Current gene co-expression databases do not support cell-specific analysis because the gene expression matrices for co-expression analysis are from multiple tissues or a mix of cells and tissues. The overall correlation in gene expression identified ...

Gemma is a database for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles. Gemma contains data from thousands of public studies, referencing thousands of published papers. ...

The Gene Expression Database (GXD) is a community resource for gene expression information from the laboratory mouse. GXD stores and integrates different types of expression data and makes these data freely available in formats appropriate for compre ...

ViBrism DB is a database for anatomical gene expression maps and topological co-expression network graphs created with original techniques of microtomy-based gene expression measurements, Transcriptome Tomography. The DB is equipped with a WebGL-base ...

Gene expression data sorted into two groups: expressed and not expressed genes

The e-Mouse Atlas of Gene Expression (EMAGE) is a freely available database of in situ gene expression patterns that allows users to perform online queries of mouse developmental gene expression. EMAGE is unique in providing both text-based descripti ...

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Gene expression and neuroanatomical data.

The GENSAT (Gene Expression Nervous System ATlas) database captures information on gene expression in mouse brain at several developmental ages. The project began at Rockefeller University in New York under the direction of Nat Heintz, and has since ...

ALEXA is a microarray design platform for 'alternative expression analysis'. This platform facilitates the design of expression arrays for analysis of mRNA isoforms generated from a single locus by the use of alternative transcription initiation, spl ...

Gene expression patterns in the mouse

microRNA Expression and Sequence Analysis Database

Database of Gene Expression in Mouse Haematopoiesis

SAGEmap provides a tool for performing statistical tests designed specifically for differential-type analyses of SAGE (Serial Analysis of Gene Expression) data. The data include SAGE libraries generated by individual labs as well as those generated b ...

Database for cross species expression pattern comparisons

This database enables the reliable identification of an individual Interferon Regulated Gene (IRG) or IRG signatures from high-throughput data sets (i.e. microarray, proteomic data etc.). It also assists in identifying regulatory elements, chromosoma ...

Expression and epigenetic data for mouse hematopoietic cell types

The explosion in the number of functional genomic datasets generated with tools such as DNA microarrays has created a critical need for resources that facilitate the interpretation of large-scale biological data. SOURCE is a web-based database that b ...

Autosomal monoallelic expression (MAE) refers to mitotically stable, epigenetically controlled allele-specific expression of autosomal genes, with the initial non-predetermined ('random') choice of thetranscriptional activity of the two alleles maint ...

Gene expression data on mouse embryos

A comprehensive database for decoding the regulatory transcription co-factors in human and mouse.

CAGE Basic and Analysis Databases store an original resource produced by CAGE (cap-analysis gene expression; 1), which measures expression levels of transcription starting sites (TSS) by sequencing large amounts of transcript 5'-ends, termed CAGE tag ...

The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) provides data and tools to facilitate research on the GenitoUrinary (GU) tract for the scientific and medical community. In addition to current GUDMAP data, this resource incorporates d ...

GeneNetwork is a group of linked data sets and tools used to study complex networks of genes, molecules, and higher order gene function and phenotypes. GeneNetwork combines more than 25 years of legacy data generated by hundreds of scientists togethe ...

A curated RNA-seq database of palmitoylating and de-palmitoylating enzyme expression in the mouse brain.

PrimerBank is a public resource for PCR primers. These primers are designed for gene expression detection or quantification (real-time PCR). PrimerBank contains over 306,800 primers covering most known human and mouse genes. There are several ways to ...

TF-target relationsips inferred from single cell and bulk RNA-seq datasets

The Mammalian Transcriptomic Database (MTD) was created to store information on mammalian transcriptomes. The MTD allows browsing of genes based on their neighboring genomic coordinates or joint KEGG pathway and provides expression information on exo ...

The cisRED database holds conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations. Sequence inputs include low-coverage genome sequence data and ENCODE data.

Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. This molecular compendium, fully accessible via a searchable web-browser interface, serves as a reliable reference of the expressed tis ...

