The Plant Organelles Database 2

	The Plant Organelles Database 2
[Organelles Movie Database] [Organellome Database] [Functional Analysis Database] [External Links] [Organelles World]

External Links

Genomics

AtPID (Arabidopsis thaliana Protein Interactome Database): http://atpid.biosino.org/
Genoscope: http://www.genoscope.cns.fr/spip/Vitis-vinifera-e.html
Gramene (A Resource for Comparative Grass Genomics): http://www.gramene.org/
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/oryzabase/top/top.jsp
PHYSCObase: http://moss.nibb.ac.jp/
PlantGDB (Plant Genome Database): http://www.plantgdb.org/
RAP-DB (Rice Annotation Project Database): http://rapdb.lab.nig.ac.jp/
Saccharomyces Genome Deletion Project: http://www-sequence.stanford.edu/group/yeast_deletion_project/
Shanghai RAPESEED Database: http://rapeseed.plantsignal.cn/welcome.do
SIGnAL (Salk Institute Genomic Analysis Laboratory): http://signal.salk.edu/
SoyBase: http://soybase.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

ACT (Arabidopsis Co-expression Tool): http://www.arabidopsis.leeds.ac.uk/act/index.php
Agilent Design Files: http://www.chem.agilent.com/cag/bsp/pp4_1.asp
Arabidopsis Coexpression Data Mining Tools: http://www.arabidopsis.leeds.ac.uk/act/
ArrayExpress: http://www.ebi.ac.uk/microarray-as/ae/
ATTED II (Arabidopsis thaliana trans-factor and cis-element prediction database): http://www.atted.bio.titech.ac.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
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
Soybean Full-Length cDNA Database: http://rsoy.psc.riken.jp/

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 (Plant Transcription Associated Proteins): http://www.cosmoss.org/bm/plantapdb
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 (A Database of Putative Protein from Plant Peroxisomes): http://www.araperox.uni-goettingen.de/
Cell Wall Navigator: http://bioweb.ucr.edu/Cellwall/index.pl
Chloroplast Genome Database: http://chloroplast.cbio.psu.edu/
ER-GolgiDB (A Database of Predicted ER and Golgi Localization Based on Sequence Homology): http://cubic.bioc.columbia.edu/db/ERGolgiDB/index.html
eSLDB (Eukaryotic Subcellular Localization DataBase): http://gpcr2.biocomp.unibo.it/esldb/index.htm
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://www.plantenergy.uwa.edu.au/applications/suba/index.php
The Arabidopsis Mitochondrial Proteome Project: http://www.gartenbau.uni-hannover.de/genetik/AMPP

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://bio.ltsn.ac.uk/imagebank/
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://www.bioimagesuite.org/
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/
GreenPhylDB (A phylogenomic database for plant comparative genomics): http://greenphyl.cirad.fr/cgi-bin/greenphyl.cgi
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 New: http://www.micro-manager.org/index.php

Others

DrugBank: http://www.drugbank.ca/
EWDB (European Wheat Database): http://genbank.vurv.cz/ewdb/default.htm
GCP Comparative Stress Gene Catalog: http://dayhoff.generationcp.org/
Gene Ontology: http://www.geneontology.org/
KaPPA-View2 (The Kazusa Plant Pathway Viewer): http://kpv.kazusa.or.jp/kappa-view/
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/
ppdb (plantpromoterdb 2.0): http://ppdb.gene.nagoya-u.ac.jp/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/