ArticleScientific reports2017
Elucidating the modes of action for bioactive compounds in a cell-specific manner by large-scale chemically-induced transcriptomics.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 83 citations in OpenAlex.
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- SIMD: Synergistic integration mutualistic platform based on single-cell and proteotranscriptomics for drug repositioning.NPJ breast cancer · 2025Article
- TheInternational journal of molecular sciences · 2025Review
- Exploiting similarity in drug molecular effects for drug repurposing.Human genomics · 2025Article
- Drug Search and Design Considering Cell Specificity of Chemically Induced Gene Expression Profiles for Disease-Associated Tissues.Molecular informatics · 2025Article
- Application of GWAS summary data and drug-induced gene expression profiles of neural progenitor cells in psychiatric drug prioritization analysis.Molecular psychiatry · 2025Article
- Merging multi-omics with proteome integral solubility alteration unveils antibiotic mode of action.eLife · 2024Article
- Deep learning of multimodal networks with topological regularization for drug repositioning.Journal of cheminformatics · 2024Article
- AutoTransOP: translating omics signatures without orthologue requirements using deep learning.NPJ systems biology and applications · 2024Article
- A polo-like kinase inhibitor identified by computational repositioning attenuates pulmonary fibrosis.Respiratory research · 2023Article
- Benchmarking causal reasoning algorithms for gene expression-based compound mechanism of action analysis.BMC bioinformatics · 2023Article
- Article
- Analyses of Transcriptomics Cell Signalling for Pre-Screening Applications in the Integrated Approach for Testing and Assessment of Non-Genotoxic Carcinogens.International journal of molecular sciences · 2022Review
- Connecting omics signatures and revealing biological mechanisms with iLINCS.Nature communications · 2022Article
- From drug repositioning to target repositioning: prediction of therapeutic targets using genetically perturbed transcriptomic signatures.Bioinformatics (Oxford, England) · 2022Article
- Chemical-induced gene expression ranking and its application to pancreatic cancer drug repurposing.Patterns (New York, N.Y.) · 2022Article
- The cellular response to drug perturbation is limited: comparison of large-scale chemogenomic fitness signatures.BMC genomics · 2022Article
- Computational analyses of mechanism of action (MoA): data, methods and integration.RSC chemical biology · 2022Review
- Evaluation of connectivity map shows limited reproducibility in drug repositioning.Scientific reports · 2021Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The identification of the modes of action of bioactive compounds is a major challenge in chemical systems biology of diseases. Genome-wide expression profiling of transcriptional responses to compound treatment for human cell lines is a promising unbiased approach for the mode-of-action analysis. Here we developed a novel approach to elucidate the modes of action of bioactive compounds in a cell-specific manner using large-scale chemically-induced transcriptome data acquired from the Library of Integrated Network-based Cellular Signatures (LINCS), and analyzed 16,268 compounds and 68 human cell lines. First, we performed pathway enrichment analyses of regulated genes to reveal active pathways among 163 biological pathways. Next, we explored potential target proteins (including primary targets and off-targets) with cell-specific transcriptional similarity using chemical-protein interactome. Finally, we predicted new therapeutic indications for 461 diseases based on the target proteins. We showed the usefulness of the proposed approach in terms of prediction coverage, interpretation, and large-scale applicability, and validated the new prediction results experimentally by an in vitro cellular assay. The approach has a high potential for advancing drug discovery and repositioning.
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