Gene expression databases | Gene expression data analysis
Determining the genes expressed for every tissue and cell type in the body has important consequences for basic cell biology, generating hypotheses for gene function and studying transcriptional changes in disease. Gene expression signatures have been used to make clinical…
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Genevestigator Genevestigator

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…

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A A A Ouija Ouija

Ouija

A statistical framework for learning pseudotimes from single-cell RNA-seq data.…

A statistical framework for learning pseudotimes from single-cell RNA-seq data. Ouija using only small panels of marker genes and prior knowledge of gene behaviour. The user can place priors on…

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A A A High-Dimensional… High-Dimensional Transposable Data

HDTD High-Dimensional Transposable Data

In multiple-tissue gene expression studies, the rows correspond to genes and…

In multiple-tissue gene expression studies, the rows correspond to genes and the columns to tissues, and genes and tissues might to be correlated with each other. The unique feature of HDTD is the…

A A A Danshen… Danshen Transcriptional Resource Database

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…

A A A Gene eXpression… Gene eXpression Database

GXD Gene eXpression Database

Offers an extensive and well-curated community resource of mouse developmental…

Offers an extensive and well-curated community resource of mouse developmental expression information. GXD collects and integrates data from RNA in situ hybridization, immunohistochemistry, RT-PCR,…

A A A CucurbiGene CucurbiGene

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…

A A A SoleaDB SoleaDB

SoleaDB

A transcriptome database for Senegalese sole (Solea senegalensis) and common…

A transcriptome database for Senegalese sole (Solea senegalensis) and common sole (Solea solea). This database includes the assemblies and annotation of new genomic resources generated from different…

A A A OryzaExpress OryzaExpress

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…

A A A Marine Microbial… Marine Microbial Eukaryotic Transcriptome…

MMETSP Marine Microbial Eukaryotic Transcriptome Sequencing Project

Provides a significant foothold for integrating microbial eukaryotes into…

Provides a significant foothold for integrating microbial eukaryotes into marine ecology by creating over 650 assembled, functionally annotated, and publicly available transcriptomes. MMETSP is…

A A A Glia Open Access… Glia Open Access Database

GOAD Glia Open Access Database

A comprehensive web-based tool to access and analyze glia transcriptome data.…

A comprehensive web-based tool to access and analyze glia transcriptome data. GOAD has several features: (i) Differential gene Expression (DE) Analysis, (ii) Quantitative gene Expression (QE)…

A A A NeuroExpresso NeuroExpresso

NeuroExpresso

A database of publicly available mouse brain cell type-specific gene expression…

A database of publicly available mouse brain cell type-specific gene expression datasets. NeuroExpresso is a database of brain cell type specific gene expression profiles. This tool can demonstrate…

A A A GENE Expression and… GENE Expression and Enrichment Vector Analyzer

GEN3VA GENE Expression and Enrichment Vector Analyzer

Enables the integrative analysis of aggregated collections of tagged gene…

Enables the integrative analysis of aggregated collections of tagged gene expression signatures identified and extracted from GEO. GEN3VA can be used to identify, aggregate, and analyze themed…

A A A The Medicago… The Medicago truncatula Gene Expression Atlas

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…

A A A Kaleidoscope of gEne… Kaleidoscope of gEne Responses to Inflammation…

KERIS Kaleidoscope of gEne Responses to Inflammation among Species

A comprehensive resource for the genome responses between human inflammatory…

A comprehensive resource for the genome responses between human inflammatory diseases and murine models. KERIS includes comparisons of the genomic response of six human inflammatory diseases (burns,…

A A A Lotus japonicus Gene… Lotus japonicus Gene Expression Atlas

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…

A A A Vitis Expression… Vitis Expression Studies Platform Using COLOMBOS…

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…

A A A The Lair The Lair

The Lair

Provides interactive access to the (re)analysis of publicly available RNA-Seq…

Provides interactive access to the (re)analysis of publicly available RNA-Seq data presented in published papers. The Lair is powered by kallisto, sleuth, the Snakemake workflow management system and…

