Evaluation of RNAi and CRISPR technologies by large-scale gene expression profiling in the Connectivity Map
Fig 4
Gene expression analysis of CRISPR-Cas9 reagents.
(A) Analysis of landmark transcript reduction, comparing CRISPR and RNAi for genes targeted by both technologies. The dotted line (blue) is a null distribution of the set of all z-scores. Both technologies show significant down-regulation of directly measured target transcripts. (B) As in Fig 2E, comparison of holdout results either retaining or removing PC1 for the CRISPR dataset. (C) Holdout analysis for genes assayed by CRISPR (left) and RNAi (right). Genes are shown for RNAi only if they were also assayed by CRISPR; furthermore, because holdout analysis requires at least 6 independent reagents, not all of the genes assayed by CRISPR have sufficient coverage by RNAi; missing values in some cell lines are indicated by black boxes. Smaller q-values (green) indicate greater statistical significance, i.e., that the CGS is valid. See S6 Data. Cas9, CRISPR-associated 9; CGS, consensus gene signature; CRISPR, clustered regularly interspaced short palindromic repeat; PC1, first principal component; RNAi, RNA interference.
doi: https://doi.org/10.1371/journal.pbio.2003213.g004