Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2019 Apr 15;35(8):1427-1429.
doi: 10.1093/bioinformatics/bty784.

The GCTx format and cmap{Py, R, M, J} packages: resources for optimized storage and integrated traversal of annotated dense matrices

Oana M Enache  1 , David L Lahr  1 , Ted E Natoli  1 , Lev Litichevskiy  1 , David Wadden  2 , Corey Flynn  3 , Joshua Gould  1 , Jacob K Asiedu  1 , Rajiv Narayan  1 , Aravind Subramanian  1
Affiliations

The GCTx format and cmap{Py, R, M, J} packages: resources for optimized storage and integrated traversal of annotated dense matrices

Oana M Enache et al. Bioinformatics. .

Abstract

Motivation: Facilitated by technological improvements, pharmacologic and genetic perturbational datasets have grown in recent years to include millions of experiments. Sharing and publicly distributing these diverse data creates many opportunities for discovery, but in recent years the unprecedented size of data generated and its complex associated metadata have also created data storage and integration challenges.

Results: We present the GCTx file format and a suite of open-source packages for the efficient storage, serialization and analysis of dense two-dimensional matrices. We have extensively used the format in the Connectivity Map to assemble and share massive datasets currently comprising 1.3 million experiments, and we anticipate that the format's generalizability, paired with code libraries that we provide, will lower barriers for integrated cross-assay analysis and algorithm development.

Availability and implementation: Software packages (available in Python, R, Matlab and Java) are freely available at https://github.com/cmap. Additional instructions, tutorials and datasets are available at clue.io/code.

Supplementary information: Supplementary data are available at Bioinformatics online.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
(a) Schematic of a GCTx file. (b) Parse times are faster for GCTx files compared with text-based files; more details in Supplementary Material S3
See this image and copyright information in PMC

References

    1. Abelin J.G. et al. (2016) Reduced-representation phosphosignatures measured by quantitative targeted MS capture cellular states and enable large-scale comparison of drug-induced phenotypes. Mol. Cell. Proteomics, 15, 1622–1641. - PMC - PubMed
    1. Bray M.-A. et al. (2016) Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes. Nat. Protoc., 11, 1757–1774. - PMC - PubMed
    1. Corsello S.M. et al. (2017) The Drug Repurposing Hub: a next-generation drug library and information resource. Nat. Med., 23, 405–408. - PMC - PubMed
    1. Eisen M.B. et al. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA, 95, 14863–14868. - PMC - PubMed
    1. Hughes T.R. et al. (2000) Functional discovery via a compendium of expression profiles. Cell, 102, 109–126. - PubMed

Publication types