ArticleBioinformatics (Oxford, England)2019
The GCTx format and cmap{Py, R, M, J} packages: resources for optimized storage and integrated traversal of annotated dense matrices.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.
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Who cites it
31 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Genome-wide meta-analyses of non-response to antidepressants provide insights into underlying molecular genetics and suggest potential pharmacotherapies.Molecular psychiatry · 2026Pooled it
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- Transcriptomic profiling of chlorogenic acid and taurine treatment in human skin cells provides insights into cellular senescence mechanisms.Frontiers in molecular biosciences · 2026Article
- Reference-based chemical-genetic interaction profiling to elucidate small molecule mechanism of action in Mycobacterium tuberculosis.Nature communications · 2025Article
- Adaptive multi-view learning method for enhanced drug repurposing using chemical-induced transcriptional profiles, knowledge graphs, and large language models.Journal of pharmaceutical analysis · 2025Article
- Establishment of interpretable cytotoxicity prediction models using machine learning analysis of transcriptome features.Acta pharmaceutica Sinica. B · 2025Article
- Next-generation precision medicine for suicidality prevention.Translational psychiatry · 2024Article
- In-Silico Identification of Novel Pharmacological Synergisms: The Trabectedin Case.International journal of molecular sciences · 2024Article
- Leveraging metabolic modeling and machine learning to uncover modulators of quiescence depth.PNAS nexus · 2024Article
- Drug repositioning targeting glutaminase reveals drug candidates for the treatment of Alzheimer's disease patients.Journal of translational medicine · 2023Article
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- The clinical and bioinformatics analysis for the role of antihypertension drugs on mortality among patients with hypertension hospitalized with COVID-19.Journal of medical virology · 2022Article
- Getting Started with LINCS Datasets and Tools.Current protocols · 2022Article
- Drug target inference by mining transcriptional data using a novel graph convolutional network framework.Protein & cell · 2022Article
- Drug repurposing candidates to treat core symptoms in autism spectrum disorder.Frontiers in pharmacology · 2022Article
- Artificial intelligence unifies knowledge and actions in drug repositioning.Emerging topics in life sciences · 2021Review
- Side effect prediction based on drug-induced gene expression profiles and random forest with iterative feature selection.The pharmacogenomics journal · 2021Article
- Noncanonical open reading frames encode functional proteins essential for cancer cell survival.Nature biotechnology · 2021Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
motivationFacilitated 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.
resultsWe 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.