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Plant gene expression databases | Gene expression data analysis

The accessibility of gene expression data in plant is a primary challenge to help researchers answer complex biological questions from related large-scale studies. The exploration of plant genome permits to develop new statistical methods or…
Ensembl
Dataset

Ensembl

A genomic interpretation system providing the most up-to-date annotations,…

A genomic interpretation system providing the most up-to-date annotations, querying tools and access methods for chordates and key model organisms. The REST server, which allows programs written in…

Genevestigator
Web

Genevestigator

An innovative online platform to help you interpret your results, prioritize…

An innovative online platform to help you interpret your results, prioritize targets and biomarkers, identify correlated genes, discover novel disease-specific genes, or simply to explore the…

RefSeq
Dataset

RefSeq Reference Sequence

Maintains and curates a publicly available database of annotated genomic,…

Maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records. The RefSeq project leverages the data submitted to the International Nucleotide…

Escherichia…
Dataset

Escherichia coli Multi-omics Database

Provides a database of E. coli. Escherichia coli Multi-omics Database offers a…

Provides a database of E. coli. Escherichia coli Multi-omics Database offers a comprehensive knowledge of the quantitative information regarding the inner molecular components of cells.

Heliagene
Dataset

Heliagene

Provides visualization, querying tools for data mining and network exploration…

Provides visualization, querying tools for data mining and network exploration around Helianthus annuus. Heliagene offers a reference genome and companion resources to accelerate breeding programs.…

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Expression…
Dataset

Expression Atlas

Provides information about gene and protein expression in animal and plant…

Provides information about gene and protein expression in animal and plant samples of different cell types, organism parts, developmental stages, diseases and other conditions. Expression Atlas…

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AtGenExpress…
Dataset

AtGenExpress JPN

Allows to work about the transcriptome of the multicellular model organism…

Allows to work about the transcriptome of the multicellular model organism Arabidopsis thaliana. The AtGenExpress JPN project includes several resources which treat gene expression patterns. These…

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CYTOMER
Dataset

CYTOMER

Provides information about organs and cell types of Arabidopsis. CYTOMER…

Provides information about organs and cell types of Arabidopsis. CYTOMER comprises more than 5236 entries whose a part is incorporated into a hierarchical system. It offers the complete vocabulary of…

diArk
Dataset

diArk

Aims to provide access to all available assembled genomes and transcriptomes.…

Aims to provide access to all available assembled genomes and transcriptomes. In September 2014, diArk contains about 2600 eukaryotes with 6000 genome and transcriptome assemblies, of which 22% are…

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AtRTD
Dataset

AtRTD Arabidopsis Thaliana Reference Transcript Dataset

Provides a comprehensive high-quality reference transcript dataset about…

Provides a comprehensive high-quality reference transcript dataset about Arabidopsis transcripts. AtRTD contains more than 82 190 unique transcript models. It was generated by integration of…

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RiceFOX
Dataset

RiceFOX Rice full-length cDNA over-expressed Arabidopsis mutant database

Contains a lot of information on mutant lines. RiceFOX includes different…

Contains a lot of information on mutant lines. RiceFOX includes different search functions and allows to refer to the introduced rice fl-cDNA in addition to the morphological features of a broad…

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Plant MPSS…
Dataset

Plant MPSS databases

Measure the expression level of most genes under defined conditions and provide…

Measure the expression level of most genes under defined conditions and provide information about potentially novel transcripts (antisense transcripts, alternative splice isoforms and regulatory…

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PLEXdb
Dataset

PLEXdb PLant EXpression database

A unified gene expression resource for plants and plant pathogens. PLEXdb is a…

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…

SoyBase
Dataset

SoyBase

A comprehensive repository for professionally curated genetics, genomics and…

A comprehensive repository for professionally curated genetics, genomics and related data resources for soybean.

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CATdb
Dataset

CATdb

Provides public access to a large collection of transcriptome data for…

Provides public access to a large collection of transcriptome data for Arabidopsis thaliana produced by a single Complete Arabidopsis Transcriptome Micro Array (CATMA) platform.

