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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…
FlyBase
Dataset

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…

Ensembl
Dataset

Ensembl

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

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

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GXD
Dataset

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,…

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
Dataset

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…

RefSeq
Dataset

RefSeq Reference Sequence

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

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

Heliagene
Dataset

Heliagene

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

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

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Expression…
Dataset

Expression Atlas

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

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

VectorBase
Dataset

VectorBase

A National Institute of Allergy and Infectious Diseases supported…

A National Institute of Allergy and Infectious Diseases supported Bioinformatics Resource Center (BRC) for invertebrate vectors of human pathogens. VectorBase currently hosts the genomes of 35…

PATRIC
Dataset

PATRIC Pathosystems Resource Integration Center

A genomics-centric relational database and bioinformatics resource designed to…

A genomics-centric relational database and bioinformatics resource designed to assist scientists in infectious-disease research. PATRIC provides researchers with an online resource that stores and…

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CYTOMER
Dataset

CYTOMER

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

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

diArk
Dataset

diArk

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

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

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AtRTD
Dataset

AtRTD Arabidopsis Thaliana Reference Transcript Dataset

Provides a comprehensive high-quality reference transcript dataset about…

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

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GENSAT
Dataset

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.

FlyMine
Dataset

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…

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SATMD
Dataset

SATMD Staphylococcus aureus Transcriptome Meta-Database

Contains information coming from manually curating papers published on…

Contains information coming from manually curating papers published on Staphylococcus aureus transcriptome studies. SATMD is the updated version of Staphylococcus aureus microarray meta-database.…

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GenePaint.org
Dataset

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.

Xenbase
Dataset

Xenbase

Integrates variety of data from biomedical model genus and archives large data…

Integrates variety of data from biomedical model genus and archives large data sets that would otherwise be unavailable to the global scientific community. Researchers can easily navigate from genome…

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Plant MPSS…
Dataset

Plant MPSS databases

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

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

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PLEXdb
Dataset

PLEXdb PLant EXpression database

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

A unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with…

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EMAGE
Dataset

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.

RSIADB
Dataset

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…

SoyBase
Dataset

SoyBase

A comprehensive repository for professionally curated genetics, genomics and…

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

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CATdb
Dataset

CATdb

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

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

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Allen Brain…
Dataset

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.

TOMATOMICS
Dataset

TOMATOMICS

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

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

ANISEED
Dataset

ANISEED

A sophisticated information system dedicated to the biology of ascidians, and…

A sophisticated information system dedicated to the biology of ascidians, and which consists of two classes of inter-linked databases. The Developmental Browser formalizes, integrates and displays an…

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FlyEx
Dataset

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,…

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FlyAtlas
Dataset

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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GeneSigDB
Dataset

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…

ZFIN
Dataset

ZFIN The Zebrafish Model Organism Database

The central resource for zebrafish genetic, genomic, phenotypic and…

The central resource for zebrafish genetic, genomic, phenotypic and developmental data.

PortEco
Dataset

PortEco

A next-generation data resource for the bacterial model organism, Escherichia…

A next-generation data resource for the bacterial model organism, Escherichia coli.

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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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RiceXPro
Dataset

RiceXPro Rice eXpression Profile database

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

A repository of gene expression profiles derived from microarray analysis of tissues/organs encompassing the entire growth of the rice plant under natural field conditions, rice seedlings treated…

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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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PlaMoM
Dataset

PlaMoM Plant Mobile Macromolecules

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

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

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KERIS
Dataset

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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BloodSpot
Dataset

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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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,…

Nematode.net
Dataset

Nematode.net

Disseminates diverse bioinformatic data sets and provide analysis tools to the…

Disseminates diverse bioinformatic data sets and provide analysis tools to the broad scientific community in a useful and user-friendly manner. Next-generation data has been added to the various…

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MTD
Dataset

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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GEISHA
Dataset

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.

