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 predictions in a number of cancers and to elucidate basic gene expression biology. Source text: McCall et al., 2014.
Curator: Babru Bahan Samal
4DXpress
4DXpress
This database provides a platform to query and compare gene expression data during the…
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 data was acquired through whole mount in situ…
Allen Brain Atlas
Allen Brain Atlas
A growing collection of online public resources integrating extensive gene expression and…
A growing collection of online public resources integrating extensive gene expression and neuroanatomical data, complete with a novel suite of search and viewing tools.
anatomic Gene Expresssion Mapping
anatomic Gene Expresssion Mapping
aGEM
Conceived to integrate phenotypic information from spatial and temporal distribution of…
Conceived to integrate phenotypic information from spatial and temporal distribution of expressed genes in human and mouse.
ArraySearch
ArraySearch
A search utility for arabidopsis thaliana genomic expression data. This resource will…
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 comparing it with expression signatures from a large…
Bgee
Bgee
A database to retrieve and compare gene expression patterns between animal species. Bgee…
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) to anatomy and development of different species.…
Bioclock
Bioclock
A searchable database of diel and circadian microarray expression data. This website…
A searchable database of diel and circadian microarray expression data. This website allows searchable browsing of this quantitative gene expression information. The visualization allows for gene-by-gene comparison of transcript expression under…
BioXpress
BioXpress
A gene expression and cancer association database in which the expression levels are…
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, Expression Atlas and publications. The BioXpress…
Blood Brain Barrier omics
Blood Brain Barrier omics
BBBomics
A comprehensive portal for blood-brain barrier transcriptomics data, obtained by…
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 coding (gene expression, alternate splice forms,…
BloodExpress
BloodExpress
A database of gene expression in mouse haematopoiesis. BloodExpress integrates 271…
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 types. Gene expression information has been…
BloodSpot
BloodSpot
Provides an expression plot of genes in healthy and cancerous haematopoietic cells at…
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 links to patient survival, investigation of…
Brain RNA-seq
Brain RNA-seq
A transcriptome database for these eight cell types by RNA sequencing and used a…
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 thousands of new cell type-enriched genes and splicing…
Cancer RNA-Seq Nexus
Cancer RNA-Seq Nexus
CRN
Provides all of the following features: (i) large-scale and comprehensive data archives…
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 networks; (ii) phenotype-oriented data organization…
CATdb
CATdb
Provides public access to a large collection of transcriptome data for Arabidopsis…
Provides public access to a large collection of transcriptome data for Arabidopsis thaliana produced by a single Complete Arabidopsis Transcriptome Micro Array (CATMA) platform.
Chickpea Transcriptome Database
Chickpea Transcriptome Database
CTDB
It has been developed with the view to provide most comprehensive information about the…
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 tools for transcriptome sequence, functional…
Circadian Expression Profiles Data Base
Circadian Expression Profiles Data Base
CircaDB
A database of circadian transcriptional profiles from time course expression experiments…
A database of circadian transcriptional profiles from time course expression experiments from mice and humans. Each transcript's expression was evaluated by three separate algorithms, JTK_Cycle, Lomb Scargle and DeLichtenberg. Users can query…
CleanEx
CleanEx
Provides access to public gene expression data via unique approved gene symbols and which…
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 analysis and cross-dataset comparisons.
COLOMBOS
COLOMBOS
A collection of expression data from both microarray and RNA-Seq experiments for several…
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 ArrayExpress. Its uniqueness resides in the ability to…
Complete Arabidopsis Transcriptome MicroArray
Complete Arabidopsis Transcriptome MicroArray
CATMA
The aim of the project was the design and production of high quality Gene-specific…
The aim of the project was the design and production of high quality Gene-specific Sequence Tags (GSTs) covering most Arabidopsis genes.
Connectivity Map
Connectivity Map
cmap
Developed with the express purpose of identifying drugs with putative efficacy against a…
Developed with the express purpose of identifying drugs with putative efficacy against a given disease, where the disease in question is characterized by a (differential) gene-expression signature.