TOMATOMICS
Dataset

TOMATOMICS

Provides an access to the information on the cDNA clone resources, full-length…

Provides an access to the information on the cDNA clone resources, full-length mRNA sequences, gene structures, expression profiles and functional annotations of genes of Solanum lycopersicum…

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RiceXPro
Dataset

RiceXPro Rice eXpression Profile database

A repository of gene expression profiles derived from microarray analysis of…

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…

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PlaMoM
Dataset

PlaMoM Plant Mobile Macromolecules

Provides convenient and interactive search tools allowing users to retrieve, to…

Provides convenient and interactive search tools allowing users to retrieve, to analyze and also to predict mobile RNAs/proteins. Each entry in the PlaMoM database contains detailed information such…

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AspWood
Dataset

AspWood Aspen Wood

Enables genomics analysis of cambial growth and wood formation. AspWood…

Enables genomics analysis of cambial growth and wood formation. AspWood contains high-spatial-resolution gene expression profiles across developing phloem and wood-forming tissues from four natural…

LSD
Dataset

LSD Leaf Senescence Database

A database of leaf senescence to collect SAGs, mutants, phenotypes and…

A database of leaf senescence to collect SAGs, mutants, phenotypes and literature references.

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TFGD
Web

TFGD Tomato Functional Genomics Database

Serves as a central repository for raw gene expression data derived from the…

Serves as a central repository for raw gene expression data derived from the public tomato cDNA microarray. The suite of tools and interfaces in TFGD allow intelligent data mining of recently…

OTL
Dataset

OTL Oryza Tag Line

Facilitates forward genetic search for specific phenotypes, putatively…

Facilitates forward genetic search for specific phenotypes, putatively resulting from gene disruption, and/or for GUSA or GFP reporter gene expression patterns, reflecting ET-mediated endogenous gene…

PlanMine
Dataset

PlanMine

Aims to provide an easily accessible and minable repository of general…

Aims to provide an easily accessible and minable repository of general planarian sequence data. Our dual mission objective is to first, provide opportunities for comparing and mining planarian…

IC4R
Dataset

IC4R Information Commons for Rice

A rice knowledgebase featuring adoption of an extensible and sustainable…

A rice knowledgebase featuring adoption of an extensible and sustainable architecture that integrates multiple omics data through community-contributed modules. Each module is developed and…

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DsTRD
Dataset

DsTRD Danshen Transcriptional Resource Database

A comprehensive transcript resource for Salvia miltiorrhiza. DsTRD contains…

A comprehensive transcript resource for Salvia miltiorrhiza. DsTRD contains 76531 transcribed sequences assembled from the RNA-seq data. DsTRD provides information regarding the sequences and…

FLAGdb++
Dataset

FLAGdb++

Helps biologists to find the flanking insertion sites (FSTs) that interrupt the…

Helps biologists to find the flanking insertion sites (FSTs) that interrupt the genes in which they are interested. The FLAGdb information system was developed with the aim of using whole plant…

Cannabis sativa
Dataset

Cannabis sativa

A database which offers gene annotation of Cannabis sativa, also know under the…

A database which offers gene annotation of Cannabis sativa, also know under the name of Marijuana. The draft genome and transcriptome of C. sativa has been presented and compared with the genomes and…

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RSOY
Dataset

RSOY RIKEN Soybean Full-Length cDNA Database

Represents a resource about large-scale collection of full-length cDNA clones…

Represents a resource about large-scale collection of full-length cDNA clones derived from a Japanese soybean cultivar. The RSOY web interface allows to retrieve sequence information of soybean…

GPI
Dataset

GPI GenoPlante-Info

Aims at developing genome analysis programs for crop species (corn, wheat,…

Aims at developing genome analysis programs for crop species (corn, wheat, rapeseed, sunflower and pea) and model plants (Arabidopsis and rice).

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PlantExpress
Dataset

PlantExpress

Represents a platform for microarray database gene expression network (GEN)…

Represents a platform for microarray database gene expression network (GEN) analysis both in a single species and cross-species. PlantExpress provides informations on global GENs constructed using…

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DRASTIC
Dataset

DRASTIC Database Resource for the Analysis of Signal Transduction in Cells

A manually derived database of plant expressed sequence tags and genes up- or…

A manually derived database of plant expressed sequence tags and genes up- or down-regulated in response to various pathogens, chemical treatments, and abiotic stress such as drought, salt and cold.