A A A OPTIMAS Data Warehouse OPTIMAS Data Warehouse

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…

IntegromeDB IntegromeDB

IntegromeDB

A biological web search engine based on the Semantic Web technologies. The…

A biological web search engine based on the Semantic Web technologies. The IntegromeDB search engine allows scanning data on gene regulation, gene expression, protein-protein interactions, pathways,…

A A A Genoplante… Genoplante Information System

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,…

A A A Tree shrew database Tree shrew database

TreeshrewDB Tree shrew database

A user-friendly web-based platform that integrates the currently available data…

A user-friendly web-based platform that integrates the currently available data from the tree shrew (Tupaia belangeri) genome, including an updated gene set, with a systematic functional annotation…

A A A Retina Retina

Retina

An accurate and high-resolution atlas of gene expression and gene co-regulation…

An accurate and high-resolution atlas of gene expression and gene co-regulation in human retina. We collected 50 high-quality post-mortem human retinas from donors and performed high-coverage…

Theba Pisana Gene… Theba Pisana Gene Database

ThebaBD Theba Pisana Gene Database

An online database committed to establishing a comprehensive gene resource for…

An online database committed to establishing a comprehensive gene resource for the land snail Theba pisana. ThebaBD includes sequence data, gene expression profiles, protein domain and biological…

A A A SpinachBase SpinachBase

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…

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A A A Analysis using… Analysis using Denoising Autoencoders for Gene…

ADAGE Analysis using Denoising Autoencoders for Gene Expression

An approach based on analysis using denoising autoencoders of gene expression,…

An approach based on analysis using denoising autoencoders of gene expression, which is capable of integrating diverse gene expression data to aid in the interpretation of existing and new…

A A A Transcriptome… Transcriptome ENcyclopedia Of Rice

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…

RSIADB RSIADB

RSIADB

A collective resource for rice sheath blight pathogen, Rhizoctonia solani AG1…

A collective resource for rice sheath blight pathogen, Rhizoctonia solani AG1 IA genome and transcritome. RSIADB enables users to search, browse, and download gene sequences for R. solani AG1 IA, and…

A A A Blood Brain Barrier… Blood Brain Barrier omics

BBBomics Blood Brain Barrier omics

A comprehensive portal for blood-brain barrier transcriptomics data, obtained…

A comprehensive portal for blood-brain barrier transcriptomics data, obtained by sequencing mRNA (mRNA-seq) and microRNA (miRNA-seq) of polarized hCMEC/D3 cell monolayers. This data encompasses…

A A A Pattern Gene Database Pattern Gene Database

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…

A A A Tissue-Specific Genes… Tissue-Specific Genes Database

TiSGeD Tissue-Specific Genes Database

Provides comprehensive information of tissue-specific genes derived from…

Provides comprehensive information of tissue-specific genes derived from biomedical literatures and data mining of more than 123,125 gene expression profiles over 107 human tissues, 67 mouse tissues…

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A A A GEMINI GEMINI

GEMINI

A fast search engine that uses a query genomic profile to search for similar…

A fast search engine that uses a query genomic profile to search for similar profiles in a very large genomic database. GEMINI enables users to identify similar profiles independent of sample label,…

A A A Mammalian… Mammalian Transcriptomic Database

MTD Mammalian Transcriptomic Database

A mammalian transcriptomic database. The MTD contains data from humans, mice,…

A mammalian transcriptomic database. The MTD contains data from humans, mice, rats and pigs. Regarding the core features, the MTD browses genes based on their neighboring genomic coordinates or joint…

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A A A D-GEX D-GEX

D-GEX

A deep learning method to infer the expression of target genes from the…

A deep learning method to infer the expression of target genes from the expression of landmark genes. We used the microarray-based GEO dataset, consisting of 111K expression profiles, to train our…

