dbMAE – the database of autosomal monoallelic expression

Recently, data on ‘random’ autosomal monoallelic expression has become available for the entire genome in multiple human and mouse tissues and cell types, creating a need for better access and dissemination. The database of autosomal monoallelic expression (dbMAE) 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 well as indirect identification, based on a specific chromatin signature present in MAE gene bodies.

Currently, dbMAE contains transcriptome-wide chromatin identification calls for 8 human and 21 mouse tissues, and describes over 16 000 murine and ∼700 human cases of directly measured biased expression, compiled from allele-specific RNA-seq and genotyping array data. All data are manually curated.

To ensure cross-publication uniformity, the developers performed re-analysis of transcriptome-wide RNA-seq data using the same pipeline. Data are accessed through an interface that allows for basic and advanced searches; all source references, including raw data, are clearly described and hyperlinked. This ensures the utility of the resource as an initial screening tool for those interested in investigating the role of monoallelic expression in their specific genes and tissues of interest.

rna-seq

Results of queries to the databases can be examined to greater specificity by clicking on fields of interest. Shown are data panels from pages resulting from simple query by gene symbol ‘Msx2’. Gene page: Indicates overall gene status in the organisms currently in the database. ‘Monoallelic’ indicates that there is some evidence for monoallelic expression in at least one tissue. Tissue page: Accessed upon clicking one of the entries in the ‘gene page’; indicates inferred and experimental status of the gene in the selected organism in each tissue. Headers can be clicked to sort alphabetically. Clicking the ‘Download as csv’ button results in a csv file with the data as presented on the page. Data page: Accessed upon clicking one of the entries in the ‘tissue page’. The chromatin mark section shows quantile rank values for the chromatin marks H3K27me3 and H3K36me3 in the selected tissue for the query gene. The experimental data section shows clonal cell lines derived from the tissue in question, and whether the query gene was positively called (“1”) or undetermined (“0”) to be either biased or unbiased in each line.

Availabilityhttps://mae.hms.harvard.edu

Savova V, Patsenker J, Vigneau S, Gimelbrant AA. (2015) dbMAE: the database of autosomal monoallelic expression. Nucleic Acids Res [Epub ahead of print]. [article]

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