ArticleEURASIP journal on bioinformatics & systems biology2012
Determination of minimal transcriptional signatures of compounds for target prediction.
Article in EURASIP journal on bioinformatics & systems biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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The trial behind it
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Who cites it
5 citing papers in PubMed.
- Harnessing AI to fuse phenotypic signatures for drug target identification: progress in computational modeling.Briefings in bioinformatics · 2026Review
- Harnessing the biological complexity of Big Data from LINCS gene expression signatures.PloS one · 2018Article
- Representing high throughput expression profiles via perturbation barcodes reveals compound targets.PLoS computational biology · 2017Article
- Transcriptional Characterization of Compounds: Lessons Learned from the Public LINCS Data.Assay and drug development technologies · 2016Article
- Dark chemical matter as a promising starting point for drug lead discovery.Nature chemical biology · 2015Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The identification of molecular target and mechanism of action of compounds is a key hurdle in drug discovery. Multiplexed techniques for bead-based expression profiling allow the measurement of transcriptional signatures of compound-treated cells in high-throughput mode. Such profiles can be used to gain insight into compounds' mode of action and the protein targets they are modulating. Through the proxy of target prediction from such gene signatures we explored important aspects of the use of transcriptional profiles to capture biological variability of perturbed cellular assays. We found that signatures derived from expression data and signatures derived from biological interaction networks performed equally well, and we showed that gene signatures can be optimised using a genetic algorithm. Gene signatures of approximately 128 genes seemed to be most generic, capturing a maximum of the perturbation inflicted on cells through compound treatment. Moreover, we found evidence for oxidative phosphorylation to be one of the most general ways to capture compound perturbation.
Identifiers
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Registered trials
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