CucurbiGene
CucurbiGene
Develops genomic tools for Squash (Cucurbita spp.) breeding: transcriptome, genetic map,…
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 cultivars, with improve fruit quality and disease…
D-GEX
D-GEX
A deep learning method to infer the expression of target genes from the expression of…
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 model and compare its performance to those from…
database of autosomal MonoAllelic Expression
database of autosomal MonoAllelic Expression
dbMAE
Incorporates data from multiple recent reports of genome-wide analyses. These include…
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 well as indirect identification, based on a…
Database of Transcriptome in Mouse Early Embryos
Database of Transcriptome in Mouse Early Embryos
DBTMEE
A searchable and browsable database designed to manipulate gene expression information…
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 understanding of the enigmatic fertilization…
Database Resource for the Analysis of Signal…
Database Resource for the Analysis of Signal Transduction in Cells
DRASTIC
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.
DB-AT
DB-AT
Contains transcriptomes of Apicomplexa parasites, as well as datasets reflecting a…
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 data of 116 Indonesian malaria patients infected with…
dbEMT
dbEMT
A literature-based gene resource for exploring epithelial-mesenchymal transition…
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 biological pathways. It is constructed as a free…
diArk
diArk
Aims to provide access to all available assembled genomes and transcriptomes. In…
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 not available via NCBI/ENA/DDBJ. Several indicators…
Drosophila Spermatogenesis Expression Database
Drosophila Spermatogenesis Expression Database
SpPress
A public database containing genome-wide expression analysis of wild-type males using…
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. melanogaster.
Drug Signatures Database
Drug Signatures Database
DSigDB
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 drugs/compounds and gene sets. DSigDB gene sets provide…
ECLAT
ECLAT
This is a server for the classification of ESTs from mixed EST pools (from fungus…
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 for discrimination between plant and fungal…
Eimeria Transcript Database
Eimeria Transcript Database
EimeriaTDB
An integrated resource of cDNA sequencing and annotation data of Eimeria spp. of domestic…
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 reconstructed transcripts.
EMAGE
EMAGE
A freely available database of in situ gene expression patterns that allows users to…
A freely available database of in situ gene expression patterns that allows users to perform online queries of mouse developmental gene expression.
Embeddr
Embeddr
Laplacian eigenmaps and principal curves for pseudotemporal ordering and clustering of…
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 high-variance gene correlation graph and laplacian…
Embryonic Stem Cell Atlas from Pluripotency…
Embryonic Stem Cell Atlas from Pluripotency Evidence
ESCAPE
A mouse and human embryonic stem cells (m/hESC)-centered database integrating data from…
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 sequencing, genome-wide inhibitory RNA screens, gene…
Erythropoiesis DataBase
Erythropoiesis DataBase
EpoDB
A database of genes that relate to vertebrate red blood cells. It includes DNA sequence,…
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.
EXPath
EXPath
A database resource that collects and utilizes gene expression profiles derived from…
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 only comprehensively congregate the public…
Expression Atlas
Expression Atlas
Provides information about gene and protein expression in animal and plant samples of…
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 consists of selected microarray and RNA-sequencing…
ExpTreeDB
ExpTreeDB
An online database which includes manually curated gene expression datasets derived from…
An online database which includes manually curated gene expression datasets derived from experiments deposited in Gene Expression Omnibus (GEO).
FANTOM4 EdgeExpressDB
FANTOM4 EdgeExpressDB
A database and set of interfaces for interpreting biological networks and comparing large…
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. The FANTOM4 EdgeExpress database summarizes gene…
FlyAtlas
FlyAtlas
Contains data on the expression of the genes of Drosophila melanogaster in different…
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 Genome 2 microarrays. A novel facility allows the…
FlyBase
FlyBase
It is the leading website and database of Drosophila genes and genomes. FlyBase curates a…
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 (genetic and physical), gene ontology (GO) information…
FlyEx
FlyEx
Stores quantitative data on gene expression in segmentation genetic network in fruit fly…
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, that makes it possible to more effectively use and…
FlyMine
FlyMine
A data warehouse that addresses one of the important challenges of modern biology: how to…
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 proteomics data for Drosophila and other insects.…
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.
