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The Expression Atlas allows searches by gene, splice variant, protein attribute, disease, treatment or organism part (cell types/tissues). Individual genes or gene sets can be searched for. All datasets in Expression Atlas have its metadata manually curated and its data analysed through standardised analysis pipelines.
EMAGE (e-Mouse Atlas of Gene Expression [note 1]) is an online biological database of gene expression data in the developing mouse (Mus musculus) embryo. [1] [2] [3] The data held in EMAGE is spatially annotated to a framework of 3D mouse embryo models produced by EMAP (e-Mouse Atlas Project).
The Immunological Genome Project (ImmGen) is a collaborative scientific research project that is currently building a gene-expression database for all characterized immune cells in the mouse. The overarching goal of the project is to computationally reconstruct the gene regulatory network in immune cells . [1]
Today the Biohub is launching Tabula Muris, an open-source database that details the biology of the average healthy mouse cell-by-cell, providing a potential gold mine for medical researchers.
Mouse Genome Informatics (MGI) is a free, online database and bioinformatics resource hosted by The Jackson Laboratory, with funding by the National Human Genome Research Institute (NHGRI), the National Cancer Institute (NCI), and the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD). [1]
Genevestigator is an application consisting of a gene expression database and tools to analyse the data. It exists in two versions, biomedical and plant, depending on the species of the underlying microarray and RNAseq as well as single-cell RNA-sequencing data.
Bgee is a database maintained by the SIB Swiss Institute of Bioinformatics and the University of Lausanne for retrieval and comparison of gene expression patterns from RNA-Seq, scRNA-Seq, Microarray, In situ hybridization and EST studies, across multiple animal species.
Mouse RNASeqMetaDB: a database and web server for navigating metadata of publicly available mouse RNA-Seq data sets. Rubus Rubus GDR RefTrans V1 - GDR Rubus RefTrans combines published RNA-Seq and EST data sets to create a reference transcriptome (RefTrans) for rubus and provides putative gene function identified by homology to known proteins.