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Links to other Databases on Plant Science

ABrowse A customizable genome browser framework
AGOS A composition-based WG/GW Argonaute-binding domains detector
AGRIS Arabidopsis Gene Regulatory Information Server
AHD2.0 Arabidopsis Hormone Database 2.0
ANAP Arabidopsis Network Analysis Pipeline
APSnet APS Education Center. The plant health instructor
Arabidopsis Metabolomics Consortium Metabolomics as a functional genomics tool for elucidating the functions of Arabidopsis genes
AraPath A knowledge base for pathway analysis in Arabidopsis
ArrayExpress A public repository for microarray data
ASIP Alternative Splicing in Plants
AthaMap A genome-wide map of potential transcription factor and small RNA binding sites in Arabidopsis.
AtmiRNET Reconstructing regulatory networks of Arabidopsis thaliana miRNAs
Altas T4SS A Database for Analysis of Type IV Secretion System
AtPAN Arabidopsis thaliana Promoter Analysis Net (for Transcription Regulatory Networks)
ATTED-II Co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis
BarleyBase Miame/Plant-compliant and Plant Ontology enhanced expression resource for barley
BESC BeoCyc A collection of Pathway / Genome Databases of sequnced Bioenergy related organisms
bEST-DRRD Barley EST DNA replication and repair database
BioCyc A collection of pathway / genome databases
BioGRID Biological General Repository for Interaction Datasets
B10NUMB3R5 The database of useful biological numbers
bfgr Biofuel Feedstock Genomics Resource
BlastR A tool for searching and clustering RNA
Bolbase Genomics database for Brassica oleracea
CastorDB Castor bean genome data
CathaCyc Metabolic Pathway Database of Catharanthus roseus
CAZy Carbohydrate-Active Enzymes Database
CIBMAN Database Exploring Citrus Biodiversity of Manipur
CIP International Potato Centre
Comparative Pathway Analyzer Allows users to investigate the reaction content of a set of organisms
CACTUS Chory Array Computational Tools User Site
CoP Co-expressed biological processes
CORNET Linking different components of a system by constructing correlation networks
Cotton EST Database Cotton EST Database
CPGR Comprehensive Phytopathogen Genomics Resource
CPRAD Cereal Pathogen Resistance Allele Database
CYPSI CYPs Structure Interface
DATF Database of Arabidopsis Transcription Factors
dbWFA A Wheat Functional Annotation Database
dcGO Database of domain centric ontologies on functions, phenotypes, diseases and more
DEBDOM Database Exploring Banana Diversity in Manipur
DeOri Database of eukaryotic DNA replication origins
DFVF Database of Virulence Factors in Fungal Pathogens
DNAtraffic A database for systems biology of DNA dynamics
DRASTIC Database Resource for the Analysis of Signal Transduction in Cells
DTS Dragon Translation Initiation Site Spotter
ECPD European Cultivated Potato Database
EMBL EMBL Nucleotide Sequence Database
ERISdb Database of Plant Splice Sites and Splicing Signals
EuPathDAB Eukaryotic Pathogen Database Resources
ExPASy Proteomics server, enzyme database, and links to biochemical pathways
EXPath Comparative expression analysis inferring metabolic pathways for plants.
FARO server Functional Association Response by Overlap
FmMDB Foxtail Millet Marker Database
From Metabolite to Metabolite Can reconstuct metabolic pathwaysfrom one metabolite to another one.
FSTVAL Flanking Sequence Tag Validator
GABI-Kat Arabidopsis T-DNA mutant database
GabiPD A repository and analysis platform for a wide array of heterogeneous data from high-throughput experiments in several plant species
GARNet A BBSRC sponsored network to support work on Arabidopsis and the wider plant community
Gene Expression Atlas Gene Expression Atlas (Array Express Atlas)
GeneMANIA A web interface for generating hypotheses about gene function
GENEVESTIGATOR the gene expression search engine
GFam gene family annotation and maintenance
Global Potato News A source of online information about potatoes
GMCC-13 Sixth International Conference on Coexistence of GM and non-GM based Agricultural Supply Chains. 12-15 November, 2013. Lisbon, Portugal.
