ArticleCommunications biology2023
Open-source curation of a pancreatic ductal adenocarcinoma gene expression analysis platform (pdacR) supports a two-subtype model.
Article in Communications biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 20 citations in OpenAlex.
- Purity Independent Subtyping of Tumors (PurIST) Pancreatic Cancer Classifier: Analytic Validation of a 16-RNA Expression Signature Distinguishing Basal and Classical Subtypes.The Journal of molecular diagnostics : JMD · 2024Trial
- Article
- Aberrant alternative splicing of purinergic receptor P2RX4 prevents sensitivity towards combinatorial treatment in colorectal and pancreatic cancer.The Journal of pathology · 2026Article
- Biomarker discovery and patient stratification in pancreatic cancer using incomplete multi-omics data.PLoS computational biology · 2026Article
- MondoA mediates transcriptional coordination between the MYC network and the integrated stress response in pancreatic cancer.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Identification and characterization of a TGF-β-independent SMAD4-NFATc1-STAT3 regulatory axis.Journal of molecular cell biology · 2026Article
- A cell-state axis underlying colonization in carcinomas with implications for metastasis risk prediction and interception.Cell reports · 2025Article
- c-Rel drives pancreatic cancer metastasis through fibronectin-integrin signaling-induced isolation stress resistance and EMT.Molecular cancer · 2025Article
- Integrative analysis of genomic and transcriptomic data informs precancer progression in the pancreas.bioRxiv : the preprint server for biology · 2025Article
- MondoA mediates transcriptional coordination between the MYC network and the integrated stress response in pancreatic ductal adenocarcinoma.bioRxiv : the preprint server for biology · 2025Article
- Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms Reveals Divergent Indolent and Malignant States.Clinical cancer research : an official journal of the American Association for Cancer Research · 2025Article
- Article
- Updates in Molecular Profiling of Pancreatic Ductal Adenocarcinoma.The Surgical clinics of North America · 2024Review
- Natural TCRs targeting KRASG12V display fine specificity and sensitivity to human solid tumors.The Journal of clinical investigation · 2024Article
- Pancreatic Ductal Adenocarcinoma (PDAC): A Review of Recent Advancements Enabled by Artificial Intelligence.Cancers · 2024Review
- Clinically relevant orthotopic pancreatic cancer models for adoptive T cell transfer therapy.Journal for immunotherapy of cancer · 2024Article
- Coordinated single-cell tumor microenvironment dynamics reinforce pancreatic cancer subtype.Nature communications · 2023Article
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9 authors at 4 institutions in 1 country.
Funding
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease for which potent therapies have limited efficacy. Several studies have described the transcriptomic landscape of PDAC tumors to provide insight into potentially actionable gene expression signatures to improve patient outcomes. Despite centralization efforts from multiple organizations and increased transparency requirements from funding agencies and publishers, analysis of public PDAC data remains difficult. Bioinformatic pitfalls litter public transcriptomic data, such as subtle inclusion of low-purity and non-adenocarcinoma cases. These pitfalls can introduce non-specificity to gene signatures without appropriate data curation, which can negatively impact findings. To reduce barriers to analysis, we have created pdacR ( http://pdacR.bmi.stonybrook.edu , github.com/rmoffitt/pdacR), an open-source software package and web-tool with annotated datasets from landmark studies and an interface for user-friendly analysis in clustering, differential expression, survival, and dimensionality reduction. Using this tool, we present a multi-dataset analysis of PDAC transcriptomics that confirms the basal-like/classical model over alternatives.
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