A A A Cancer RNA-Seq Nexus Cancer RNA-Seq Nexus

CRN Cancer RNA-Seq Nexus

Provides all of the following features: (i) large-scale and comprehensive data…

Provides all of the following features: (i) large-scale and comprehensive data archives and analyses, including coding-transcript profiling, long non-coding RNA (lncRNA) profiling and coexpression…

A A A RNA-Seq Atlas RNA-Seq Atlas

RNA-Seq Atlas

A web-based repository of RNA-Seq gene expression profiles and query tools. The…

A web-based repository of RNA-Seq gene expression profiles and query tools. The website offers open and easy access to RNA-Seq gene expression profiles and tools to both compare tissues and find…

A A A hematopoietic Systems… hematopoietic Systems Biology Repository

SBR-Blood hematopoietic Systems Biology Repository

Enables the user to conduct cell type correlations with previously published…

Enables the user to conduct cell type correlations with previously published data sets and data sets currently under investigation. By reproducing concepts manually validated in the community, it has…

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A A A Metabolic gEne RApid… Metabolic gEne RApid Visualizer

MERAV Metabolic gEne RApid Visualizer

A web-based tool that can query a database comprising ∼4300 microarrays,…

A web-based tool that can query a database comprising ∼4300 microarrays, representing human gene expression in normal tissues, cancer cell lines and primary tumors. MERAV has been designed as a…

Information Commons… Information Commons for Rice

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…

A A A database of autosomal… database of autosomal MonoAllelic Expression

dbMAE database of autosomal MonoAllelic Expression

Incorporates data from multiple recent reports of genome-wide analyses. These…

Incorporates data from multiple recent reports of genome-wide analyses. These include transcriptome-wide analyses of allelic imbalance in clonal cell populations based on sequence polymorphisms, as…

A A A Medaka Expression… Medaka Expression Pattern Database

MEPD Medaka Expression Pattern Database

A repository of medaka expression data for the scientific community. In this…

A repository of medaka expression data for the scientific community. In this update we present two main improvements. First, we have changed the previous clone-centric view for in situ data to a…

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A A A Embeddr Embeddr

Embeddr

Laplacian eigenmaps and principal curves for pseudotemporal ordering and…

Laplacian eigenmaps and principal curves for pseudotemporal ordering and clustering of single-cell RNA-seq data. Embeddr creates a reduced dimensional representation of the gene space using a…

A A A Lygodium japonicum… Lygodium japonicum Transcriptome Database

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…

A A A MeloGen MeloGen

MeloGen

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…

A A A MOROKOSHI MOROKOSHI

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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A A A LINCS Canvas Browser LINCS Canvas Browser

LCB LINCS Canvas Browser

An interactive HTML5 web-based software application that facilitates querying,…

An interactive HTML5 web-based software application that facilitates querying, browsing and interrogating many of the currently available LINCS L1000 data. LCB implements two compacted layered…

A A A Shared Harvard Inner… Shared Harvard Inner Ear Laboratory Database

SHIELD Shared Harvard Inner Ear Laboratory Database

A resource for dissemination and comparison of inner-ear gene expression…

A resource for dissemination and comparison of inner-ear gene expression datasets, initially developed by laboratories associated with Harvard Medical School and now including Creighton University…

A A A EXPath EXPath

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…

dbEMT dbEMT

dbEMT

A literature-based gene resource for exploring epithelial-mesenchymal…

A literature-based gene resource for exploring epithelial-mesenchymal transition (EMT)-related human genes. dbEMT includes literature data, clinical relevant variants, gene expression profiles and…

A A A Medicago sativa Gene… Medicago sativa Gene Index

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).…

Embryonic Stem Cell… Embryonic Stem Cell Atlas from Pluripotency…

ESCAPE Embryonic Stem Cell Atlas from Pluripotency Evidence

A mouse and human embryonic stem cells (m/hESC)-centered database integrating…

A mouse and human embryonic stem cells (m/hESC)-centered database integrating data from many recent diverse high-throughput studies including chromatin immunoprecipitation followed by deep…