PRIMeLink
Dataset

PRIMeLink

Allows to search and analyze ranging from metabolomics to transcriptomics.…

Allows to search and analyze ranging from metabolomics to transcriptomics. Provides users an access to data resources of PRIMe. The PRIMeLink web interface integrates three databases: the MS2T…

Coffee Genome…
Dataset

Coffee Genome Hub

An integrative genome information system that allows centralized access to…

An integrative genome information system that allows centralized access to genomics and genetics data and analysis tools to facilitate translational and applied research in coffee. The hub relies on…

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Allium TDB
Dataset

Allium TDB Allium Transcript DataBase

Provides access to RNA-Seq data set including contigs length, nucleotide…

Provides access to RNA-Seq data set including contigs length, nucleotide sequences, amino acid sequences, annotation, and expression values. Allium TDB provides an overview of transcriptome dynamics…

MODEM
Dataset

MODEM Multi-Omics Data Envelopment and Mining in maize

A comprehensive database to collect maize multidimensional omics data including…

A comprehensive database to collect maize multidimensional omics data including genomic variation, transcriptomic quantification, metabolic identification and phenotypic traits from cellular to…

CAP
Dataset

CAP Citrus sinensis annotation project

Collects information about genomic and transcriptomic data. CAP aims to…

Collects information about genomic and transcriptomic data. CAP aims to simplify understanding about the genome structure and function of sweet orange by using annotation. The database contains…

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CATMA
Dataset

CATMA Complete Arabidopsis Transcriptome MicroArray

The aim of the project was the design and production of high quality…

The aim of the project was the design and production of high quality Gene-specific Sequence Tags (GSTs) covering most Arabidopsis genes.

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SustainPine DB
Dataset

SustainPine DB

Provides access to a sequence collection for Pinus pinaster. SustainPine DB was…

Provides access to a sequence collection for Pinus pinaster. SustainPine DB was designed to gather the most reliable pre-processed, assembled, and annotated P. pinaster sequences using different…

MAGIC
Dataset

MAGIC

A maize expression compendium, making use of an integration methodology and a…

A maize expression compendium, making use of an integration methodology and a consistent probe to gene mapping based on the 5b.60 sequence release of Zea mays.

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VESPUCCI
Dataset

VESPUCCI Vitis Expression Studies Platform Using COLOMBOS Compendia Instances

A gene expression compendium for grapevine that integrates publicly available…

A gene expression compendium for grapevine that integrates publicly available transcriptomics data from several microarray and RNA-Seq platforms into one coherent database, queryable via a web or…

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TENOR
Dataset

TENOR Transcriptome ENcyclopedia Of Rice

A database that encompasses large-scale mRNA sequencing (mRNA-seq) data…

A database that encompasses large-scale mRNA sequencing (mRNA-seq) data obtained from rice under a wide variety of conditions. We used mRNA-seq and performed a time-course transcriptome analysis of…

SIFGD
Dataset

SIFGD Setaria italica Functional Genomics Database

Provides search and analysis tools for bioinformatics analyses of gene function…

Provides search and analysis tools for bioinformatics analyses of gene function or regulatory modules. SIFGD was designed to integrate existing data from publications, to improve the proportion of…

UniVIO
Dataset

UniVIO Uniformed Viewer for Integrative Omics

Provides an integrated data set of hormonome and transcriptome analyses in 14…

Provides an integrated data set of hormonome and transcriptome analyses in 14 organs of the rice plant at the reproductive stage and in gibberellin-related mutants. UniVIO allows users to search…

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RED
Dataset

RED Rice Expression Database

Integrates rice gene expression profiles under various tissues and experimental…

Integrates rice gene expression profiles under various tissues and experimental conditions. RED is based on more than 284 high-quality RNA-Seq experiments. It provides large-scale whole-genome…

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OmicsDI
Dataset

OmicsDI Omics Discovery Index

Permits to access, discover and disseminate omics data sets. OmicsDI is an…

Permits to access, discover and disseminate omics data sets. OmicsDI is an open-source platform that can integrate proteomics, genomics, metabolomics and transcriptomics data sets. This platform…

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The Tomato…
Desktop

The Tomato Expression Atlas

Facilitates effective data analysis and allowing the simultaneous visualization…

Facilitates effective data analysis and allowing the simultaneous visualization of groups of genes at a cell/tissue level of resolution within an organ, enhancing hypothesis development and testing…

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RBFLDB
Dataset

RBFLDB RIKEN Brachypodium FLcDNA database

Allows users to specify queries with keywords to retrieve relevant gene…

Allows users to specify queries with keywords to retrieve relevant gene information. RBFLDB provides a web-based search interface enabling keyword and sequence similarity searches. It is possible to…

JCDB
Dataset

JCDB Jatropha curcas DataBase

A database which offers gene annotation of Jatropha curcas, also known as…

A database which offers gene annotation of Jatropha curcas, also known as Barbados nut, purging nut or physic nut. Jatropha curcas is currently attracting much attention as a plant with high…

