Potato Metabolic Pathways

Bringing together information on plant metabolism

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Links to databases related to 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.
 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
 BESC BeoCyc A collection of Pathway / Genome Databases of sequnced Bioenergy related organisms
 bEST-DRRD Barley EST DNA replication and repair database
 Bio3graph Enables automatic extraction of biological relations from the literature
 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
 Bolbase Genomics database for Brassica oleracea
 BlastR A tool for searching and clustering RNA
 CACTUS Chory Array Computational Tooles User Service
 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
 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
 CyanoPhyChe A Database for Physico-chemical properties of cyanobacterial proteins
 dcGO Database of domain-centric ontologies on functions, phenotypes, diseases and more
 CYPSI CYPs Structure Interface
 DATF Database of Arabidopsis Transcription Factors
 dbWFA A Wheat Functional Annotation Database
 DEBDOM Database Exploring Banana Divesity 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
 EuPathDB Eukaryotic Pathogen Database Resources
 ExPASy Proteomics server, enzyme database, and links to biochemical pathways
 FARO server Functional Association Response by Overlap
 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
 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
 MediPIExMedicago 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
 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
 PhosPhat 4.0 The Arabidopsis Protein Phosphorylation Site Database
 Phytozome To facilitate comparative genomic studies between green plants
 PIECE Plant Introl 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
 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
 RiceSRTFDB Rice Stress-Responsive Transcription Factor Database
 RiceWiki An open 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 Systmatic 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
 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
 SMR SWISS-MODEL Repository
 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
 Sol Genomics Sol Genomics Network
 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 localization 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
 TF Database Predicted 3D structures  for all Transcription Factors in Arabidopsis
 TFGD Tomato functional genomics database
 TGP Database on Plant Promoters for Transgenesis
 TreeTFDB A database of transcription factors for 6 tree species
 TSdb Transporter substrate database
 UniGene UniGene
 VIGGS Vigna Genome Server
 Wall COX Cell Wall Coexpression Database
 WheatGenome Wheat Genome Information
 WoLF PSORT Protein Subcellular Localization Prediction

 

 

 Page last updated 9 December 2015