A A A Drug Signatures… Drug Signatures Database

DSigDB Drug Signatures Database

A collection of drug and small molecule related gene sets based on quantitative…

A collection of drug and small molecule related gene sets based on quantitative inhibition and/or drug-induced gene expression changes data. DSigDB allows users to search, view, and download…

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A A A Transcriptomine Transcriptomine

Transcriptomine

A tool for mining tissue-specific nuclear receptor transcriptomes based on…

A tool for mining tissue-specific nuclear receptor transcriptomes based on annotated published genome wide transcriptional profiling experiments in the field of nuclear receptor signaling.…

Drosophila… Drosophila Spermatogenesis Expression Database

SpPress Drosophila Spermatogenesis Expression Database

A public database containing genome-wide expression analysis of wild-type males…

A public database containing genome-wide expression analysis of wild-type males using three cell populations isolated from mitotic, meiotic and post-meiotic phases of spermatogenesis in D.…

BioXpress BioXpress

BioXpress

A gene expression and cancer association database in which the expression…

A gene expression and cancer association database in which the expression levels are mapped to genes using RNA-seq data obtained from The Cancer Genome Atlas, International Cancer Genome Consortium,…

Gene Expression… Gene Expression database of Normal and Tumor…

GENT Gene Expression database of Normal and Tumor tissues

A web-accessible database which provides gene expression patterns across…

A web-accessible database which provides gene expression patterns across diverse human cancer and normal tissues. More than 34000 samples, profiled by Affymetrix U133A or U133plus2 platforms, are…

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A A A Staphylococcus aureus… Staphylococcus aureus Transcriptome Meta-Database

SATMD Staphylococcus aureus Transcriptome Meta-Database

A meta-database that contains the post-analysis data from all transcriptome…

A meta-database that contains the post-analysis data from all transcriptome experiments done in Staphylococcus aureus. SATMD contains all the genes identified as regulated by either a locus or a…

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A A A GenoExp GenoExp

GenoExp

A web-based tool in which users can upload their individual SNP data and obtain…

A web-based tool in which users can upload their individual SNP data and obtain predicted expression levels for the set of predictable genes across the 14 different cell types. GenoExp thus allows…

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Gemma Gemma

Gemma

A database, analysis software system and web site for genomics data re-use and…

A database, analysis software system and web site for genomics data re-use and meta-analysis. Currently, Gemma contains analyzed data from over 3300 expression profiling studies, yielding hundreds of…

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A A A Pattern Gene Finder Pattern Gene Finder

PaGeFinder Pattern Gene Finder

A web-based server for on-line detection of gene expression patterns from…

A web-based server for on-line detection of gene expression patterns from serial transcriptomic data generated by high-throughput technologies like microarray or next-generation sequencing. Three…

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A A A GeneHub-GEPIS GeneHub-GEPIS

GeneHub-GEPIS

A bioinformatics tool for inferring gene expression patterns in a large panel…

A bioinformatics tool for inferring gene expression patterns in a large panel of normal and cancer tissues based on human and mouse EST sequence abundance. This tool is built upon the GeneHub…

PD_NGSAtlas PD_NGSAtlas

PD_NGSAtlas

Aims at providing a reference resource combining both next-generation…

Aims at providing a reference resource combining both next-generation sequencing epigenomic and transcriptomic data and quantitative analysis of epigenetic and transcriptional alternations involved…

A A A FANTOM4 EdgeExpressDB FANTOM4 EdgeExpressDB

FANTOM4 EdgeExpressDB

A database and set of interfaces for interpreting biological networks and…

A database and set of interfaces for interpreting biological networks and comparing large high-throughput expression datasets that requires minimal development for new data types and search patterns.…

