GeneQuery - веб-сервер для генерации биологических гипотез на основании транскрипции.

Current version: https://artyomovlab.wustl.edu/genequery/

New (alpha)-version: http://genome.ifmo.ru/genequery/

GeneQuery is an expression-based phenotype searching engine for mouse and human. Unlike other tools, like DAVID or MsigDB, GeneQuery does not use manually curated gene sets associated with a particular pathway or perturbation. Instead, we use WGCNA clustering to obtain a vast database of co-expression clusters from available GEO microarray experiments. The data used span ~ 3,000 mouse and ~ 3,800 human data series that included 8-100 samples, thus covering a substantial fraction (30% for mouse, 17% for human) of all published microarray expression profiling experiments. We believe that this approach finds more meaningful results and better accounts for biological complexity and variation.

To start using GeneQuery, all you need is a list of genes that you have found to be significant in your experiment. It can be a list of differentially expressed genes (we suggest using up- and down-regulated signatures separately), or candidate regulated genes from a DNase-Seq or a ChIP-Seq experiment. GeneQuery accepts the following types of gene IDs: Entrez, universal gene symbol (HGNC/MGNC), RefSeq, and Ensembl. It is also natively supports a search with orthologous genes – that is, you can search a list of human genes against the mouse database, and still get meaningful results. In fact, we encourage you to try it. This feature only works on lists of universal gene symbols.