LINCS gene overexpression signatures
Transcriptional signatures of gene overexpression based on L1000 assay. The signatures consist of differential gene expressions and p-values for 978 Landmark Genes measured by L1000 assay. The signatures were created by aggregating (ie averaging) Level 4 data for biological replicates as defined by the signatures metadata. Only signatures designated to be reproducible and self-connected ("gold") by the Broad institute are represented.
"Differential expression values" are constructed as the moderated-Z (modZ) weighted averages of replicated Level 4 signatures, which are themselves calculated by comparing the log-2 gene expression levels to the "population control" (median of all measurements for the gene on the same plate), as described in the L1000 paper (see reference below). The P-Value of modZ is generated using lmFit and eBayes function in limma R package. It is a weighted T-test with a hypothesis that the weighted mean of level4 Z-scores equals to zero. P-values are not adjusted for multiple comparisons.
For more information about L1000, please refer to https://dx.doi.org/10.1016%2Fj.cell.2017.10.049