)
- http://compsysbio.achs.virginia.edu/tobfac/