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Lygodium…
Dataset

Lygodium japonicum Transcriptome Database

Provides important opportunities to accelerate molecular research in ferns. In…

Provides important opportunities to accelerate molecular research in ferns. In this study, to identify a comprehensive catalog of transcripts and characterize their expression traits in the fern…

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MOROKOSHI
Dataset

MOROKOSHI

In this database, users can access predominantly two types of transcriptome…

In this database, users can access predominantly two types of transcriptome data; correct TSSs and structural gene annotation based on approximately 40,000 FL-cDNAs, and expression profiles from…

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Cassava Online…
Dataset

Cassava Online Archive

Provides expressed sequence tags (ESTs) currently available from NCBI…

Provides expressed sequence tags (ESTs) currently available from NCBI (Genbank/EMBL/DDBJ) and cassava mRNA sequences and their annotations. Cassava Online Archive simplifies the cassava genomics…

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EXPath
Dataset

EXPath

A database resource that collects and utilizes gene expression profiles derived…

A database resource that collects and utilizes gene expression profiles derived from microarray platforms under various conditions to infer metabolic pathways for plants. EXPath was developed to not…

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MSGI
Dataset

MSGI Medicago sativa Gene Index

An online resource for analyses of gene expression in M. sativa for six…

An online resource for analyses of gene expression in M. sativa for six distinct tissue types derived from two biologically distinct subspecies (M. sativa ssp. falcata and M. sativa ssp. sativa).…

STPD
Dataset

STPD Salinity Tolerant Poplar Database

An integrative database for salt-tolerant poplar genome biology. Currently the…

An integrative database for salt-tolerant poplar genome biology. Currently the STPD contains Populus euphratica genome and its related genetic resources. P. euphratica, with a preference of the salty…

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MtGEA
Dataset

MtGEA The Medicago truncatula Gene Expression Atlas

Analyzes the Medicago transcriptome. MtGEA web server hosts gene expression…

Analyzes the Medicago transcriptome. MtGEA web server hosts gene expression data from 156 Affymetrix GeneChip Medicago genome arrays in 64 different experiments, covering a broad range of…

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CucurbiGene
Dataset

CucurbiGene

Develops genomic tools for Squash (Cucurbita spp.) breeding: transcriptome,…

Develops genomic tools for Squash (Cucurbita spp.) breeding: transcriptome, genetic map, SNP collections and high throughput genotyping platforms applied to the competitive development of new…

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MeloGene
Dataset

MeloGene

Develops genomic tools for Melon (Cucumis melo) breeding: transcriptome, SSR,…

Develops genomic tools for Melon (Cucumis melo) breeding: transcriptome, SSR, SNP collections and high throughput genotyping platforms. Melogene includes a new version of the melon transcriptome with…

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PvGEA
Dataset

PvGEA Phaseolus vulgaris Gene Expression Atlas

These data provide the basis for a gene expression atlas, which will facilitate…

These data provide the basis for a gene expression atlas, which will facilitate functional genomic studies in common bean. Analysis of this dataset has identified genes important in regulating seed…

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CTDB
Dataset

CTDB Chickpea Transcriptome Database

It has been developed with the view to provide most comprehensive information…

It has been developed with the view to provide most comprehensive information about the chickpea transcriptome, the most relevant part of the genome. The database contains various information and…

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SpinachBase
Dataset

SpinachBase

A genomic database for spinach (Spinacia oleracea L.) which is an annual or…

A genomic database for spinach (Spinacia oleracea L.) which is an annual or biennial plant which belongs to the family Amaranthaceae. Spinachbase is designed to allow users to easily retrieve and…

KIR
Dataset

KIR Kiwifruit Information Resource

Hosts a wide range of kiwifruit genomics and genetics datasets based on the…

Hosts a wide range of kiwifruit genomics and genetics datasets based on the latest and most accurate genome annotation. KIR aims to be a comprehensive online platform for users to search, visualize,…

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ECLAT
Web

ECLAT

This is a server for the classification of ESTs from mixed EST pools (from…

This is a server for the classification of ESTs from mixed EST pools (from fungus infected plants). ECLAT is based on the machine learning algorithm Support Vector Machines and uses codon frequencies…

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LjGEA
Dataset

LjGEA Lotus japonicus Gene Expression Atlas

Provides a global view of gene expression in all organ systems of Lotus…

Provides a global view of gene expression in all organ systems of Lotus japonicus, including roots, nodules, stems, petioles, leaves, flowers, pods and seeds. Time-series data covering multiple…

