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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…

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ReCount
Dataset

ReCount

Summarizes analysis-ready expression data for genes, exons, exon–exon splice…

Summarizes analysis-ready expression data for genes, exons, exon–exon splice junctions and base-level coverage. ReCount is an online resource that uses analysis pipelines that are annotation agnostic…

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BrainTx
Dataset

BrainTx Brain Transcriptome Database

Provides data on the transcriptome related to mouse cerebellar development.…

Provides data on the transcriptome related to mouse cerebellar development. BrainTx is a neuroinformatics database that contains gene expression information related to various stages and states of…

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…

Escherichia…
Dataset

Escherichia coli Multi-omics Database

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

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

Heliagene
Dataset

Heliagene

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

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

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Expression…
Dataset

Expression Atlas

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

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

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AtGenExpress…
Dataset

AtGenExpress JPN

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

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

PATRIC
Dataset

PATRIC Pathosystems Resource Integration Center

Aims to assist scientists in infectious-disease research. PATRIC is a National…

Aims to assist scientists in infectious-disease research. PATRIC is a National Institute of Health (NIH) supported bioinformatics resource center that has been built to enable comparative genomic…

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…

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OASIS
Dataset

OASIS

Provides a central repository and a web-based analytical platform for cancer…

Provides a central repository and a web-based analytical platform for cancer multi-omics data. OASIS contains sample-level annotations and gene level mutation, copy number variation (CNV) and…

EMAP
Dataset

EMAP e-Mouse Atlas Project

Gathers digital models of mouse development. EMAP allows users to visualize…

Gathers digital models of mouse development. EMAP allows users to visualize embryo anatomy and gene expression of mice in 3D.

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BASiCz
Web

BASiCz Blood Atlas of Single Cells in zebrafish

Allows easy access and retrieval of sequencing data from zebrafish myeloid…

Allows easy access and retrieval of sequencing data from zebrafish myeloid cells. BASiCz is a user-friendly cloud repository, (Blood Atlas of Single Cells in zebrafish) for interactive exploration…

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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…

HipSci
Dataset

HipSci human induced pluripotent Stem cells initiative

Generates human induced pluripotent stem cells (iPSCs) from hundreds of healthy…

Generates human induced pluripotent stem cells (iPSCs) from hundreds of healthy individuals as well as patients diagnosed with selected diseases. HipSci is a powerful resource to evaluate and…

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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.

ParameciumDB
Dataset

ParameciumDB

Provides data about the model organism Paramecium tetraurelia. ParameciumDB was…

Provides data about the model organism Paramecium tetraurelia. ParameciumDB was created by using components of the Generic Model Organism Database (GMOD). It offers data about gene expression data…

ZFIN
Dataset

ZFIN The Zebrafish Information Network

Provides genetic and genomic data involving zebrafish. ZFIN is composed of…

Provides genetic and genomic data involving zebrafish. ZFIN is composed of mutants, gene expression, phenotypes, knockdown reagents, antibodies, transgenic constructs, and reporter lines. It offers…

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The NAISTrap…
Dataset

The NAISTrap database

Compiles the nucleotide sequences of about 900 cDNA fragments derived from the…

Compiles the nucleotide sequences of about 900 cDNA fragments derived from the mouse trapped genes candidates. The NAISTrap database provides a description of the genes for each embryonic stem (ES)…

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LIFEdb
Dataset

LIFEdb

Provides integrated access to complementary DNA (cDNA)-data, experimental…

Provides integrated access to complementary DNA (cDNA)-data, experimental results and bioinformatics information. LIFEdb is a database enabling researchers to systematically select and characterize…

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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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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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RiceFOX
Dataset

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

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

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

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Plant MPSS…
Dataset

Plant MPSS databases

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

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

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PLEXdb
Dataset

PLEXdb PLant EXpression database

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

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

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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…

LGEA
Dataset

LGEA Lung Gene Expression Analysis

Provides useful graphical interfaces with new interactive options to uses…

Provides useful graphical interfaces with new interactive options to uses increasingly comprehensive RNA expression data sets. LGEA offers an extended database enabling rapid analysis of (i)…

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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SpBase
Dataset

SpBase Strongylocentrotus purpuratus database

Provides genomic information about the purple sea urchin and comparative…

Provides genomic information about the purple sea urchin and comparative sequence information from other echinoderms. SpBase contains more than 10 000 gene annotations and includes sequence…

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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.

