Please cite the following paper: Zhou et al., Nature Communications 2019, 10(1):1523.. We will really appreciate if you also show our URL [https://metascape.org] in your text. Please avoid citing [https://metascape.org/gp/index.html#/main/step1], as that URL may be changed in the future. If you like Metascape, help us spread the word. (Note: please do not cite Tripathi 2015 anymore, it was meant to be a placeholder.)

On the Analysis Report page, Download the Zip package that contains high-quality .pdf files. High-quality Circos plots are available in .svg format. Heatmap file .cdt can be opened in JTreeView. The enrichment network .cys file can be opened in Cytoscape. Files such as .pdf and .svg can be edited with Adobe Illustrator. You may be interested in checking out how others use Metascape visualizations in their publications, as listed under the menu About > Citations.

Entrez Gene ID, RefSeq (RNA and Proteins), Gene Symbol and aliases, Ensembl (Gene, Transcript, Protein), UCSC, UniProt.

Major model organisms and request-driven. We currently support ten species: H. sapiens, M. musculus, R. norvegicus, D. rerio, D. melanogaster, C. elegans, S. cerevisiae, A. thaliana, S. pombe, and P. falciparum. Statisitcs shows there is a diminishing usage of new species, so we do not plan to support ALL species. Nevertheless, we plan to support additional species nominated by users from time to time. By default, all input gene identifiers are converted into their human orthologs for annotation and enrichment analysis, as the knowledge base for the humans is the most comprehensive, however, you can choose other organisms for analysis purposes as well.

The Metascape team commits to update data sources frequently. We have been maintaining a quarterly database update using a semi-automatic workflow. Metascape always uses the latest data content it has; it does not take snapshots of older databases.

Yes. Metascape takes multiple gene lists as input (using file upload), if a gene list is named "_BACKGROUND", it will be automatically recognized and used as the background for enrichment analysis (you must check the "multiple gen lists" box). Alternatively, you may choose "Custom Analysis" and upload your background gene list, before you trigger the "Enrichment Analysis". Here is a blog discussing the background gene list in detail.

Given there are only 20,000 genes in typical genomes, a reasonable-quality gene list should not contain thousands of genes. The signal of driver pathways will be too weak to detect. It is not the more genes the better when it comes to function enrichment analysis; our limit of 3000 is more than generous. In our own research, we typically limit the gene lists to under 300 genes. Please try to trim down your gene lists to get more meaningful results.

No. Express Analysis is designed to be one-click. Custom Analysis allows us to control annotation fields and more.

There is no API to automate web-based Metascape submission. The backend server is unable to handle the number of anticipated API requests, due to most Metascape analyses being very resource intensive. We would like to reserve the Metascape server for biologists.
We currently provide a powerful Docker-based offline version called Metascape for Bioinformaticians (MSBio) [more ...]. MSBio enables bioinformaticians to perform an unlimited amount of offline analyses using users' own hardware. A commercial license is required for non-academic users, which unlocks the capability of adding a proprietary knowlegebase.

Metascape tracks the standard site usage data (IP, timestamp, URL visited). It keeps users upload files for up to maximum 3 days in order to provide analysis reports and download support by the owner later on. User files are automatically deleted upon expiration. We do not peek into your data files and have no plan to do so in the future. We already have enough challenges in understanding our own data, why bother with yours without biological context :-). Metascape does not receive private funding, nevertheless, corporate users are advised to check with their legal teams before using Metascape.org. You may also contact us to obtain a commercial license for "Metascape for Bioinformaticians", which enables you to run a command-line version of Metascape in-house (no data transmission to the Internet).