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Silene…
Dataset

Silene vulgaris Transcriptome

Provides access to data generated from high throughput sequencing of expressed…

Provides access to data generated from high throughput sequencing of expressed genes in the flowering plant Silene vulgaris, a widely used model in studies of ecology and evolution. In Silene…

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dbWFA
Dataset

dbWFA Database of Wheat Functional Annotation

Integrates numerous data sources. dbWFA is an open-access database and is a…

Integrates numerous data sources. dbWFA is an open-access database and is a source of heterogeneous data for functional annotation of Triticum aestivum transcripts and UniGenes. It also provides the…

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OryzaExpress
Dataset

OryzaExpress

Provides information of gene expression network and biological annotations in…

Provides information of gene expression network and biological annotations in rice. OryzaExpress is a comprehensive rice database that exploits powerful omics approaches from all perspectives in…

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OsMes
Dataset

OsMes Oryza sativa Mitochondria expression server

Provides information of transcribed regions and gene annotations in the rice…

Provides information of transcribed regions and gene annotations in the rice mitochondrial genome. In OsMES, information on the transcribed regions and the gene annotations are presented using the…

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Optimas-DW
Dataset

Optimas-DW OPTIMAS Data Warehouse

A comprehensive data collection for maize. Optimas-DW integrates data from…

A comprehensive data collection for maize. Optimas-DW integrates data from different data domains such as transcriptomics, metabolomics, ionomics, proteomics and phenomics. A web interface allows…

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SoySeq
Dataset

SoySeq

Provides a record of high-resolution gene expression in a set of fourteen…

Provides a record of high-resolution gene expression in a set of fourteen diverse tissues. Hierarchical clustering of transcriptional profiles for these tissues suggests three clades with similar…

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PaGenBase
Dataset

PaGenBase Pattern Gene Database

Provides information of pattern genes (specific genes, selective genes,…

Provides information of pattern genes (specific genes, selective genes, housekeeping genes and repressed genes) of 11 model organisms identified from serial gene expression profiles of multiple…

MorusDB
Dataset

MorusDB Morus genome database

Provides important genomic resources for scientists working with mulberry and…

Provides important genomic resources for scientists working with mulberry and other Moraceae species, which include many important fruit crops.

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GnpIS
Dataset

GnpIS Genoplante Information System

A multispecies integrative information system dedicated to plant and fungi…

A multispecies integrative information system dedicated to plant and fungi pests. GnpIS bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps,…

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EimeriaTDB
Dataset

EimeriaTDB Eimeria Transcript Database

An integrated resource of cDNA sequencing and annotation data of Eimeria spp.…

An integrated resource of cDNA sequencing and annotation data of Eimeria spp. of domestic fowl. In addition to sequencing data, Eimeria TDB provides an organized catalogue of functionally annotated…

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Orchidstra
Dataset

Orchidstra

Collects, annotates and shares genomic information for orchid functional…

Collects, annotates and shares genomic information for orchid functional genomics studies. Orchidstra is an integrated orchid functional genomics database that include transcriptome information for…

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RecountDB
Dataset

RecountDB

Provides a secondary database derived from primary data in NCBI's short…

Provides a secondary database derived from primary data in NCBI's short read archive. RecountDB holds sequence counts from RNA-seq and 5′ capped transcription start site experiments, corrected…

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Shanghai…
Dataset

Shanghai RAPESEED Database

Provides the solid platform for functional genomics studies of oilseed crops…

Provides the solid platform for functional genomics studies of oilseed crops with the emphasis on seed development and fatty acid metabolism. The RAPESEED includes the resource of 8462 unique ESTs,…

BFGR
Dataset

BFGR

Provides uniform annotation of gene and transcript assembly sequences. BFGR…

Provides uniform annotation of gene and transcript assembly sequences. BFGR contains sequence data from 54 species and assists users to analyze, view and obtain annotation at the transcript, protein,…

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Oak Contig…
Dataset

Oak Contig Browser

Aims to produce and maintain an automatic annotation of Oak EST libraries. The…

Aims to produce and maintain an automatic annotation of Oak EST libraries. The Oak Contig Browser is an INRA Project. This database will support ecosystem genomics studies, where geneticists,…

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SoyXpress
Dataset

SoyXpress

A database (MySQL) designed for exploring the soybean transcriptome. SoyXpress…

A database (MySQL) designed for exploring the soybean transcriptome. SoyXpress is designed for the purpose of exploring potential transcriptome differences in different plant genotypes, including…

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