BDGP
Dataset

BDGP Berkeley Drosophila Genome Project

Provides sequence of euchromatic genome of Drosophila melanogaster in high…

Provides sequence of euchromatic genome of Drosophila melanogaster in high quality. BDGP is a resource developed to (i) produce gene disruptions using P element-mediated mutagenesis on a scale…

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PRIGEN
Dataset

PRIGEN PRImate GENes

Stores Pan troglodytes verus cDNAs. PRIGEN is a database that provides a…

Stores Pan troglodytes verus cDNAs. PRIGEN is a database that provides a keyword and a BLAST search. It contains sequences derived from full-length cDNAs (FLcDNA) libraries constructed by the…

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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CAGE
Dataset

CAGE Cap-Analysis Gene Expression

Compiles information derived from Cap-Analysis Gene Expression (a…

Compiles information derived from Cap-Analysis Gene Expression (a high-throughput method) tags from humans and mice. The CAGE database is composed of: (i) CAGE Basic Database which gathers…

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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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GATHER
Dataset

GATHER Gene Annotation Tool to Help Explain Relationships

Allows to study the Retinoblastoma/E2 Factor (Rb/E2F) pathway. GATHER permits…

Allows to study the Retinoblastoma/E2 Factor (Rb/E2F) pathway. GATHER permits to find common aspects of biology in these otherwise dissimilar expression profiles showing both the power of expression…

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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…

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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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…

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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AspWood
Dataset

AspWood Aspen Wood

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

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

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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…

Globin Gene…
Dataset

Globin Gene Server

Supplies contents and method to study DNA sequences. Globin Gene Server informs…

Supplies contents and method to study DNA sequences. Globin Gene Server informs about human hemoglobin mutations. It offers a list of experimental data and several types of software allowing…

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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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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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Orchidstra
Dataset

Orchidstra

Collects, annotates and shares genomic information for orchid functional…

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

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CATchUP
Dataset

CATchUP

Provides information on spatiotemporal specific gene expression for eight plant…

Provides information on spatiotemporal specific gene expression for eight plant species. CATchUP provides information on approximately 70000 transcripts including the δdmax values, functional…

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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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SPIED
Dataset

SPIED Searchable Platform Independent Expression Database

Contains transcriptional data covering multiple platforms and species. SPIED…

Contains transcriptional data covering multiple platforms and species. SPIED includes more than 100,000 expression fold profiles defined independently of control/treatment assignment. This database…

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Sheep Atlas
Dataset

Sheep Atlas

Gathers information about sheep. Sheep Atlas is a dataset that presents a poll…

Gathers information about sheep. Sheep Atlas is a dataset that presents a poll concerning gene expression across a wide range of tissues taken from the domestic sheep. The information is presented…

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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…

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

Gathers information about rice. IC4R provides a reference genome with…

Gathers information about rice. IC4R provides a reference genome with standardized and accurate gene annotations based on huge amounts of omics data and large quantities of rice-related literatures.…

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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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The Tolerome
Dataset

The Tolerome

Provides transcriptome-level information from microarray, RNA-sequencing, and…

Provides transcriptome-level information from microarray, RNA-sequencing, and quantitative polymerase chain reaction (PCR) datasets while maintaining records on mutations in a variety of stress…

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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…

G T A T C G C T A
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…

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EPConDB
Dataset

EPConDB Endocrine Pancreas Consortium DataBase

Provides information about genes expressed in the pancreas. EPConDB is a…

Provides information about genes expressed in the pancreas. EPConDB is a resource of the Beta Cell Biology Consortium that collects information and data from public sources. Users can query this…

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GermSAGE
Dataset

GermSAGE

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

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

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VuGEA
Dataset

VuGEA Vigna unguiculata Gene Expression Atlas

Allows users to detect transcript sequence. VuGEA is a web accessible database…

Allows users to detect transcript sequence. VuGEA is a web accessible database allowing to understand the molecular mechanisms. This online resource stores information about sequences and…

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…

OikoBase
Dataset

OikoBase

Provides information on expressed sequence tags (ESTs), transcripts, proteins…

Provides information on expressed sequence tags (ESTs), transcripts, proteins and genome-wide expression profiles for the urochordate Oikopleura dioica. OikoBase is a tiling array-based developmental…