A A A Non-Human Primate… Non-Human Primate Reference Transcriptome Resource

NHPRTR Non-Human Primate Reference Transcriptome Resource

Aims to generate comprehensive RNA-seq data from a wide variety of non-human…

Aims to generate comprehensive RNA-seq data from a wide variety of non-human primates (NHPs), from lemurs to hominids. This resource will continue to host additional RNA-Seq data, alignments and…

A A A DB-AT DB-AT

DB-AT

Contains transcriptomes of Apicomplexa parasites, as well as datasets…

Contains transcriptomes of Apicomplexa parasites, as well as datasets reflecting a diverse nature of the transcriptomes in individual parasites both in vivo and in vitro. Furthermore, the RNA-Seq…

FlyView FlyView

FlyView

An image database for Drosophila development and genetics, particularly for…

An image database for Drosophila development and genetics, particularly for gene-expression patterns. The concept of FlyView includes compatibility to FlyBase, the main Drosophila database.

A A A SuperFly SuperFly

SuperFly

A relational database for quantified spatio-temporal expression data of…

A relational database for quantified spatio-temporal expression data of segmentation genes during early development in different species of dipteran insects (flies, midges and mosquitoes). SuperFly…

MethHC MethHC

MethHC

A database comprising a systematic integration of a large collection of DNA…

A database comprising a systematic integration of a large collection of DNA methylation data and mRNA/microRNA expression profiles in human cancer. MethHC integrates data such as DNA methylation,…

MyMpn MyMpn

MyMpn

An online resource devoted to studying the human pathogen Mycoplasma…

An online resource devoted to studying the human pathogen Mycoplasma pneumoniae, a minimal bacterium causing lower respiratory tract infections. MyMpn hosts a wealth of omics-scale datasets generated…

A A A Eimeria Transcript… Eimeria Transcript Database

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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A A A ECLAT ECLAT

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…

A A A Tissue-specific Gene… Tissue-specific Gene Expression and Regulation

TiGER Tissue-specific Gene Expression and Regulation

A database developed by the Bioinformatics Lab at Wilmer Eye Institute of Johns…

A database developed by the Bioinformatics Lab at Wilmer Eye Institute of Johns Hopkins University. TiGER contains tissue-specific gene expression profiles or expressed sequence tag (EST) data,…

A A A TissueInfo TissueInfo

TissueInfo

A program that determines the tissue expression profile of a sequence.…

A program that determines the tissue expression profile of a sequence. TissueInfo does this by comparing the given sequence against the EST database. Each EST comes from a library derived from a…

A A A Brain RNA-seq Brain RNA-seq

Brain RNA-seq

A transcriptome database for these eight cell types by RNA sequencing and used…

A transcriptome database for these eight cell types by RNA sequencing and used a sensitive algorithm to detect alternative splicing events in each cell type. Bioinformatic analyses identified…

A A A Database of… Database of Transcriptome in Mouse Early Embryos

DBTMEE Database of Transcriptome in Mouse Early Embryos

A searchable and browsable database designed to manipulate gene expression…

A searchable and browsable database designed to manipulate gene expression information from our ultralarge-scale whole-transcriptome analysis of mouse early embryos. DBTMEE will help to promote our…

A A A Phaseolus vulgaris… Phaseolus vulgaris Gene Expression Atlas

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…

A A A SoySeq SoySeq

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…

A A A ExpTreeDB ExpTreeDB

ExpTreeDB

An online database which includes manually curated gene expression datasets…

An online database which includes manually curated gene expression datasets derived from experiments deposited in Gene Expression Omnibus (GEO).

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A A A Gene Expression data… Gene Expression data Mining Toward RElevant…

GEM-TREND Gene Expression data Mining Toward RElevant Network Discovery

A web tool for searching gene expression data, allows users to search data from…

A web tool for searching gene expression data, allows users to search data from GEO using gene-expression signatures or gene expression ratio data as a query and retrieve gene expression data by…

Web app
A A A MARQ MARQ

MARQ

A web-based application that allows researchers to compare a query set of…

A web-based application that allows researchers to compare a query set of genes, e.g. a set of over- and under-expressed genes, against a signature database built from GEO datasets for different…

A A A yStreX yStreX

yStreX

An online database that collects, stores and distributes genome-wide expression…

An online database that collects, stores and distributes genome-wide expression data generated in the studies of stress responses using yeast Saccharomyces cerevisiae as the model organism.

