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…
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…

dbEMT
Data

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…

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GiSAO.db
Data

GiSAO.db Genes involved in senescence, apoptosis and oxidative stress database

Provides a database for the storage and management of ageing-related data. The…

Provides a database for the storage and management of ageing-related data. The core of GiSAO.db consists of normalized gene expression and miRNA expression data retrieved from microarray experiments.…

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TBrowser
Desktop

TBrowser TranscriptomeBrowser

Hosts a large database of transcriptional signatures (TS, n~40 000) extracted…

Hosts a large database of transcriptional signatures (TS, n~40 000) extracted from Gene Expression Omnibus (~4 000 experiments) using the DBF-MCL algorithm. TBrowser constitutes a highly powerful…

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cerebroViz
Desktop

cerebroViz

Maps spatiotemporal brain data to vector graphic diagrams of the human brain.…

Maps spatiotemporal brain data to vector graphic diagrams of the human brain. cerebroViz allows rapid generation of publication-quality figures that highlight spatiotemporal trends in the input data,…

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SAGEnhaft
Desktop

SAGEnhaft

Implements several functions useful for analysis of gene expression data by…

Implements several functions useful for analysis of gene expression data by sequencing tags as done in SAGE (Serial Analysis of Gene Expressen) data. For example, SAGEnhaft permits extraction of a…

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AtlasRDF
Desktop

AtlasRDF

Query the Gene Expression AtlasRDF data at the European Bioinformatics…

Query the Gene Expression AtlasRDF data at the European Bioinformatics Institute using genes, experimental factors (such as disease, cell type, compound treatments), pathways and proteins. AtlasRDF…

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scRNASeqDB
Data

scRNASeqDB

Collects and curates gene expression profiles of the transcriptome of human…

Collects and curates gene expression profiles of the transcriptome of human single cells. scRNASeqDB provides various features such as gene expression in different cell types, expression patterns at…

TOMATOMICS
Data

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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PlaMoM
Data

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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Ouija
Desktop

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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HDTD
Desktop

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…

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DsTRD
Data

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…

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GXD
Data

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,…

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CucurbiGene
Data

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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SoleaDB
Data

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…

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OryzaExpress
Data

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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EeelBase
Data

EeelBase

Provides picture of the genomic transcriptional activity of this economically…

Provides picture of the genomic transcriptional activity of this economically important but endangered species. EeelBase is a dedicated database of annotated transcriptome sequences of the European…

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Eurexpress
Data

Eurexpress

Provides a simultaneous visualization of thoroughly annotated gene expression…

Provides a simultaneous visualization of thoroughly annotated gene expression patterns at cellular resolution at one developmental stage. The Eurexpress atlas is a digital transcriptome atlas that…

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HEM
Data

HEM Human Erythroblast Maturation Database

Contains differentially regulated and continuously expressed transcripts. HEM…

Contains differentially regulated and continuously expressed transcripts. HEM is a comprehensive reference expression database of pure populations of normal human erythroblasts, including several…

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A Transcriptomi…
Web

A Transcriptomic Atlas of Mouse Neocortical Layers

Permits to query specific genes and transcripts. The Transcriptomic Atlas of…

Permits to query specific genes and transcripts. The Transcriptomic Atlas of Mouse Neocortical Layers extends currently available resources, such as the Allen Mouse Brain Atlas and microarray data…

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OsMes
Data

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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Silene…
Data

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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PocilloporaBase
Data

PocilloporaBase

Hosts mRNA sequencing data of the cauliflower coral, Pocillopora damicornis, a…

Hosts mRNA sequencing data of the cauliflower coral, Pocillopora damicornis, a geographically widespread Indo-Pacific species that exhibits a great diversity of colony forms and is able to thrive in…

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MTD
Data

MTD Microbial Transcriptome Database

Provides tools and information for studying the microbial transcriptome…

Provides tools and information for studying the microbial transcriptome profiles, in particular the transcriptome data derived from the high-throughput technologies. MTD accepts request for custom…

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KrillDB
Data

KrillDB

Contains 133,962 transcribed sequences assembled from the combined new Illumina…

Contains 133,962 transcribed sequences assembled from the combined new Illumina sequences and previously published 454 assembled pyrosequencing data. KrillDB gives access to: 1) the full list of…

