“We designed FITdb to be extremely user-friendly,” says Reina-Campos. “This is a very intuitive and fast platform for immunologists aiming to understand the immune cells, genomes, and proteins they are working with.”
With FITdb, researchers can enter the name of a gene and learn how its functional perturbation affects immune cell function. Or scientists can go in the opposite direction, exploring which genes or regulators may make promising targets for manipulating immune cells to better fight cancers or even viruses.
FITdb currently integrates data from 43 independent functional genetics screens, including 31 bulk and 12 single-cell screens, spanning 20,696 mouse genes and 22,293 human genes across 199 immune cell types and cell states across 29 conditions.
“Now you don’t need to look through hundreds of papers and comb through the supplementary files to find that information,” says Reina-Campos.
Reina and his LJI colleagues recently shared their work in Nucleic Acids Research. They highlight the FITdb tools “Compare MyGeneSet,” which reveals overlaps between user-defined gene lists and functional gene sets in FITdb, and “Compare MyScreen,” which lets scientists directly compare user-generated screening data with existing datasets.
FITdb users can also generate gene-centric visualizations and expand data for individual screens. “Then if you find something interesting, you read more and dig even deeper,” says Reina-Campos. For example, researchers in drug development can use FITdb to investigate whether potential drug molecules cause off-target effects in specific immune cell types.
Researchers in the Reina Lab recently used FITdb to better understand the functional effects and genetic regulators that direct “transporter” proteins called LAT and LAT2. FITdb allowed the team to examine, compare, and visualize data across complementary CRISPR datasets.
By querying FITdb, the researchers identified several regulators of LAT and LAT2 expression, including two unique inhibitors and two unique promoters. This finding gave the team a deeper understanding of the factors at play in T cell rest and activation.
“We wanted to know what others had found,” says Reina. “This might be a transporter in my setting, but it might be something very important for the cell in another setting.”
The launch of FITdb was made possible through LJI start-up funding to the Reina Lab and through the support of the LJI Information Technology Department. Reina-Campos credits LJI VP of Information Technology and Core Services Michael Scarpelli, LJI IT Director Michael Talbott, and LJI Professor Bjoern Peters, Ph.D., for their support and guidance during FITdb’s development.
Reina-Campus also worked closely with LJI Full-Stack Developer Kevin Kim to develop FITdb and organize a wealth of screening data.
“It was important to us that FITdb be extremely user-friendly with no coding needs—and you don’t need a long tutorial,” says Reina-Campos. “In the last calendar year, nearly 10,000 people have visited FITdb. This is huge, because this is just the beginning for FITdb.”
