ArticleBMC medical genomics2020
Cancer gene expression profiles associated with clinical outcomes to chemotherapy treatments.
Article in BMC medical genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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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.
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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
17 citing papers in PubMed, 29 citations in OpenAlex.
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- Reclassification of TCGA Diffuse Glioma Profiles Linked to Transcriptomic, Epigenetic, Genomic and Clinical Data, According to the 2021 WHO CNS Tumor Classification.International journal of molecular sciences · 2022Article
- Transcriptomic Harmonization as the Way for Suppressing Cross-Platform Bias and Batch Effect.Biomedicines · 2022Review
- CTR-DB, an omnibus for patient-derived gene expression signatures correlated with cancer drug response.Nucleic acids research · 2022Article
- Gene Expression-Based Signature Can Predict Sorafenib Response in Kidney Cancer.Frontiers in molecular biosciences · 2022Article
- Transcriptomic Portraits and Molecular Pathway Activation Features of Adult Spinal Intramedullary Astrocytomas.Frontiers in oncology · 2022Article
- LRRC4 mediates the formation of circular RNA CD44 to inhibitGBM cell proliferation.Molecular therapy. Nucleic acids · 2021Article
- Algorithmically DeducedCancers · 2021Article
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- Experimental and Meta-Analytic Validation of RNA Sequencing Signatures for Predicting Status of Microsatellite Instability.Frontiers in molecular biosciences · 2021Article
- Machine Learning Applicability for Classification of PAD/VCD Chemotherapy Response Using 53 Multiple Myeloma RNA Sequencing Profiles.Frontiers in oncology · 2021Article
- RNA Sequencing Data for FFPE Tumor Blocks Can Be Used for Robust Estimation of Tumor Mutation Burden in Individual Biosamples.Frontiers in oncology · 2021Article
- Medical genomics at the Systems Biology and Bioinformatics (SBB-2019) school.BMC medical genomics · 2020Article
- Editorial: Next Generation Sequencing Based Diagnostic Approaches in Clinical Oncology.Frontiers in oncology · 2020Article
- Activation of the ERK1/2 Molecular Pathways and Its Relation to the Pathogenicity of Human Malignant Tumors.Acta naturaeArticle
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundMachine learning (ML) methods still have limited applicability in personalized oncology due to low numbers of available clinically annotated molecular profiles. This doesn't allow sufficient training of ML classifiers that could be used for improving molecular diagnostics.
methodsWe reviewed published datasets of high throughput gene expression profiles corresponding to cancer patients with known responses on chemotherapy treatments. We browsed Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA) and Tumor Alterations Relevant for GEnomics-driven Therapy (TARGET) repositories.
resultsWe identified data collections suitable to build ML models for predicting responses on certain chemotherapeutic schemes. We identified 26 datasets, ranging from 41 till 508 cases per dataset. All the datasets identified were checked for ML applicability and robustness with leave-one-out cross validation. Twenty-three datasets were found suitable for using ML that had balanced numbers of treatment responder and non-responder cases.
conclusionsWe collected a database of gene expression profiles associated with clinical responses on chemotherapy for 2786 individual cancer cases. Among them seven datasets included RNA sequencing data (for 645 cases) and the others - microarray expression profiles. The cases represented breast cancer, lung cancer, low-grade glioma, endothelial carcinoma, multiple myeloma, adult leukemia, pediatric leukemia and kidney tumors. Chemotherapeutics included taxanes, bortezomib, vincristine, trastuzumab, letrozole, tipifarnib, temozolomide, busulfan and cyclophosphamide.
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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.