Abstract

We previously piloted the concept of a Connectivity Map (CMap), whereby genes, drugs and disease states are connected by virtue of common gene-expression signatures. Here, we report more than a 1,000-fold scale-up of the CMap as part of the NIH LINCS Consortium, made possible by a new, low-cost, high throughput reduced representation expression profiling method that we term L1000. We show that L1000 is highly reproducible, comparable to RNA sequencing, and suitable for computational inference of the expression levels of 81% of non-measured transcripts. We further show that the expanded CMap can be used to discover mechanism of action of small molecules, functionally annotate genetic variants of disease genes, and inform clinical trials. The 1.3 million L1000 profiles described here, as well as tools for their analysis, are available at https://clue.io.\n\nHIGHLIGHTSO_LIA new gene expression profiling method, L1000, dramatically lowers cost\nC_LIO_LIThe Connectivity Map database now includes 1.3 million publicly accessible L1000 perturbational profiles\nC_LIO_LIThis expanded Connectivity Map facilitates discovery of small molecule mechanism of action and functional annotation of genetic variants\nC_LIO_LIThe work establishes feasibility and utility of a truly comprehensive Connectivity Map\nC_LI