Table 1 List of bioinformatics databases and tools applied in plant biotechnology

Genome Database

ArrayExpress

www.ebi.ac.uk/arrayexpress

Archive for functional genomics data from microarray and sequencing platforms

BarleyGenes

https://ics.hutton.ac.uk/barleyGenes/

Gene and RNA-seq database for Barley

Chrysanthemum Transcriptome Database

http://www.icugi.org/chrysanthemum

Database of chrysanthemum’s gene and transcripts

Cottongen

https://www.cottongen.org/

Genomics, genetics, and breeding database for cotton

Expression Atlas EMBL-EBI

www.ebi.ac.uk/gxa/home

Open resource platform for gene and protein expression information

Ensembl Plants

https://plants.ensembl.org/index.html

Genomic database (genome sequence, gene models, functional annotation) of more than 33 plant species

Gene Expression Omnibus

www.ncbi.nlm.nih.gov/projects/geo

Functional genomics data repository

MaizeDIG

https://maizedig.maizegdb.org/

Genotypic-phenotypic database for maize

MaizeGDB

https://www.maizegdb.org/

Genetic and genomics database for maize

MaizeMine

https://maizemine.rnet.missouri.edu/maizemine/begin.domine/begin.do

Archive to access literature, genomic, interaction and proteomic data for maize

VvGDB

www.plantgdb.org/VvGDB/

Database for grape genome

Phytozome

https://phytozome-next.jgi.doe.gov/

Comparative genomics portal of plants

Plant Promoter Database

http://linux1.softberry.com/berry.phtml?topic=plantprom&group=data&subgroup=plantprom

Database of plant promoter sequences and experimentally determined transcription start site of various plant species

PLEXdb

http://www.plantgdb.org/prj/PLEXdb/

Plant expression database with gene expression profile data sets, structural genomics, and phenotypic data

Pomamo

https://www.gabipd.org/projects/Pomamo/

Archive of potato sequences, literature, maps, and tools

PRGdb

http://prgdb.org/prgdb/

Archive of pathogen receptor genes of various plant species

Rice Expression Database

http://expression.ic4r.org/

Repository of gene expression profiles of rice from RNA-seq data on tissues spanning an entire range of rice growth

Rice expression profile Database

http://ricexpro.dna.affrc.go.jp/

Repository of gene expression profiles of rice from microarray analysis

SolGenomics Network

https://solgenomics.net/gem/experimental_design.pl?id=2

Database and tool of genomics and genetics approach for tomato and some other plant species such as eggplant

TAIR

https://www.arabidopsis.org/

Database of genetic and molecular biology data for Arabidopsis thaliana

The Rice Annotation Project Database

https://rapdb.dna.affrc.go.jp/

Archive of rice genome sequence, structure, and function

Tomato Functional Genomics Database

http://ted.bti.cornell.edu

Archive of tomato microarray data, metabolite and RNA-seq

Metabolomic Database

Metabolights

www.ebi.ac.uk/metabolights/

Metabolomics database (cross-species, metabolite structures, biological role)

Pathway Database

Reactome

www.reactome.org

Pathway interaction repository

RiceCyc

http://pathway.gramene.org/gramene/ricecyc.shtml

Database of known and predicted biochemical pathways from rice

PlantCyc

http://plantcyc.org

Metabolic pathway reference database from over 350 plant species

RNA Analysis Tool

qTeller

https://qteller.maizegdb.org/

Comparative RNA-seq expression tool

Chemical Compound Database

ChEBI

www.ebi.ac.uk/chebi/

Archive of molecular entities that focuses on small chemical compounds

PubChem

http://pubchem.ncbi.nlm.nih.gov/

Archive of chemical information of various chemical compounds

Mass Spectrum Database

ReSpect for Phytochemicals

http://spectra.psc.riken.jp/menta.cgi/index

Database for phytochemicals MS spectra data and literature

Metlin

http://metlin.scripps.edu/

Comprehensive MS/MS database

Resistance Analysis

Disease Resistance Analysis and Gene Orthology (DRAGO2)

http://prgdb.org/prgdb/drago2

Annotate resistance genes

Networking and Interaction Analysis

PathoPlant

www.pathoplant.de/

Database of plant-pathogen interaction and components related to plant pathogenesis

AraNet

www.inetbio.org/aranet/

Probabilistic functional gene network tool for Arabidopsis thaliana

PLANET

http://aranet.mpimp-golm.mpg.de/

Platform for visualization and analysis of co-function networks of photosynthetic organisms

Genomics Tool

The Bio-Analytic Resource

http://bar.utoronto.ca/

Plant bioinformatics tools resource platform (gene expression, mapping, molecular markers, and genomics)