Plant Database

[Arabidopsis thaliana]

AGNS(Arabidopsis GeneNet supplementary) database is an Internet-available resource that provides access to description of the functions of the known Arabidopsis genes at various levels-the levels of mRNA, protein, cell, tissue, and ultimately at the levels of organs and the organism in both wild type and mutant backgrounds.

The Arabidopsis Gene Regulatory Information Server (AGRIS) is a new information resource of Arabidopsis promoter sequences, transcription factors and their target genes. AGRIS currently contains three databases.

Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis.

Arabidopsis Mitochondrial Protein Database

ARAMEMNON is a resource designed for scientists, who look for a convenient way to access data about individual plant membrane proteins and membrane protein families. Currently, the database provides membrane protein data of nine plant species

ARTADE (ARabidopsis Tiling-Array-based Detection of Exons) is a standard tool for the annotation of genome-wide tiling-array data in Arabidopsis.

Arabidopsis MPSS
Search for gene expression data in Arabidopsis generated by MPSS (massively parallel signature sequencing) technology, as well as information on Arabidopsis small RNAs.

The purpose of the Arabidopsis Small RNA Project (ASRP) website is to provide access to data and resources from the Carrington laboratory.

ATTED-II is a database of coexpressed genes that was originally developed to identify functionally related genes in Arabidopsis and rice.

Arabidopsis Nucleolar Protein Database

AtREA is a collection of programs for analysis of distribution, features and combination of known and novel CREs (Cis-Regulatory Elements ) in Arabidopsis functional classes, metabolic pathways, genome wide microarray and user defined datasets.

Complete Arabidopsis Transcript MicroArray.

CATdb collects together all the information on transcriptome experiments done at URGV with CATMA microarrays, a database for the functional analysis of plant genomes that graphically displays a wide range of Arabidopsis genome annotations including complete information concerning micro array probes.

A tool for large-scale mining of expression data from Arabidopsis. CressExpress is a user-friendly, online, coexpression analysis tool for Arabidopsis (Arabidopsis thaliana) microarray expression data that computes patterns of correlated expression between user-entered query genes and the rest of the genes in the genome.

The Database of Arabidopsis Transcription Factors (DATF) collects all arabidopsis transcription factors (totally 1922 Loci; 2290 Gene Models) and classifies them into 64 families.(Contain MADS family)

eFP Browser
Create 'electronic fluorescent protein' representations of your gene of interest's expression patterns based on the Schmid et al. (2005) Map of Arabidopsis Development.

A database for the functional analysis of the Arabidopsis genome. FLAGdb++ is dedicated to the integration and visualization of data for high-throughput functional analysis of a fully sequenced genome, as illustrated for Arabidopsis. FLAGdb++ displays the predicted or experimental data in a position-dependent way and displays correlations and relationships between different features. FLAGdb++ provides for a given genome region, summarized characteristics of experimental materials like probe lengths, locations and specificities having an impact upon the confidence we will put in the experimental results.

Novel webtools that combine BLAST and co-expression analyses.

Protein Localization Database for Human and Arabidopsis. LocDB is a expert curated database that collects experimental annotations for the subcellular localization of proteins in Human (Homo sapiens) and Weed (Arabidopsis thaliana). The database also contains predictions of subcellular localization from a variety of state-of-the-art prediction methods for all proteins with experimental information.

MIPS Arabidopsisthaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome .Search genomic information and knowledge about Arabidopsis from this comprehensive resource.

OmicBrowse is a browser to explore multiple datasets coordinated in the multidimensional omic space integrating omics knowledge ranging from genomes to phenomes and connecting evolutional correspondences among multiple species.

a plant protein phosphorylation database.

PAIR: the predicted Arabidopsis interactome resource. PAIR comprised of 5990 experimentally reported molecular interactions in Arabidopsis thaliana together with 145,494 predicted interactions, is currently the most comprehensive data set of the Arabidopsis interactome with high reliability.

PPDB is a Plant Proteome DataBase for Arabidopsis thaliana and maize (Zea mays).

PathoPlant is a database on plant-pathogen interactions and components of signal transduction pathways related to plant pathogenesis. PathoPlant also harbors gene expression data from Arabidopsis thaliana microarray experiments to enable searching for specific genes regulated upon certain stimuli like pathogen infection, elicitor treatment, or abiotic stress. Validation of short DNA sequences as cis-elements responsive to different stimuli can also be performed in PathoPlant.