GnpIS Genetic and Genomic Information System
GO Gene Ontology
Gramene Gramene Database
iHUB Collaborative International Network for ionomics
GreenPhylDB A phylogenomic database for plant comparative genomics
HOGENOM Database of Complete Genome Homologous Gene Families
InterStoreDB A generic integration resource for genetic and genomic data
IPPO International Plant Proteomics Organization
iRootHair Root Hair Genomics Database
I-TASSER Protein Structure and Function Predictions
KaPPA - View 4 A metabolic pathway database
KEGG Kyoto Encyclopedia of Genes and Genomes
LegumeIP An integrative platform to study gene function and genome evolution in legumes
LIPABASE A compilation of data related to lipases
Lipid Library The Lipid Library (good links to plant lipids)
LSD Leaf Senescence Database
LTPDB non-specific Lipid Transfer Protein Database for Plant
MaizeGDB Maize genetics and genomics database
MapMan A user-driven tool to display large datasets (eg from microarrays) onto diagrams of metabolic pathways
MASiVEdb Sirevirus Plant Retrotransposon Database
MassTRIX Mass Translator into Pathways
MEDDB Medicinal Plants Database
MediPIEx Medicago truncatula multiple expression analysis
MEROPS The Peptidase Database
MERYB Metabolomic Repository Bordeaux
Metabolights Database for metabolomics experiments and derived information
Metabolomics Society Dedicated to promoting the growth, use and understanding of metabolomics in the life sciences
MetaCrop MetaCrop database summarizes diverse information about metabolic pathways in crop plants
MetaCyc A database of nonredundant, experimentally elucidated metabolic pathways
MetNet Database contains integrative information on networks of metabolic and regulatory interactions in Arabidopsis and soybean
META-PHOR Metabolomics for plants, health and outreach
mGOASVM Multi-Label Protein Subcellular Localization Prediction
MIPS Munich Information Center for Protein Sequences
miRBase The microRNA database
miRDeepFinder Package for analyzing data from plant microRNA deep sequencing
miREvo A platform for miRNA evolution analysis
mirEX Arabidopsis pri-miRNA Expression Atlas
miRFANS Arabidopsis thaliana microRNA Function Annotations
miRTour Plant miRNA and target prediction tool.
MirtronPred Intronic MiRNA - Mirtrons
MiSolRNA A tomato micro RNA relational database
Morph-R Module guided Ranking of candidate Pathway genes
Nematic Nematode-Arabidopsis Transcriptomic Interaction Compendium
NeMedPlant A database of medicinal plants from Northeast India
NetAligner Alignment of protein interaction networks
NIASGBdb NIAS Genebank databases for genetic resources and plant disease information
Non-B DB A Database for Integrated Annotations and Analysis of non-B DNA Forming Motifs
OrysPSSP A comparative platform for small secreted proteins from rice and other plants
Oryzabase An integrated database of rice genome resources
OryzaExpress Gene Expression Database for Rice
P3DB Plant protein phosphorylation database
PaintOmics Painting omics data in biological pathways
PAIR Predicted ArabidopsisInteractome Resource
PASmiR Database for miRNA molecular regulation in plant abiotic stress
PathLocdb Pathway Localization Database
PathoPlant Database on plant-pathogen interactions and components of signal transduction pathways
PathPred Pathway Prediction server
PathText A text mining integrator for biological pathway visualizations
PCoM-DB Protein co-migration database for photosynthetic organisms
PDBe Protein Data Bank in Europe
pep2pro high-throughput proteomics data processing, analysis, and visualisation tool
Pfam Database of protein families
PGDD Plant Genome Duplication Database
PGIR Plant Genomics Initiative at Rutgers
PGSC Potato Genome Sequencing Consortium
PHI-base 4 Database containing pathogenicity, virulence and effector genes from fungal, Oomycete, and bacterial pathogens, which infect animal, plant, fungal and insect hosts.
