%0 Generic %A Team, LINCS L1000 %D 2016 %T modzs.gctx: a legacy LINCS L1000 dataset of differential expression signatures %U https://figshare.com/articles/dataset/modzs_gctx_a_legacy_LINCS_L1000_dataset_of_differential_expression_signatures/3759129 %R 10.6084/m9.figshare.3759129.v1 %2 https://ndownloader.figshare.com/files/5905200 %K LINCS %K L1000 %K modzs %K signature %K probe %K Rephetio %K Gene Expression (incl. Microarray and other genome-wide approaches) %K Bioinformatics %K Computational Biology %K Genomics %K Systems Biology %X 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 https://doi.org/bp22 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 (c3.lincscloud.org): /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 (https://git.io/vieCF) states that data files cannot be redistributed, which conflicts the NIH LINCS Data Release Policy. See https://doi.org/bfmn for more information.
%I figshare