Plant transcription factor (TF) database. PlnTFDB is a public database arising from efforts to identify and catalogue all Plant genes involved in transcriptional control.

ppdb is a plant promoter database that provides promoter annotation of Arabidopsis and rice. The database contains information on promoter structures, transcription start sites (TSSs) that have been identified from full-length cDNA clones and also a vast amount of TSS tag data.

SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis.

The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community.


CSRDB: a small RNA integrated database and browser resource for cereals, consisting of large-scale datasets of maize and rice smRNA sequences generated by high-throughput pyrosequencing.

The Database of Rice Transcription Factors (DRTF) is a collection of known and predicted transcription factors of Oryza sativa L. ssp. indica and Oryza sativa L. ssp. japonica.

GreenPhylDB ( is a comprehensive platform designed to facilitate comparative functional genomics in Oryza sativa and Arabidopsis thaliana genomes.

The MOsDB is a resource for publicly available sequences of the rice (Oryza sativa L.)

MSU Rice Genome Annotation Project Database
The objective of this project has always been to provide high quality annotation for the rice genome. We generated, refined and updated gene models for the estimated 40,000-60,000 total rice genes, provided standardized annotation for each model, linked each model to functional annotation including expression data, gene ontologies, and tagged lines.

Information about approximately 38,000 full-length cDNA clones that were completely sequenced in the Rice full-length cDNA project is shown in the database. The full-length cDNA clones were collected from various tissues treated under various stress conditions. The database contains not only information about complete nucleotide sequences and encoded amino acid sequences, but also results of homology searches against public databases, mapping information, information about patterns of alternative splicing, protein domains and transmembrane structures, and information about cellular localizations and gene functions annotated with Gene Ontology.

The MIPS Rice (Oryza sativa) database provides a comprehensive data collection dedicated to the genome information of rice.

Oryza Tag Line
Oryza Tag Line consists in a searchable database integrating phenotypic data resulting from the evaluation of the Genoplante rice insertion line library. To display the sequence information (Flanking Sequence Tags) resulting from the molecular characterization of the mutagen insertion sites in the collection, Oryza Tag Line is linked to OryGenesDB a GGB-derived interface.

The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan. The database is originally aimed to gather as much knowledge as possible ranging from classical rice genetics to recent genomics and from fundamental information to hot topics.

The PlantTribes database is a plant gene family database based on the inferred proteomes of five sequenced plant species: Arabidopsis thaliana, Carica papaya, Medicago truncatula, Oryza sativa and Populus trichocarpa.

The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc.

Rice Mutant Database is an archive for collecting, managing and searching information of the T-DNA insertion mutants generated by an enhancer trap system. We have generated 129000 rice mutant (enhancer trap) lines that are now being gathered in the database.

Rice Information System (BGI-RIS) is targeted to be the most up-to-date integrated information resource for rice genomes as well as a workbench for comparative genomic analysis among cereal crops.In addition to the comprehensive data of Oryza sativa L. ssp. indica sequenced by BGI, BGI-RIS will host carefully curated genome information of Oryza sativa L. ssp. japonica (Syngenta).

Rice Functional Genomic Express Database

Rice Proteome Database
The Rice Proteome Database is the first detailed database to describe the proteome of rice. The current release contains 21 reference maps based on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) of proteins from rice tissues and subcellular compartments. These reference maps comprise 11 941 identified proteins showing tissue and subcellular localization, corresponding to 4180 separate protein entries in the database. The Rice Proteome Database contains the calculated properties of each protein such as molecular weight, isoelectric point and expression.

RiceGAAS: an automated annotation system and database for rice genome sequence. This system integrates programs for prediction and analysis of protein-coding gene structure.

The Rice Expression Profile Database (RiceXPro) is a repository of gene expression profiles derived from microarray analysis of tissues/organs encompassing the entire growth of the rice plant under natural field conditions, rice seedlings treated with various phytohormones, and specific cell types/tissues isolated by laser microdissection (LMD). This database is part of a project on rice transcriptome analysis using microarray technology aimed at characterizing the expression profile of all predicted genes in rice and providing reference information that can be used in functional genomics.

[Other plants]

AgBase provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes.

BarleyBase(BB) is an online database for plant microarrays with integrated tools for data visualization and statistical analysis.BB houses raw and normalized expression data from the two publicly available Affymetrix genome arrays,Barley1 and Arabidopsis ATH1 with plans to include the new Affymetrix 61K wheat, maize, soybean and rice arrays, as they become available.

Brassica Genome
An integrated database for Brassica genomic research

The Crop EST Database (CR-EST) is a public available online resource providing access to sequence, classification, clustering, and annotation data of crop EST projects at the IPK.