PhosPhAt The Arabidopsis Protein Phosphorylation Site Database
Phytozome To facilitate comparative genomic studies between green plants
PIECE Plant Intron Exon Comparison and Evolution Database
PlaNet Plant Co-expression Network Browser
PLANEX Plant co-expression database
PlantGSEA Plant GeneSet Enrichment Analysis Toolkit
Plant Image Analysis Plant Image Analysis Software
Plant Metabolic Network A collection of plant metabolic pathway databases (includes AraCyc, PlantCyc and PoplarCyc)
Plantmetabolomics Arabidopsis metabolomics
Plant MetGenMAP A visualization and analysis package to identify changed pathways and enriched GO terms from gene expression and/or metabolite profile data
PlantMiRNAPred Plant MiRNA Prediction
PlantNATsDB Plant Natural Antisense Transcripts Database
Plant Ontology Plant Ontology Database
Plant Organelles Database Designed to promote an understanding of organelle dynamics
Plant rDNA database Provides information on ribosomal DNA loci
Plant Reactome Plant metabolic and regulatory pathways
plantRNA Database of plant tRNA gene sequences
PlantPhos A plant phosphorylation prediction tool
Plants and Microbes

Everything related to the science of plant-microbe interactions

Plantstress Links to information on abiotic plant stresses
PlantsP Functional Genomics of Plant Phosphorylation
Plants UPS Database of plants ubiquitin proteasome system
PlantTFDB Plant Transcription Factor Database
PLEXdb Plant Expression Database
PLncDB Plant Long noncoding RNA Database
PlnTFDB Plant transcription factor database
PmiRKB Plant microRNA Knowledge Base
PMN Plant Metabolic Network
PMRD plant microRNA database
PMTED Plant MicroRNA Target Expression Database
PODB Plant organelles database
POGs2 Search for Putative Orthologous Groups
PoMaMo Potato datases, chromosome maps, genome maps and more
POPcorn Project Portal for corn
Potato Genome Sequencing Consortium An international group committed to sequencing the complete potato genome
PPIRA Protein Protein Interactions between Ralstonia solanacearum and Arabidopsis thaliana
ppt-miRBase Physcomitrella patens microRNA Database
PredPlantPTS1 Plant PTS1 Protein Prediction
PRI-CAT Plant Research International ChIP-seq Analysis Tool
PRIMEe Platform for RIKEN Metabolomics
PRIN Oryza sativa protein-protein interactions network
PRINTS A compendium of protein fingerprints
PRGdb Plant resistance gene database
ProFITS Protein families involved in the transduction of signalling (ProFITS) in the maize genome
Promex A mass spectral reference database
Prosite Database of protein domains, families and functional sites
ProtClustDB Protein Clusters
psRNATarget A plant small RNA target analysis server
psRobot Plant Small RNA Analysis Toolbox
QlicRice A web interface for abiotic stress responsive QTL and loci interaction channel in rice
Q-TARO QTL Annotation Rice Online Database
RAP-DB Rice Annotation Project Database
RFET Prediction of drought-resistant genes in Arabidopsis thaliana using SVM-RFE
Rice kinase Database Rice kinase database
RiceRBP Experimentally Identified RNA Binding Proteins in Oryza sativa
Rice PIPELINE A unification tool for rice data from various databases
RiceSRTFDBA Rice Stress-Responsive Transcription Factor Database
RiceWiki An open content platform for community curation of rice genes
RiceXPro Rice Expression Profile Database
RMOS Rice microarray opening site
RNApathwaysDB A database of RNA maturation and decay
SABRE2 DB Systematic consolidation of Arabidopsis and other Botanical Resources
Sciencewatch Tracking trends and performance in basic research
SecretomeP Prediction of non-classical protein secretion
Seed proteome Seed proteome web portal
Sol Genomics Sol Genomics Network
SIGnAL / CCSB Cytoscape Web Plant-Pathogen Immune Network and Arabidopsis Interactome
SIMAP A database containing the similarity space formed by about all amino-acid sequences from public databases and completely sequenced genomes
SINEBase A database and tool for SINE analysis
Solanaceae Genomics Network A collection of Pathway Genome Databases for Solanaceae species
solArray Potato Microarray Database
SolCAP Solanaceae Coordinated Agricultural Project
Solestdb Solanaceae EST Database
SOLmiRNA Solanaceae miRNA database
SolRgene Resource for Solanum resistance genes
SoSMART Plant miRNA/tasiRNA Analysis Resources and Tools
SPD Soybean Proteome Database
SplamiR Predicting miRNAs in plants
SpliceGrapher creates splice graphs from RNA-Seq data
STIFDB Stress responsive transcription factor database
SUBA3 SUBcellular localisation database for Arabidopsis proteins
SUPFAM Database of structural and functional annotation for all proteins and genomes
Swiss Plant Science Web Swiss portal for plant sciences
Swiss-Prot A curated protein sequence database
TAIR The Arabidopsis Information Resource
TENOR Transcriptome Encyclopedia of Rice
TF Database Predicted 3D structures for all Transcription Factors in Arabidopsis
TFGD Tomato functional genomics database
TGP Database on Plant Promoters for Transgenesis
TreeTFDAB A database of transcription factors for 6 tree species
TSdb Transporter substrate database
UniGene UniGene
Wall COX Cell Wall Coexpression Database
WheatGenome Wheat Genome Information
WoLF PSORT Protein Subcellular Localization Prediction

Last updated  24 November 2015                                                                                                                                Gary Lyon