GEISHA
GEISHA
An online repository of in situ hybridization and corresponding metadata for genes…
An online repository of in situ hybridization and corresponding metadata for genes expressed in the chicken embryo during the first six days of development.
GEMINI
GEMINI
A fast search engine that uses a query genomic profile to search for similar profiles in…
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, data origin or other meta-data information. GEMINI…
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 millions of differential expression results and…
Gene Expression Barcode
Gene Expression Barcode
Seeks to determine the genes expressed for every tissue and cell type in humans and mice.…
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 preprocessing, quality control and analysis…
Gene Expression data Mining Toward RElevant…
Gene Expression data Mining Toward RElevant Network Discovery
GEM-TREND
A web tool for searching gene expression data, allows users to search data from GEO using…
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 comparing gene-expression pattern between the query…
Gene eXpression Database
Gene eXpression Database
GXD
A community resource of mouse developmental expression information. GXD collects and…
A community resource of mouse developmental expression information. GXD collects and integrates the gene expression information in MGI.
Gene Expression database of Normal and Tumor…
Gene Expression database of Normal and Tumor tissues
GENT
A web-accessible database which provides gene expression patterns across diverse human…
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 consistently processed and combined into two…
Gene Expression Nervous System ATlas
Gene Expression Nervous System ATlas
GENSAT
Captures information on gene expression in mouse brain at several developmental ages.
Captures information on gene expression in mouse brain at several developmental ages.
Gene Signature DataBase
Gene Signature DataBase
GeneSigDB
A database of gene signatures that have been extracted and manually curated from the…
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 gene signatures of cancer and related disease to the…
GeneChaser
GeneChaser
A web server that enables biologists and clinicians without bioinformatics skills to…
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.
GeneHub-GEPIS
GeneHub-GEPIS
A bioinformatics tool for inferring gene expression patterns in a large panel of normal…
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 database, which integrates gene and protein information…
GenePaint.org
GenePaint.org
A digital atlas of gene expression patterns in the mouse. Expression patterns are…
A digital atlas of gene expression patterns in the mouse. Expression patterns are determined by non-radioactive in situ hybridization on serial tissue sections.
GeneTide
GeneTide
An automated system for human transcripts (mRNA & ESTs) annotation and elucidation of…
An automated system for human transcripts (mRNA & ESTs) annotation and elucidation of de-novo genes.
Genevestigator
Genevestigator
An innovative online platform to help you interpret your results, prioritize targets and…
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 world's gene expression data. The search engine…
GenitoUrinary Development Molecular Anatomy…
GenitoUrinary Development Molecular Anatomy Project
GUDMAP
An international consortium working to generate gene expression data and transgenic mice.…
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 gene expression data of microdissected,…
GenoExp
GenoExp
A web-based tool in which users can upload their individual SNP data and obtain predicted…
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 users with biological knowledge to study the…
GermSAGE
GermSAGE
A collection of male germ cell transcriptiome information derived from Serial Analysis of…
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 type A spermatogonia (Spga), pachytene…
GonadSAGE
GonadSAGE
A publicly available web-based SAGE database on male gonad development that covers six…
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 of each SAGE library is beyond 150K, 'which…
hematopoietic Systems Biology Repository
hematopoietic Systems Biology Repository
SBR-Blood
Enables the user to conduct cell type correlations with previously published data sets…
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 been shown to be correct in terms of…
Hembase
Hembase
An integrated browser and genome portal designed for web-based examination of the human…
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 approach toward the study of erythroid biology.
