How perturbagen connectivity analysis is performed in iLINCS

The perturbagen connectivity analysis compares the query signature to all signatures for a given perturbagen as a group, thus extending the pair-wise connectivity analysis to account for diversity of responses in different cellular contexts. This is accomplished by performing the enrichment analysis of individual connectivity scores between the query signature and set of all L1000 signatures of a perturbagen (for all cell lines, time points and concentrations). The analysis establishes whether the connectivity scores as a set are “unusually” high in comparison to all positive and all negative connectivity scores between the query signature and all iLINCS signatures of the same type based on the Random Set analysis.