modzs.gctx: a legacy LINCS L1000 dataset of differential expression signatures

2016-08-29T16:14:36Z (GMT) by LINCS L1000 Team
modzs.gctx contains a probe (rows) × signature (columns) matrix of differential expression z-scores from the LINCS L1000 project. The file uses a compressed binary encoding that can be read using the `cmap/l1ktools` drivers.

modzs.gctx is an input for the dhimmel/lincs repository, but is too large to be uploaded to GitHub. dhimmel/lincs extracts signatures from modzs.gctx to compute consensus signatures for perturbagens. Consensus signatures from dhimmel/lincs are available at as user-friendly TSV files. modzs.gctx is uploaded for reproducibility of dhimmel/lincs and longterm preservation. Users who need raw LINCS L1000 data are encouraged to use the Broad Production Data hosted on GEO rather than the legacy modzs.gctx file.

I (Daniel Himmelstein) originally retrieved modzs.gctx from the following path on the L1000 C3 Cloud ( /xchip/cogs/data/build/a2y13q1/modzs.gctx. However, the original hosting is no longer operating. Therefore, I am uploading this file to figshare.

I am choosing a CC BY license with the requirement to attribute the LINCS L1000 Team at the Broad Institute. However, users should note that the licensing of modzs.gctx is murky. The Broad license ( states that data files cannot be redistributed, which conflicts the NIH LINCS Data Release Policy. See for more information.