LSD
Dataset

LSD Leaf Senescence Database

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

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

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BloodExpress
Dataset

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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MEPD
Dataset

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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4DXpress
Dataset

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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COLOMBOS
Dataset

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…

OTL
Dataset

OTL Oryza Tag Line

Facilitates forward genetic search for specific phenotypes, putatively…

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

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GXB
Web
Desktop

GXB Gene Expression Browser

Enables interactive query and navigation of transcriptome datasets relevant to…

Enables interactive query and navigation of transcriptome datasets relevant to human immunology research. GXB can be used to browse context-rich systems-scale data within and across systems…

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Retina
Dataset

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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CRN
Dataset

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…

PlanMine
Dataset

PlanMine

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

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

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SBR-Blood
Dataset

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…

InsectBase
Dataset

InsectBase

Provides a comprehensive platform for researchers who have interests in…

Provides a comprehensive platform for researchers who have interests in analyzing insect genes. InsectBase contains more than 12 millions of sequences, encompassing the genomes of 138 insects,…

IC4R
Dataset

IC4R Information Commons for Rice

A rice knowledgebase featuring adoption of an extensible and sustainable…

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

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dbMAE
Dataset

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…

CauloBrowser
Dataset

CauloBrowser

An online resource for Caulobacter studies. CauloBrowser provides a…

An online resource for Caulobacter studies. CauloBrowser provides a user-friendly interface for quickly searching genes of interest and downloading genome-wide results. Search results about…

PomBase
Dataset

PomBase

It is the model organism database for the fission yeast Schizosaccharomyces…

It is the model organism database for the fission yeast Schizosaccharomyces pombe. PomBase provides a central hub for the fission yeast community, supporting both exploratory and hypothesis-driven…

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DsTRD
Dataset

DsTRD Danshen Transcriptional Resource Database

A comprehensive transcript resource for Salvia miltiorrhiza. DsTRD contains…

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

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HIVed
Dataset

HIVed HIV expression database

Contains curated human proteins with differential expression during the human…

Contains curated human proteins with differential expression during the human immunodeficiency virus (HIV) infection, replication and latency. HIVed aims to display unbiased data reported by authors…

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scRNASeqDB
Dataset

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…

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EpoDB
Dataset

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.

FLAGdb++
Dataset

FLAGdb++

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

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

Cannabis sativa
Dataset

Cannabis sativa

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

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

GPI
Dataset

GPI GenoPlante-Info

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

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

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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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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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DRASTIC
Dataset

DRASTIC Database Resource for the Analysis of Signal Transduction in Cells

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

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

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NHPRTR
Dataset

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
Dataset

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…

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SuperFly
Dataset

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…

Coffee Genome…
Dataset

Coffee Genome Hub

An integrative genome information system that allows centralized access to…

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

MethHC
Dataset

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,…

Trematode.net
Dataset

Trematode.net

A site dedicated to the dissemination of data from flukes, flatworm parasites…

A site dedicated to the dissemination of data from flukes, flatworm parasites of the class Trematoda, phylum Platyhelminthes. Trematode.net is an independent component of Helminth.net and currently…

Helminth.net
Dataset

Helminth.net

A collection of worm-related databases and analysis tools. Currently the sites…

A collection of worm-related databases and analysis tools. Currently the sites Nematode.net and Trematode.net fall under the Helminth.net umbrella. The databases' interface, with a sophisticated…

MyMpn
Dataset

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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DBTMEE
Dataset

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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KrillDB
Dataset

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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CleanEx
Dataset

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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SlideBase
Dataset

SlideBase

Offers a way of selecting genes, promoters, enhancers and microRNAs that are…

Offers a way of selecting genes, promoters, enhancers and microRNAs that are preferentially expressed/used in a specified set of cells/tissues, based on the use of interactive sliders. SlideBase…

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Inner Ear…
Dataset

Inner Ear Transcriptome

Provides a glimpse of the transcriptional landscape of the adult human inner…

Provides a glimpse of the transcriptional landscape of the adult human inner ear. Inner Ear Transcriptome provides a package that offers a useful reference for neurobiologists studying any candidate…

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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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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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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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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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CATMA
Dataset

CATMA Complete Arabidopsis Transcriptome MicroArray

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

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

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MGDB
Dataset

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…

MAGIC
Dataset

MAGIC

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

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

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VESPUCCI
Dataset

VESPUCCI Vitis Expression Studies Platform Using COLOMBOS Compendia Instances

A gene expression compendium for grapevine that integrates publicly available…

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

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TENOR
Dataset

TENOR Transcriptome ENcyclopedia Of Rice

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

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

SIFGD
Dataset

SIFGD Setaria italica Functional Genomics Database

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

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

YeastMine
Dataset

YeastMine

Allows users to query the different types of data present in the Saccharomyces…

Allows users to query the different types of data present in the Saccharomyces Genome Database (SGD) data. YeastMine is an integrated data warehouse with precomputed tables based on the InterMine…