Stemformatics is an established gene expression data portal containing over 420 public gene expression datasets derived from microarray, RNA sequencing and single cell profiling technologies. Developed for the stem cell community, it has a major focu ...

With the rapid progress of the HLPP (Human Liver Proteome Project), a massive quantity of liver proteome expression profile data has been generated. To manage the valuable resource effectively and present it for researchers, a web-based database of l ...

EpiFactors is a web-accessible database that provides broad information about human proteins and complexes involved in epigenetic regulation. It also lists corresponding genes and their expression levels in several samples, in particular 458 human pr ...

T1DBase focuses on two research areas in type 1 diabetes (T1D): the genetics of T1D susceptibility and beta cell biology.

Spatial organization of metabolic reactions in the mouse

ABA Adult Mouse Brain is a standardised collection of the expression patterns of thousands of adult brain genes. This resource can be used for a vast array of research on brain organisation and function. There are lighter versions of this ontology th ...

AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-align ...

SEA (Super-Enhancer Archive) is a web-based comprehensive resource focusing on the collection, storage and online analysis of super-enhancers. It focuses on integrating super-enhancers in multiple species and annotating their potential roles in the r ...

FANTOM (Functional ANnoTation Of the Mammalian genome) is a worldwide collaborative project aiming at identifying all functional elements in mammalian genomes.

Many animal species present sex differences. Sex-associated genes (SAGs), which have female-biased or male-biased expression, have major influences on the remarkable sex differences in important traits such as growth, reproduction, disease resistance ...

A manually curated database of human and mouse essential lncRNA genes.

International mouse Gene Trap Consortium data

syngeneic mouse tumor database to model tumor immunity and immunotherapy response.

The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.

NONCODE is a database of noncoding RNAs (except tRNAs and rRNAs), including long noncoding (lnc) RNAs. Information contained within the database includes human lncRNA–disease relationships and single nucleotide polymorphism-lncRNA–disease relationshi ...

smiRNAdb is a database containing expression information for human, mouse, rat, zebrafish, worm and fruitfly small RNAs (mostly miRNAs).

Despite the known existence of distant-acting cis-regulatory elements in the human genome, only a small fraction of these elements has been identified and experimentally characterized in vivo. This paucity of enhancer collections with defined activit ...

The Resource of Asian Primary Immunodeficiency Diseases (RAPID) is a repository of molecular alterations in primary immunodeficiency diseases (PID). It hosts information on sequence variations and expression at the mRNA and protein levels of all gene ...

The ESTs and mRNAs from GenBank have been used to identify chimeric RNAs of two or more different genes. By analyzing thousands of chimeric ESTs by RNA sequencing, we found that the expression level of chimeric ESTs is generally low and they are high ...

User-editable lineage maps illustrating both endogenous development and the directed differentiation of human and mouse embryonic stem cells.

lncRNASNP is an integrated database of SNPs in lncRNAs and their potential functions in human and mouse. It integrated several public databases and tools, including LNCipedia, NONCODE, dbSNP, miRBase, TCGA and so on. Its aim is to provide information ...

MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.

The Array Clone Information Database (ACID) is a searchable resource for information about human, mouse, and rat cDNA clones. Each clone contains information about the assigned UniGene cluster(s), location in the full-length transcript, assigned gene ...

A database and web application for analyzing embryonic stem cells differentiation process on mouse model. The data is collected by FunGenES consortium and organized into six clusters to facilitate data mining.

The NIDDK Information Network provides access to large pools of data relevant to the mission of NIDDK. The dkNET portal contains information about research resources such as antibodies, vectors and mouse strains, data, protocols, and literature.

A database of integrated mouse data from MGI, powered by InterMine. MouseMine is member of InterMOD, a consortium of model organism databases dedicated to making cross-species data analysis easier through ongoing coordination and collaborative system ...

Genome assemblies and aligned annotations for a wide range of vertebrates and model organisms, along with an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic datasets.

The e-Mouse Atlas (EMA) is a detailed model of the developing mouse. Its purpose is not only to provide information about the shape, gross anatomy and detailed histological structure of the mouse, but also to provide a framework into which informatio ...