About the HMS LINCS Center

The Harvard Medical School (HMS) LINCS Center is part of the NIH Library of Integrated Network-based Cellular Signatures Program. The goal of this program is to collect and disseminate the data and analytical tools needed to understand how human cells respond to perturbations created by exposure to drugs, changes in the environment and mutation (“perturbagens”). LINCS is supported by the NIH Common Fund and the HMS program is funded by NIH grant U54 HG006097.

Cellular response to growth factors and kinase inhibitors

We focus on (i) small molecule kinase inhibitors, which are a leading class of therapeutic agents for treatment of cancer, autoimmune and other diseases and (ii) growth factors and inflammatory cytokines. Overall, we are profiling responses of ~100 cell lines/cell types to over 300 inhibitors. We also collaborate with the MGH Center for Molecular Therapeutics.

Assays

We measure perturbagen responses at multiple doses, monitored at multiple time points using a range of biochemical, imaging and functional assays. The Center also develops new algorithms for large-scale analysis of drug response.

Access to data, models and algorithms

HMS LINCS provides access to data through explore, search and programmatic interfaces. This data comprises multiplex biochemical, proteomic and imaging data on the responses of human cancer and primary cells to perturbagens that include naturally occurring ligands and small molecules drugs. We collaborate with the Broad LINCS Center on the collection and analysis of gene expression data.

Explore and browse functions provide tools for analyzing specific data sets using different algorithms and visualization tools (these tools are themselves freely available via our tools and software page). The analyses we provide are by no means the only or optimal way of using LINCS data, but they do highlight some obvious applications. As part of the explore functionality, we make it possible to browse responses by cell type or perturbagen. Further information on LINCS publications is also provided, with interactive versions of key figures and direct access to relevant primary data.

Search functions make it possible to search the LINCS Database for specific datasets, cell types or perturbagens. Semantic search is by far the best way to query across LINCS data and we are working with the Miami LINCS Center on the LINCS Information FramEwork (LIFE) which supports effective querying and reasoning across complex data sets.

Programmatic interfaces make it possible to download LINCS data in large batches for further analysis.