Installation

1. Install MongoDB.

2. Download the two files listed under "Signatures" and place them into the MongoDB database folder.

3. Start mongod.

4. Open a mongo shell and switch to LINCS_L1000_CD db. The cpc2014 collection in the db stores all the processed LINCS L1000 data.

5. Optionally it is suggested to download and install Robomongo which provides a nice GUI to browse the data.

6. Refer to the MongoDB documentation for query specifications and drivers for different languages.

Genes' Meta-data

rid.json is an array of probe IDs mapping to the order of the genes in the processed data.

apiRowMeta.json is the meta-data information for each probe ID downloaded from the Broad API and can be used to convert probe IDs to gene symbols and determine if a probe ID is a landmark gene.

Signatures

MongoDB files are listed here:

• cpcd-gse70138.metadata.json
• cpcd-gse70138.bson (WARNING: This is 37.53 GB!)

Original Data

1.3 million gene expression profiles generated by the Broad Institute's LINCS Project team. The matrices are stored in a binary format called GCTX that provides efficient random access subsets of the data. Matlab and Python and R routines to parse GCTX files are available here.

• q2norm_n1328098x22268.gctx (110.28 GB): Gene expression profiles of both directly measured landmark transcripts plus imputed genes. Normalized using invariant set scaling followed by quantile normalization.
• modzs_n476251x22268.gctx (39.56 GB): Moderated z-scores, where replicate signatures are condensed using a weighted averaging procedure.

Contact

Please contact Avi Ma’ayan and Qiaonan Duan for comments, suggestions, and support: avi.maayan@mssm.edu, qiaonan.duan@mssm.edu.