A A A Chickpea… Chickpea Transcriptome Database

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…

A A A BloodSpot BloodSpot

BloodSpot

Provides an expression plot of genes in healthy and cancerous haematopoietic…

Provides an expression plot of genes in healthy and cancerous haematopoietic cells at specific differentiation stages. BloodSpot facilitates the easy assessment of gene-expression data and how this…

A A A Hembase Hembase

Hembase

An integrated browser and genome portal designed for web-based examination of…

An integrated browser and genome portal designed for web-based examination of the human erythroid transcriptome. Hembase provides interested scientists and clinical hematologists with a genome-based…

A A A Human Plasma Membrane… Human Plasma Membrane Receptome

HPMR Human Plasma Membrane Receptome

Receptome genes have been matched with their ligands for surveying DNA…

Receptome genes have been matched with their ligands for surveying DNA microarray datasets.

Web app
A A A Gene Expression… Gene Expression Barcode

Gene Expression Barcode

Seeks to determine the genes expressed for every tissue and cell type in humans…

Seeks to determine the genes expressed for every tissue and cell type in humans and mice. This project uses the abundant publicly available microarray data sets combined with a suite of single-array…

A A A COLOMBOS COLOMBOS

COLOMBOS

A collection of expression data from both microarray and RNA-Seq experiments…

A collection of expression data from both microarray and RNA-Seq experiments for several prokaryotic species, taken from publicly available database such as the Gene Expression Omnibus (GEO) and…

A A A GenitoUrinary… GenitoUrinary Development Molecular Anatomy…

GUDMAP GenitoUrinary Development Molecular Anatomy Project

An international consortium working to generate gene expression data and…

An international consortium working to generate gene expression data and transgenic mice. GUDMAP includes data from large-scale in situ hybridisation screens (wholemount and section) and microarray…

A A A Bgee Bgee

Bgee

A database to retrieve and compare gene expression patterns between animal…

A database to retrieve and compare gene expression patterns between animal species. Bgee first maps heterogeneous expression data (currently RNA-Seq, Affymetrix, in situ hybridization, and EST data)…

A A A Molecular Signatures… Molecular Signatures DataBase

MSigDB Molecular Signatures DataBase

Collection of annotated gene sets for use with GSEA software. MSigDB is freely…

Collection of annotated gene sets for use with GSEA software. MSigDB is freely available for non-commercial use.

A A A MGDB MGDB

MGDB

This database contains the marker genes from all GEO expression datasets and it…

This database contains the marker genes from all GEO expression datasets and it is actualized monthly with new microarrays. Thus, researchers can see whether the marker genes of their microarray are…

diArk diArk

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…

A A A Expression Atlas Expression Atlas

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…

A A A GEISHA GEISHA

GEISHA

An online repository of in situ hybridization and corresponding metadata for…

An online repository of in situ hybridization and corresponding metadata for genes expressed in the chicken embryo during the first six days of development.

A A A Gene Expression… Gene Expression Nervous System ATlas

GENSAT Gene Expression Nervous System ATlas

Captures information on gene expression in mouse brain at several developmental…

Captures information on gene expression in mouse brain at several developmental ages.

A A A Gene Signature… Gene Signature DataBase

GeneSigDB Gene Signature DataBase

A database of gene signatures that have been extracted and manually curated…

A database of gene signatures that have been extracted and manually curated from the published literature. GeneSigDB provides a standardized resource of published prognostic, diagnostic and other…

A A A GenePaint.org GenePaint.org

GenePaint.org

A digital atlas of gene expression patterns in the mouse. Expression patterns…

A digital atlas of gene expression patterns in the mouse. Expression patterns are determined by non-radioactive in situ hybridization on serial tissue sections.