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DGET
Web

DGET Drosophila Gene Expression Tool

Stores and facilitates search of RNA-Seq based expression profiles available…

Stores and facilitates search of RNA-Seq based expression profiles available from the modENCODE consortium and other public data sets. DGET provides a flexible tool for expression data retrieval and…

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Siamese
Desktop

Siamese

Converts the expression changes of the landmark genes into a perturbation…

Converts the expression changes of the landmark genes into a perturbation barcode that reveals important features of the underlying data. Siamese uses deep learning techniques. The barcode captures…

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LungGENS
Web

LungGENS Lung Gene Expression iN Single-cell

Facilitates the retrieval of lung cell-specific gene expression information…

Facilitates the retrieval of lung cell-specific gene expression information from extensive data sets derived from RNA sequencing of single cells. LungGENS is a web-based bioinformatics resource for…

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BrainScope
Web

BrainScope

Enables the linked, all-in-one visualization of genes and samples across the…

Enables the linked, all-in-one visualization of genes and samples across the whole brain and genome, and across developmental stages. BrainScope is a web portal for fast, interactive visual…

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Horse_Trans
Desktop

Horse_Trans Horse Transcriptome

Provides a scientific collaborative platform for laboratories interested in the…

Provides a scientific collaborative platform for laboratories interested in the horse functional genomics and provide a replicable model for other organisms. The Horse_Trans is a pipeline for…

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MMETSP
Data

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…

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GOAD
Data

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)…

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NeuroExpresso
Data

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…

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GEN3VA
Data

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…

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MtGEA
Data

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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KERIS
Data

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,…

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LjGEA
Data

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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VESPUCCI
Data

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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The Lair
Data

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…

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Optimas-DW
Data

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
Data

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,…

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GnpIS
Data

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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TreeshrewDB
Data

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…

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Retina
Data

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…

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SpinachBase
Data

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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ADAGE
Desktop

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…

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TENOR
Data

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
Data

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…

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BBBomics
Data

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…

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PaGenBase
Data

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…

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TiSGeD
Data

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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GEMINI
Desktop
Web

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,…

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MTD
Data

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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D-GEX
Desktop

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…

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CRN
Data

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…

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RNA-Seq Atlas
Data

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…

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SBR-Blood
Data

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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MERAV
Web

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…

IC4R
Data

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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dbMAE
Data

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…

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MEPD
Data

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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Embeddr
Desktop

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…

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Lygodium…
Data

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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MeloGen
Data

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…

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MOROKOSHI
Data

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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LCB
Web

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…

TISSUES
Data

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…

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SHIELD
Data

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…

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EXPath
Data

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
Data

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).…

ESCAPE
Data

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…

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DSigDB
Data

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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Transcriptomine
Web

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.…

SpPress
Data

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
Data

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,…

GENT
Data

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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SATMD
Web

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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GenoExp
Desktop
Web

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…

Gemma
Web

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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PaGeFinder
Web

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…

PD_NGSAtlas
Data

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…

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FANTOM4…
Data

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.…

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NHPRTR
Data

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…

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DB-AT
Data

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
Data

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.

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SuperFly
Data

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
Data

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
Data

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…

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SpiroESTdb
Data

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,…

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EimeriaTDB
Data

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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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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TiGER
Data

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,…

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Brain RNA-seq
Data

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…

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DBTMEE
Data

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…

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PvGEA
Data

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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SoySeq
Data

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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GEM-TREND
Web

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…

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yStreX
Data

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.

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CTDB
Data

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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BloodSpot
Data

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…

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Hembase
Data

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…

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HPMR
Data

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.

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Gene…
Web

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…

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COLOMBOS
Data

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…

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GUDMAP
Data

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…

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Bgee
Data

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)…

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MSigDB
Data

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.

diArk
Data

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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Expression…
Data

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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GEISHA
Data

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.

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GENSAT
Data

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.

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GeneSigDB
Data

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…

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GenePaint.org
Data

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.

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CleanEx
Data

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…

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EMAGE
Data

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.

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EpoDB
Data

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.

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4DXpress
Data

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…

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Allen Brain…
Data

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.

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BloodExpress
Data

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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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…

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RiceXPro
Data

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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CATMA
Data

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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CATdb
Data

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.

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Plant MPSS…
Data

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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DRASTIC
Data

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.

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PLEXdb
Data

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…

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FlyAtlas
Data

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…

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FlyEx
Data

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
Data

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
Data

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
Data

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…