Human Gene Expression Index
Human Gene Expression Index
HuGEIndex
Aims to provide a comprehensive database to aid in understanding the expression of human…
Aims to provide a comprehensive database to aid in understanding the expression of human genes in normal human tissues.
Human Plasma Membrane Receptome
Human Plasma Membrane Receptome
HPMR
Receptome genes have been matched with their ligands for surveying DNA microarray…
Receptome genes have been matched with their ligands for surveying DNA microarray datasets.
Information Commons for Rice
Information Commons for Rice
IC4R
A rice knowledgebase featuring adoption of an extensible and sustainable architecture…
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 maintained by different committed groups, deals with data…
LINCS Canvas Browser
LINCS Canvas Browser
LCB
An interactive HTML5 web-based software application that facilitates querying, browsing…
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 canvases, one to visualize clustered L1000 expression…
Lygodium japonicum Transcriptome Database
Lygodium japonicum Transcriptome Database
Provides important opportunities to accelerate molecular research in ferns. In this…
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 Lygodium japonicum, nine different RNA samples…
Mammalian Transcriptomic Database
Mammalian Transcriptomic Database
MTD
A mammalian transcriptomic database. The MTD contains data from humans, mice, rats and…
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 KEGG pathway and provides expression information…
MARQ
MARQ
A web-based application that allows researchers to compare a query set of genes, e.g. a…
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 organisms and platforms.
Medaka Expression Pattern Database
Medaka Expression Pattern Database
MEPD
A repository of medaka expression data for the scientific community. In this update we…
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 gene-centric view. This is possible because now we…
Medicago sativa Gene Index
Medicago sativa Gene Index
MSGI
An online resource for analyses of gene expression in M. sativa for six distinct tissue…
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). This publicly available resource is a valuable tool…
MeloGen
MeloGen
Develops genomic tools for Melon (Cucumis melo) breeding: transcriptome, SSR, SNP…
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 of 49,741 unigenes generated at COMAV. These…
Metabolic gEne RApid Visualizer
Metabolic gEne RApid Visualizer
MERAV
A web-based tool that can query a database comprising ∼4300 microarrays, representing…
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 powerful tool for whole genome analysis which offers…
MethHC
MethHC
A database comprising a systematic integration of a large collection of DNA methylation…
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, mRNA expression, DNA methylation of microRNA gene and…
MGDB
MGDB
This database contains the marker genes from all GEO expression datasets and it is…
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 marker genes in other microarrays in the database,…
Molecular Signatures DataBase
Molecular Signatures DataBase
MSigDB
Collection of annotated gene sets for use with GSEA software. MSigDB is freely available…
Collection of annotated gene sets for use with GSEA software. MSigDB is freely available for non-commercial use.
MOROKOSHI
MOROKOSHI
In this database, users can access predominantly two types of transcriptome data; correct…
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 RNA-Seq analysis. In MOROKOSHI, users can access…
Multi-Omics Profiling Expression Database
Multi-Omics Profiling Expression Database
MOPED
Presents consistently processed data for gene, protein and pathway expression. To improve…
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 methods. The multi-omics data are integrated through…
MyMpn
MyMpn
An online resource devoted to studying the human pathogen Mycoplasma pneumoniae, a…
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 by hundreds of experimental and computational…
Non-Human Primate Reference Transcriptome Resource
Non-Human Primate Reference Transcriptome Resource
NHPRTR
Aims to generate comprehensive RNA-seq data from a wide variety of non-human primates…
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 assemblies as they are generated over the coming years…
OryzaExpress
OryzaExpress
Provides information of gene expression network and biological annotations in rice.…
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 plant science and leads to systems biology.
