ArticleScientific reports2021
Evaluation of connectivity map shows limited reproducibility in drug repositioning.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
33 citing papers in PubMed, 48 citations in OpenAlex.
- FBX-DMEP suppresses hepatocellular carcinoma through tubulin-associated mitotic dysregulation.Journal of translational internal medicine · 2026Article
- Computational identification of novel therapeutic candidates for Streptococcus pyogenes and influenza A coinfections through transcriptomic-based drug repositioning.BMC microbiology · 2026Article
- Leveraging drug-specific genes to identify sensitizers for resistant cancer cell lines.Cell death discovery · 2026Article
- A Tumor-Agnostic, Topology-Informed Scoring Framework for Drug Repurposing: Application to CDK4/6 Inhibitor Resistance in HRBiomedicines · 2026Article
- Harnessing AI to fuse phenotypic signatures for drug target identification: progress in computational modeling.Briefings in bioinformatics · 2026Review
- Harnessing Single-Cell RNA-Seq for Computational Drug Repurposing in Cancer Immunotherapy.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Exploiting similarity in drug molecular effects for drug repurposing.Human genomics · 2025Article
- Identifying a Vaginal Microbiome-Derived Selective Antibiotic Metabolite via Microbiome Pharmacology Analysis.bioRxiv : the preprint server for biology · 2025Article
- Comprehensive analysis of high-throughput transcriptomics to distinguish drug-induced liver injury (DILI) phenotypes.Archives of toxicology · 2025Review
- A heterogeneous pharmaco-transcriptomic landscape induced by targeting a single oncogenic kinase.bioRxiv : the preprint server for biology · 2025Article
- Integrating pharmacogenomics and cheminformatics with diverse disease phenotypes for cell type-guided drug discovery.Genome medicine · 2025Article
- Application of GWAS summary data and drug-induced gene expression profiles of neural progenitor cells in psychiatric drug prioritization analysis.Molecular psychiatry · 2025Article
- Development of Drug-Induced Gene Expression Ranking Analysis (DIGERA) and Its Application to Virtual Screening for Poly (ADP-Ribose) Polymerase 1 Inhibitor.International journal of molecular sciences · 2024Article
- Drug repurposing for glomerular diseases: an underutilized resource.Nature reviews. Nephrology · 2024Review
- Integrated transcriptomics- and structure-based drug repositioning identifies drugs with proteasome inhibitor properties.Scientific reports · 2024Article
- Article
- A Proteomics Approach Identifies RREB1 as a Crucial Molecular Target of Imidazo-Pyrazole Treatment in SKMEL-28 Melanoma Cells.International journal of molecular sciences · 2024Article
- Repositioning VU-0365114 as a novel microtubule-destabilizing agent for treating cancer and overcoming drug resistance.Molecular oncology · 2024Article
- Drug Repurposing Using FDA Adverse Event Reporting System (FAERS) Database.Current drug targets · 2024Review
- In silico discovery of small molecules for efficient stem cell differentiation into definitive endoderm.Stem cell reports · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
The Connectivity Map (CMap) is a popular resource designed for data-driven drug repositioning using a large transcriptomic compendium. However, evaluations of its performance are limited. We used two iterations of CMap (CMap 1 and 2) to assess their comparability and reliability. We queried CMap 2 with CMap 1-derived signatures, expecting CMap 2 would highly prioritize the queried compounds; the success rate was 17%. Analysis of previously published prioritizations yielded similar results. Low recall is caused by low differential expression (DE) reproducibility both between CMaps and within each CMap. DE strength was predictive of reproducibility, and is influenced by compound concentration and cell-line responsiveness. Reproducibility of CMap 2 sample expression levels was also lower than expected. We attempted to identify the "better" CMap by comparison with a third dataset, but they were mutually discordant. Our findings have implications for CMap usage and we suggest steps for investigators to limit false positives.
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Registered trials
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 Socratic graph.