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SpermBase
Dataset

SpermBase

Contains sperm-borne RNA profiling expression data for mouse, rat, rabbit, and…

Contains sperm-borne RNA profiling expression data for mouse, rat, rabbit, and human. SpermBase provides large and small RNA expression data, total sperm and sperm heads. It will be expanded to other…

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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…

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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…

BmuG@Sbase
Dataset

BmuG@Sbase

Contains microbial gene expression and comparative genomic hybridization…

Contains microbial gene expression and comparative genomic hybridization experimental data. BµG@Sbase is a web-browsable Minimum Information about a Microarray Experiment (MIAME)-compliant database…

CMGSDB
Dataset

CMGSDB Database for Computational Modeling of Gene Silencing

An integration of heterogeneous data sources about Caenorhabditis elegans with…

An integration of heterogeneous data sources about Caenorhabditis elegans with capabilities for compositional data mining (CDM) across diverse domains.

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RED
Dataset

RED Rice Expression Database

Integrates rice gene expression profiles under various tissues and experimental…

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

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CSTEA
Web

CSTEA Cell State Transition Expression Atlas

Provides both visualization and analysis of valuable time-series gene…

Provides both visualization and analysis of valuable time-series gene expression data during cell state transitions. CSTEA focuses on expounding important genes and their corresponding functions at…

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OmicsDI
Dataset

OmicsDI Omics Discovery Index

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

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

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The Tomato…
Desktop

The Tomato Expression Atlas

Facilitates effective data analysis and allowing the simultaneous visualization…

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

Listeriomics
Dataset

Listeriomics

Integrates different tools for omics data analyses. Listeriomics integrates all…

Integrates different tools for omics data analyses. Listeriomics integrates all the complete Listeria species genomes, transcriptomes, and proteomes published to date. It allows navigation among all…

SilkPathDB
Dataset

SilkPathDB

Proposes a comprehensive resource for studying on pathogens of silkworm,…

Proposes a comprehensive resource for studying on pathogens of silkworm, including microsporidia, fungi, bacteria and virus. SilkPathDB provides access to not only genomic data including functional…

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GOAD
Dataset

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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HEM
Dataset

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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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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DSigDB
Dataset

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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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…

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MMETSP
Dataset

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…

JCDB
Dataset

JCDB Jatropha curcas DataBase

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

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

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GEN3VA
Dataset

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…

BorreliaBase
Dataset

BorreliaBase

An online database for comparative browsing of borrelia genomes. BorreliaBase…

An online database for comparative browsing of borrelia genomes. BorreliaBase is currently populated with sequences from 35 genomes of eight lyme-borreliosis group borrelia species and 7…

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The Lair
Dataset

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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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,…

croc genomes
Dataset

croc genomes the crocodilian genomes project

A database which offers gene annotation of crocodilian. This base offers…

A database which offers gene annotation of crocodilian. This base offers completed genome assemblies for three important crocodilians: Alligator mississippiensis (the American alligator), Crocodylus…

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FANTOM4…
Dataset

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.…

ESCAPE
Dataset

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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Lygodium…
Dataset

Lygodium japonicum Transcriptome Database

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

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

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MOROKOSHI
Dataset

MOROKOSHI

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

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

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GiSAO.db
Dataset

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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EXPath
Dataset

EXPath

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

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

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MSGI
Dataset

MSGI Medicago sativa Gene Index

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

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

ExPASy
Dataset

ExPASy Expert Protein Analysis System

Provides a comprehensive list of resources in different domains, such as…

Provides a comprehensive list of resources in different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics and transcriptomics. ExPASy is the Swiss…

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Hembase
Dataset

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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HuGEIndex
Dataset

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.

INsPeCT
Web

INsPeCT INtegrative Platform for Cancer Transcriptomics

Allows to perform comprehensive in-silico analyses of microarray, ChIP-seq, and…

Allows to perform comprehensive in-silico analyses of microarray, ChIP-seq, and RNA-seq data. INsPeCT is a web-application which provides an easy-to-use interface to a comprehensive, integrated suite…

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NeuroExpresso
Dataset

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…

ThebaBD
Dataset

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…

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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…