Pattern Gene Database
Pattern Gene Database
PaGenBase
Provides information of pattern genes (specific genes, selective genes, housekeeping…
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 physiological conditions. PaGenBase has collected 143…
Pattern Gene Finder
Pattern Gene Finder
PaGeFinder
A web-based server for on-line detection of gene expression patterns from serial…
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 particular parameters, the specificity measure, the…
PD_NGSAtlas
PD_NGSAtlas
Aims at providing a reference resource combining both next-generation sequencing…
Aims at providing a reference resource combining both next-generation sequencing epigenomic and transcriptomic data and quantitative analysis of epigenetic and transcriptional alternations involved in psychiatric disorders. The current release of…
Phaseolus vulgaris Gene Expression Atlas
Phaseolus vulgaris Gene Expression Atlas
PvGEA
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 composition and has increased our understanding of…
PLant EXpression database
PLant EXpression database
PLEXdb
A unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype…
A unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic, physical, and…
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 intergenic transcripts).
ProfileChaser
ProfileChaser
A web server that allows for querying the Gene Expression Omnibus based on genome-wide…
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 profiles that match the differentially regulated…
Rice eXpression Profile database
Rice eXpression Profile database
RiceXPro
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 with various phytohormones, and specific cell…
RNA-Seq Atlas
RNA-Seq Atlas
A web-based repository of RNA-Seq gene expression profiles and query tools. The website…
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 genes with specific expression patterns. To enlarge…
RSIADB
RSIADB
A collective resource for rice sheath blight pathogen, Rhizoctonia solani AG1 IA genome…
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 mine the data using BLAST, sequence extractor,…
Shared Harvard Inner Ear Laboratory Database
Shared Harvard Inner Ear Laboratory Database
SHIELD
A resource for dissemination and comparison of inner-ear gene expression datasets,…
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 School of Medicine, Oregon Health & Science…
SoleaDB
SoleaDB
A transcriptome database for Senegalese sole (Solea senegalensis) and common sole (Solea…
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 tissues, developmental stages or stimuli…
SoySeq
SoySeq
Provides a record of high-resolution gene expression in a set of fourteen diverse…
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 profiles: aerial, underground and seed tissues.
SoyXpress
SoyXpress
A database (MySQL) designed for exploring the soybean transcriptome. SoyXpress is…
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 genetically modified crops. Soybean EST sequences,…
SpiroESTdb
SpiroESTdb
A web-based information resource that is built upon the annotation and curation of 5,655…
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, functional genes, genetic markers including single…
Staphylococcus aureus Transcriptome Meta-Database
Staphylococcus aureus Transcriptome Meta-Database
SATMD
A meta-database that contains the post-analysis data from all transcriptome experiments…
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 growth condition, using microarray and other…
SuperFly
SuperFly
A relational database for quantified spatio-temporal expression data of segmentation…
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 has a special focus on emerging non-drosophilid…
Tissue-specific Gene Expression and Regulation
Tissue-specific Gene Expression and Regulation
TiGER
A database developed by the Bioinformatics Lab at Wilmer Eye Institute of Johns Hopkins…
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, cis-regulatory module (CRM) data, and combinatorial…
Tissue-Specific Genes Database
Tissue-Specific Genes Database
TiSGeD
Provides comprehensive information of tissue-specific genes derived from biomedical…
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 and 30 rat tissues. A statistical parameter SPM is…
TissueInfo
TissueInfo
A program that determines the tissue expression profile of a sequence. TissueInfo does…
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 specific tissue type. By collating the library…
TISSUES
TISSUES
Integrates evidence on tissue expression from manually curated literature, proteomics and…
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 with a body map that provides a complete overview…
Tomato Functional Genomics Database
Tomato Functional Genomics Database
TFGD
Serves as a central repository for raw gene expression data derived from the public…
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 released and continually expanding large-scale tomato…
Transcriptomine
Transcriptomine
A tool for mining tissue-specific nuclear receptor transcriptomes based on annotated…
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. Transcriptomine allows for multiple, menu-driven querying…
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 all data for a single species, and now extends to…
yStreX
yStreX
An online database that collects, stores and distributes genome-wide expression data…
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.