The Brief History of Metascape Since 2014

Five years ago (2014), we were looking for a gene-list analysis resource to recommend to biologists in our own research organizations. DAVID stood out in terms of functionality and usability, however, we noticed DAVID did not appear to be maintained. Its databases were over four years old (eventually became six-year old) and questions on user forum were unanswered. More than 10% of genes in our typical submissions were not recognized and thus ignored. See our earlier analysis here.

In the meantime we had delivered a number of high-profile multi-OMICs publications ourselves. Despite each study required specific bioinformatics analyses, especially in terms of calling gene candidates, we nevertheless saw a pattern emerged in the down-stream gene list analysis. Some analysis approaches and visualization styles were found particularly helpful in explaining the biological stories behind datasets. These analyses and visualizations were not easy to program even by seasoned bioinformaticians like ourselves, let alone experimental biologists.

The combination of these two factors led us to start the Metascape journey aiming for providing a resource that would be truly biologist friendly. Many bioinformatics portals have emerged, disappeared, or improved over the past five years, nevertheless, biologist-friendly gene-list analysis web tools remain an unmet need in our opinion (see our survey of 25 gene-list analysis resources). Some most popular tools, such as DAVID, are more than two-year old. Many tools only provide pathway enrichment analysis without the data-driven interactome analysis component. Few tools can consider multiple gene lists and allow cross dataset meta analysis. Therefore, all the motivations for the creation of Metascape remain present even today.

The Metascape team has an interesting composition: bioinformaticians such as Benner’s lab at UCSD developed a popular NGS analysis package called Homer before; Chanda’s lab at SBP generates immense amount of OMICs datasets; Volunteers from GNF have over a decade of individual experience in developing user-friendly tools in a pharmaceutical service environment. This formulation and a year of coordinated efforts led to the beta-release of the Metascape web site, which was announced at a talk at UCSD on Oct 8, 2015 (reported here). As there was no official publication on the Metascape tool itself, we had to use our first Metascape application paper published on Dec 9, 2015 as a place holder for citation purpose.

Metascape user base has been slowly growing through word of mouth and occasionally it was discovered and recommended by social media. With the growing number of published studies using Metascape and its attractive visualizations, new biologists discover this valuable resource every day. After five years of patience and hard work, the Metascape portal itself is now published by Nature Communication on April 3, 2019 (link).

On this special day, we at Metascape are thankful to our user community members for their valuable bug reports, suggestions, and referrals. We also thank NIH NIAID for fundings that has supported the UCSD and SBP labs, as well as the hardware infrastructure enabling this journey. We are looking forward to serving the broader biomedical community by continue to provide a free, fresh, and easy system-level analysis tool for OMICs datasets.

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