A A A CleanEx CleanEx

CleanEx

Provides access to public gene expression data via unique approved gene symbols…

Provides access to public gene expression data via unique approved gene symbols and which represents heterogeneous expression data produced by different technologies in a way that facilitates joint…

A A A EMAGE EMAGE

EMAGE

A freely available database of in situ gene expression patterns that allows…

A freely available database of in situ gene expression patterns that allows users to perform online queries of mouse developmental gene expression.

A A A Erythropoiesis… Erythropoiesis DataBase

EpoDB Erythropoiesis DataBase

A database of genes that relate to vertebrate red blood cells. It includes DNA…

A database of genes that relate to vertebrate red blood cells. It includes DNA sequence, structural features, protein information, gene expression information and transcription factor binding sites.

A A A 4DXpress 4DXpress

4DXpress

This database provides a platform to query and compare gene expression data…

This database provides a platform to query and compare gene expression data during the development of the major model animals (zebrafish, drosophila, medaka, mouse). The high resolution expression…

A A A Allen Brain Atlas Allen Brain Atlas

Allen Brain Atlas

A growing collection of online public resources integrating extensive gene…

A growing collection of online public resources integrating extensive gene expression and neuroanatomical data, complete with a novel suite of search and viewing tools.

A A A BloodExpress BloodExpress

BloodExpress

A database of gene expression in mouse haematopoiesis. BloodExpress integrates…

A database of gene expression in mouse haematopoiesis. BloodExpress integrates 271 individual microarray experiments derived from 15 distinct studies done on most characterised mouse blood cell…

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A A A Tomato Functional… Tomato Functional Genomics Database

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…

A A A Rice eXpression… Rice eXpression Profile database

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…

A A A Complete Arabidopsis… Complete Arabidopsis Transcriptome MicroArray

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.

A A A CATdb CATdb

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.

A A A Plant MPSS databases Plant MPSS databases

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…

A A A Database Resource for… Database Resource for the Analysis of Signal…

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.

A A A PLant EXpression… PLant EXpression database

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…

A A A FlyAtlas FlyAtlas

FlyAtlas

Contains data on the expression of the genes of Drosophila melanogaster in…

Contains data on the expression of the genes of Drosophila melanogaster in different tissues (currently 25-17 adult and 8 larval) obtained by hybridization of messenger RNA to Affymetrix Drosophila…

A A A FlyEx FlyEx

FlyEx

Stores quantitative data on gene expression in segmentation genetic network in…

Stores quantitative data on gene expression in segmentation genetic network in fruit fly Drosophila melanogaster. FlyEx supports the data downloads and construction of personal reference datasets,…

FlyMine FlyMine

FlyMine

A data warehouse that addresses one of the important challenges of modern…

A data warehouse that addresses one of the important challenges of modern biology: how to integrate and make use of the diversity and volume of current biological data. Its main focus is genomic and…

WormBase WormBase

WormBase

A central repository for research data on the biology, genetics and genomics of…

A central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans and other nematodes. The project has evolved from its original remit to collect and integrate…

FlyBase FlyBase

FlyBase

It is the leading website and database of Drosophila genes and genomes. FlyBase…

It is the leading website and database of Drosophila genes and genomes. FlyBase curates a variety of data from published biological literature, including phenotype, gene expression, interactions…

Web app
A A A ProfileChaser ProfileChaser

ProfileChaser

A web server that allows for querying the Gene Expression Omnibus based on…

A web server that allows for querying the Gene Expression Omnibus based on genome-wide patterns of differential expression. Using a novel, content-based approach, ProfileChaser retrieves expression…

A A A CyanoEXpress CyanoEXpress

CyanoEXpress

A user-friendly web-server, which enables interactive exploration of curated…

A user-friendly web-server, which enables interactive exploration of curated genome-wide expression data for the cyanobacterium Synechocystis sp. PCC 6803. CyanoEXpress is regularly updated with new…