The Genome Database for Rosaceae (GDR) is a central repository of curated and integrated genetics and genomics data of Rosaceae, an economically important family which includes apple, cherry, peach, pear, raspberry, rose and strawberry. GDR contains annotated databases of all publicly available Rosaceae ESTs, the genetically anchored peach physical map, Rosaceae genetic maps and comprehensively annotated markers and traits.

Gramene(Cold Spring Harbor Laboratory)
Gramene is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species.

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.

GrainGenes is the international database for the wheat, barley, rye and oat genomes. For these species it is the primary repository for information about genetic maps, mapping probes and primers, genes, alleles and QTLs.

The Maize Genetics and Genomics Database (MaizeGDB) is a central repository for maize sequence, stock, phenotype, genotypic and karyotypic variation, and chromosomal mapping data.

Medicago truncatula
Annotating the genome of Medicago truncatula

An Orchid Genome Database

Tools and resources for plant genomics

PoMaMo--a comprehensive database for potato genome data.he database contains molecular maps of all twelve potato chromosomes with about 1000 mapped elements, sequence data, putative gene functions, results from BLAST analysis, SNP and InDel information from different diploid and tetraploid potato genotypes, publication references, links to other public databases like GenBank or SGN , etc.

Wheat transcript analysis

SoyBase, the USDA-ARS soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics and related data resources for soybean.

SoyXpress is a database designed for exploring the soybean transcriptome.

TFGD -- Tomato Functional Genomics Database. This module contains the annotation and sequence information of all probes on the tomato TOM1 cDNA array, TOM2 oligo array and Affymetrix genome array, and provides tools to query or batch retrieve the desired information.

TomatEST database
SolEST database: a "one-stop shop" approach to the study of Solanaceae transcriptomes

TropGeneDB is organized on a crop basis with currently nine public modules (banana, cocoa, coconut, coffee, cotton, oil palm, rice, rubber tree, sugarcane).


GEO Overview
Gene Expression Omnibus (GEO) Overview. Depend on DataSet / Sample / Platform.

Genomes Online Database, is a World Wide Web resource for comprehensive access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world.

Phytozome v.10
Phytozome is the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute.

Plant Repeat Databases
The TIGR plant repeat database is a repository of repetitive sequences in plants.

Plant Proteome Database
The Plant Proteome Database is a National Science Foundation-funded project to determine the biological function of each protein in plants.It includes data for two plants that are widely studied in molecular biology, Arabidopsis thaliana and maize (Zea mays).

Plant DNA C-values Database
The Plant DNA C-values Database is a comprehensive catalogue of C-value (nuclear DNA content, or in diploids, genome size) data for land plants and algae.

Plant transcription factor database, a portal for the functional and evolutionary study of plant transcription factors.

GrassPROMDB, the promoter database for the grasses, is designed to provide a collection of sequences for promoters from maize, sugarcane, sorghum and rice. In these promoters, experimentally verified cis-regulatory elements (CREs), presumably recognized by transcription factors, are indicated.

PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic, physical, and pathway data.

Rice Oligonucleotide Array Database (ROAD) is a public resource for gene expression and coexpression analysis in rice, the most important staple food over the world. Over 1,000 microarray slides were incorporated and several kinds of analysis tools are available in ROAD.

The integrated database "OryzaExpress" provides information of gene expression network and biological annotations in rice.

microRNA Database

The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download.

miRTarBase has accumulated more than fifty thousand miRNA-target interactions (MTIs), which are collected by manually surveying pertinent literature after data mining of the text systematically to filter research articles related to functional studies of miRNAs.

PMRD try to integrate the available large information of plant microRNAs data, consisting of microRNA sequence and their target genes, secondary dimension structure, expression profiling, genome browser, etc.

PMTED is a Plant MicroRNA Target Expression Database to study the microRNA (miRNA) functions by inferring their target gene expression profiles among the large amount of existing microarray data.

Plant snoRNA Database
The plant snoRNA Database and web-site brings together information from three independent computer-assisted searches of the Arabidopsis genome for box C/D snoRNA genes and from studies of ncRNAs. To date, the Arabidopsis box C/D snoRNAs have been used to identify approximately 250 genes from different non-Arabidopsis plant species and these sequences are included as alignments in the Database.

Plant microRNA Knowledge Base (PmiRKB)! MicroRNAs (miRNAs), one kind of well-defined plant small RNAs, exert essential roles in numerous biological pathways through repressive effects on their targets. PmiRKB includes the miRNAs of two model plants, Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). Four major functional modules, "SNPs", "Pri-miRNAs", "MiR-Tar", and "Self-reg", are provided.

A plant small RNA target analysis server.