MGEx-Udb: A Mammalian Uterus Database for Expression-Based Cataloguing of Genes across Conditions, Including Endometriosis and Cervical Cancer

Gene expression profiling of uterus tissue has been performed in various contexts, but a significant amount of the data remains underutilized as it is not covered by the existing general resources.). The database can be queried with gene names/IDs, sub-tissue locations, as well as various conditions such as the cervical cancer, endometrial cycles and disorders, and experimental treatments. Accordingly, the output would be a) transcribed and dormant genes listed for the queried condition/location, or b) expression profile of the gene of interest in various uterine conditions. The results also include the reliability score for the expression status of each gene. MGEx-Udb also provides information related to Gene Ontology annotations, protein-protein interactions, transcripts, promoters, and expression status by other sequencing techniques, and facilitates various other types of analysis of the individual genes or co-expressed gene clusters.In brief, MGEx-Udb enables easy cataloguing of co-expressed genes and also facilitates bio-marker discovery for various uterine conditions

Schematic representation of MGEx-Udb.

<p>The figure represents the data collection (top portion), architecture (central portion) and operation (bottom portion) of the database.</p

Example hierarchy of the conditions and sub-conditions.

<p>An example <i>(“stage IIA non-keratinizing squamous cell cervical carcinoma”)</i> hierarchy of the conditions and sub-conditions, for which data have been collected, and drop-down options provided in the query and upload pages of MGEx-Udb. Currently the database allows up to four levels of the hierarchy to query.</p

Number of datasets

<p>(<b>and studies</b>) <b>in MGEx-Udb corresponding to various physiological and pathological uterine conditions.</b> ‘Others’ represent post-parturition, genetic-ablation, artificial insemination and embryo implantation. Studies considering tissues that are used as controls but may not be absolutely ‘normal’ have been grouped in <i>‘may be normal’</i> category (examples: “normal tissue adjacent to tumor/cancer tissue”, “vehicle-treated”).</p

Datasets

<p>(<b>with gene count</b>) <b>collected from various sources.</b> In case of “PubMed & GEO” and “PubMed & ArrayExpress”, smaller gene lists came from validation experiments and were collected from PubMed, while raw/processed data were always collected from the repositories (GEO/ArrayExpress).</p

Source of data across various mammalian species in MGEx-Udb.

<p>Other species include cow and pig. Among the data collected from GEO or “PubMed & GEO”, 85% of the studies were also present in ArrayExpress, even though this is not indicated in the figure.</p