A A A Hipposeq Hipposeq

Hipposeq

Allows you to interactively analyze and visualize RNA-seq data for all…

Allows you to interactively analyze and visualize RNA-seq data for all excitatory cell populations in the hippocampus at multiple levels of granularity. Hipposeq clarifies the transcriptional…

TISSUES TISSUES

TISSUES

Integrates evidence on tissue expression from manually curated literature,…

Integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. When searching for a human protein, the user is presented…

GonadSAGE Deprecated GonadSAGE

GonadSAGE

A publicly available web-based SAGE database on male gonad development that…

A publicly available web-based SAGE database on male gonad development that covers six male mouse embryonic gonad stages, including E10.5, E11.5, E12.5, E13.5, E15.5 and E17.5. The sequence coverage…

A A A SpiroESTdb SpiroESTdb

SpiroESTdb

A web-based information resource that is built upon the annotation and curation…

A web-based information resource that is built upon the annotation and curation of 5,655 ESTs data. SpiroESTdb provides an integrated platform for expressed sequence data, expression dynamics,…

A A A Sentra Deprecated Sentra

Sentra

A database of signal transduction proteins encoded in completely sequenced…

A database of signal transduction proteins encoded in completely sequenced prokaryotic genomes. Sentra consists of two principal components, a manually curated list of signal transduction proteins in…

A A A Human Gene Expression… Human Gene Expression Index

HuGEIndex Human Gene Expression Index

Aims to provide a comprehensive database to aid in understanding the expression…

Aims to provide a comprehensive database to aid in understanding the expression of human genes in normal human tissues.

Web app
A A A GeneTide Deprecated GeneTide

GeneTide

An automated system for human transcripts (mRNA & ESTs) annotation and…

An automated system for human transcripts (mRNA & ESTs) annotation and elucidation of de-novo genes.

A A A SoyXpress Deprecated SoyXpress

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…

A A A anatomic Gene… anatomic Gene Expresssion Mapping

aGEM anatomic Gene Expresssion Mapping

Conceived to integrate phenotypic information from spatial and temporal…

Conceived to integrate phenotypic information from spatial and temporal distribution of expressed genes in human and mouse.

Web app
A A A ArraySearch Deprecated ArraySearch

ArraySearch

A search utility for arabidopsis thaliana genomic expression data. This…

A search utility for arabidopsis thaliana genomic expression data. This resource will empower biological researchers with a statistical method to explore expression data from their own research by…

Web app
A A A Connectivity Map Connectivity Map

cmap Connectivity Map

A reference collection of gene-expression profiles from cultured human cells…

A reference collection of gene-expression profiles from cultured human cells treated with bioactive small molecules, together with pattern-matching software to mine these data. CMAP resource can be…

Web app
A A A GeneChaser GeneChaser

GeneChaser

A web server that enables biologists and clinicians without bioinformatics…

A web server that enables biologists and clinicians without bioinformatics skills to easily identify biological and clinical conditions in which a gene or set of genes was differentially expressed.

Multi-Omics Profiling… Multi-Omics Profiling Expression Database

MOPED Multi-Omics Profiling Expression Database

Presents consistently processed data for gene, protein and pathway expression.…

Presents consistently processed data for gene, protein and pathway expression. To improve data quality, consistency and use, MOPED includes metadata detailing experimental design and analysis…

A A A GermSAGE Deprecated GermSAGE

GermSAGE

A collection of male germ cell transcriptiome information derived from Serial…

A collection of male germ cell transcriptiome information derived from Serial Analysis of Gene Expression (SAGE). GermSAGE includes the three key germ cell stages in spermatogenesis, including mouse…

Curators for Gene expression data

  • Babru Bahan Samal's avatar image
    Babru Bahan Samal
    Section on Molecular Neuroscience,…
  • Shweta Bagewadi's avatar image
    Shweta Bagewadi
    Department of Bioinformatics,…
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