Snapshots of GREAM illustrating use of ‘analyze orthologous gene-set’ on human transcription factor genes and their mouse orthologs from Steinhoff et al [48].

<p>Snapshots of GREAM illustrating use of ‘analyze orthologous gene-set’ on human transcription factor genes and their mouse orthologs from Steinhoff et al [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133647#pone.0133647.ref048" target="_blank">48</a>].</p

Workflow of the GREAM web server.

<p>Workflow of the GREAM web server.</p

Snapshots of GREAM illustrating use of ‘analyze gene-set’ option on a gene-set from Tawa et al [46].

<p>Snapshots of GREAM illustrating use of ‘analyze gene-set’ option on a gene-set from Tawa et al [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133647#pone.0133647.ref046" target="_blank">46</a>].</p

The contribution of repeat elements to nuclear genomes in 17 mammalian species.

<p>The contribution of repeat elements to nuclear genomes in 17 mammalian species.</p

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

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

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

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