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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 projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, MouseMine Project, MouseCyc Project at MGI
The Expression Atlas provides information on gene expression patterns under different biological conditions such as a gene knock out, a plant treated with a compound, or in a particular organism part or cell. It includes both microarray and RNA-seq data. The data is re-analysed in-house to detect interesting expression patterns under the conditions of the original experiment. There are two components to the Expression Atlas, the Baseline Atlas and the Differential Atlas. The Baseline Atlas displays information about which gene products are present (and at what abundance) in "normal" conditions (e.g. tissue, cell type). It aims to answer questions such as "which genes are specifically expressed in human kidney?". This component of the Expression Atlas consists of highly-curated and quality-checked RNA-seq experiments from ArrayExpress. It has data for many different animal and plant species. New experiments are added as they become available. The Differential Atlas allows users to identify genes that are up- or down-regulated in a wide variety of different experimental conditions such as yeast mutants, cadmium treated plants, cystic fibrosis or the effect on gene expression of mind-body practice. Both microarray and RNA-seq experiments are included in the Differential Atlas. Experiments are selected from ArrayExpress and groups of samples are manually identified for comparison e.g. those with wild type genotype compared to those with a gene knock out. Each experiment is processed through our in-house differential expression statistical analysis pipeline to identify genes with a high probability of differential expression.
ArrayExpress is one of the major international repositories for high-throughput functional genomics data from both microarray and high-throughput sequencing studies, many of which are supported by peer-reviewed publications. Data sets are either submitted directly to ArrayExpress and curated by a team of specialist biological curators, or are imported systematically from the NCBI Gene Expression Omnibus database on a weekly basis. Data is collected to MIAME and MINSEQE standards.
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The Taenia solium genome project is a whole genome sequencing project of the parasite Taenia solium, the causal agent of human and porcine cysticercosis; a disease that is still a public health problem of relevance in Mexico. It is being carried out by a consortium of scientists belonging to diverse institutions of the Universidad Nacional Autónoma de México (UNAM, the National Autonomous University of Mexico).
This site provides access to complete, annotated genomes from bacteria and archaea (present in the European Nucleotide Archive) through the Ensembl graphical user interface (genome browser). Ensembl Bacteria contains genomes from annotated INSDC records that are loaded into Ensembl multi-species databases, using the INSDC annotation import pipeline.
The NCBI Trace Archive is a permanent repository of DNA sequence chromatograms (traces), base calls, and quality estimates for single-pass reads from various large-scale sequencing projects. The Trace Archive serves as the repository of sequencing data from gel/capillary platforms such as Applied Biosystems ABI 3730®. The Sequence Read Archive (SRA) stores sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome Analyzer®, Applied Biosystems SOLiD® System, Helicos Heliscope®, and others. The Trace Assembly Archive stores pairwise alignment and multiple alignment of sequencing reads, linking basic trace data with finished genomic sequence.