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RSOY
Dataset

RSOY RIKEN Soybean Full-Length cDNA Database

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

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

Acytostelium…
Dataset

Acytostelium Gene Database

Provides gene models for Acytostelium subglobosum. Acytostelium Gene Database…

Provides gene models for Acytostelium subglobosum. Acytostelium Gene Database was constructed by combining three sets of gene models, transcript sequences thank to data from cDNA and EST analyses,…

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DBTGR
Dataset

DBTGR

Provides a comprehensive access to published information regarding regulation…

Provides a comprehensive access to published information regarding regulation of gene expression in tunicates. DBTGR is a database that mainly consists of a collection of experimentally characterized…

GPI
Dataset

GPI GenoPlante-Info

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

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

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PlantExpress
Dataset

PlantExpress

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

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

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MAGEST
Dataset

MAGEST Maboya Gene Expression patterns and Sequence Tags

Gathers information concerning maternal gene expression information for…

Gathers information concerning maternal gene expression information for Halocynthia roretzi. MAGEST is a database assisting in prediction of amino acid fragment sequences. This resource is dedicated…

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DRASTIC
Dataset

DRASTIC Database Resource for the Analysis of Signal Transduction in Cells

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

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

PRIMeLink
Dataset

PRIMeLink

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

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

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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…

XenMine
Dataset

XenMine

Provides a platform to query publicly available Xenopus genomic data. XenMine…

Provides a platform to query publicly available Xenopus genomic data. XenMine permits the access of user-friendly tools for further hypothesis generation. This online resource (i) recovers genomic…

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Allium TDB
Dataset

Allium TDB Allium Transcript DataBase

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

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

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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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TargetMine
Dataset

TargetMine

An integrated data warehouse based on the versatile InterMine framework, which…

An integrated data warehouse based on the versatile InterMine framework, which models biological entities (such as genes and proteins) as ‘objects’ and their relationships as ‘references’ to other…

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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…

MODEM
Dataset

MODEM Multi-Omics Data Envelopment and Mining in maize

A comprehensive database to collect maize multidimensional omics data including…

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

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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…

CAP
Dataset

CAP Citrus sinensis annotation project

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

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

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PAGER
Dataset

PAGER Pathways Annotated list and Gene-sets Electronic Repository

Contains Pathways, Annotated lists and Gene-signature (PAG) data from…

Contains Pathways, Annotated lists and Gene-signature (PAG) data from heterogeneous sources including ontology, pathway, omics, and public databases. PAGER is a comprehensive database infrastructure…

LiverWiki
Dataset

LiverWiki

Provides the research community with comprehensive liver-related data, as well…

Provides the research community with comprehensive liver-related data, as well as to allow the community to share their liver-related data flexibly and efficiently. LiverWiki integrates liver-related…

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ATGC…
Desktop

ATGC transcriptomics

Provides non-expert computer users with accessible biological data management…

Provides non-expert computer users with accessible biological data management and simple data integration, as it can be used without any prior knowledge of programming, database administration. ATGC…

PHYSCObase
Dataset

PHYSCObase

Provides Physcomitrella patens DNA sequences. PHYSCObase is an online resource…

Provides Physcomitrella patens DNA sequences. PHYSCObase is an online resource that gathers full-length enriched cDNA libraries of P. patens from auxin- and cytokinin-treated gametophytes, as well as…

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Sparus aurata…
Dataset

Sparus aurata transcriptomic database

Provides a high confidence of functional annotation for Sparus aurata by means…

Provides a high confidence of functional annotation for Sparus aurata by means of similarity searches, gene ontology (GO) terms and detailed insights on pathway analysis. Sparus aurata transcriptomic…

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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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SustainPine DB
Dataset

SustainPine DB

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

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

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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…

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FFGED
Dataset

FFGED Filamentous Fungal Gene Expression Database

Gathers comparisons of multiple experimental designs and correlations from…

Gathers comparisons of multiple experimental designs and correlations from different experimental results about filamentous fungi. FFGED allows users to share gene expression data, automatically…

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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C-It
Dataset

C-It

Permits to detect uncharacterized genes. C-It offers access to comprehensive…

Permits to detect uncharacterized genes. C-It offers access to comprehensive transcriptional profiles by combining microarray and Serial Analysis of Gene Expression (SAGE) data. It permits a…