ArticleComputational and structural biotechnology journal2021
Survival analysis across the entire transcriptome identifies biomarkers with the highest prognostic power in breast cancer.
Article in Computational and structural biotechnology journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 642 papers, 1 of them a synthesis that pooled it.
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Who cites it
642 citing papers in PubMed, 1 synthesis or guideline pooled it.
- RGS Family Remodeling in Breast Cancer: A Meta-Analysis and Multi-Omics Profiling of Prognostic Biomarkers.Cancer medicine · 2026Pooled it
- Home-based high-intensity exercise training during neoadjuvant chemotherapy is associated with favorable chemotherapy outcomes and tumor microenvironment remodeling in breast cancer.Cell communication and signaling : CCS · 2026Trial
- Tracking CDK1 Dynamics With a Novel Biosensor Mouse and Clinical Cohorts to Predict CDK4/6 Inhibitor Sensitivity in ER+ Breast Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- AKAP13 regulates GLI1/ULK1 axis and drive tumor resistance to next-generation HER2-targeted therapies.Oncogene · 2026Article
- Spatiotemporal regulation of DNA repair proteins between Golgi and nucleus maintains genome stability.The Journal of cell biology · 2026Article
- Role of orphan G protein-coupled receptor GPR52 in breast cancer cell multicellular organization and collective invasion.British journal of cancer · 2026Article
- Targeting breast cancer stem cells by restoring RBM38 function: mechanism and protein delivery therapy.Biomarker research · 2026Article
- A dual role for miR-210-3p in hypoxia-driven signaling and mitotic regulation in cancer.Molecular biomedicine · 2026Article
- Integrated Bioinformatics Analysis Identifies NCAPG2 as an Immune-Related Prognostic Biomarker in Breast Cancer.World journal of oncology · 2026Article
- Multi-scale transcriptomic integration reveals LINC00152-high tumor cells promote TGCT progression and T cell exhaustion.British journal of cancer · 2026Article
- ABHD17C-Mediated S-Depalmitoylation of BCL6B Enhances CD24 Transcription to Resist Macrophage Phagocytosis in Pancreatic Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Enzymatic activity-independent NANS stabilizes LATS2 to drive growth and therapeutic resistance in HR+/HER2- breast cancer.Nature communications · 2026Article
- A peripheral blood-based approach involving vimentin along with AURKA enabled efficient tracking of elusive Oct4/Sox2-expressing disseminated breast cancer stem cells.Bioscience reports · 2026Article
- Identification of E3 Ubiquitin Ligases Associated with Survival in Soft Tissue Sarcomas.International journal of molecular sciences · 2026Article
- High TRIM28 Expression Defines an Aggressive, Immune-Cold Phenotype with Worse Survival Outcomes in ERα-Positive Breast Cancer.Biomedicines · 2026Article
- GALNT5 drives colorectal cancer progression and chemoresistance via PI3K/Akt/ABCC1 axis.Journal of cancer research and clinical oncology · 2026Article
- Mechanisms of active wetting and fluidification in epithelial cell collectives.Nature materials · 2026Article
- TMEM216 inhibits breast cancer lung metastasis by modulating IGF1R-IRS4 signaling pathway.Nature communications · 2026Article
- Expression and Survival Analysis Show High Mobility Group (HMG) Family as Prognostic Biomarkers in Breast Cancer.European journal of breast health · 2026Article
- HER2∆16 directs luminal cell identity and estrogen receptor signaling in HER2+ breast cancer.Nature communications · 2026Article
582 more citing papers are in PubMed but not listed here.
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Abstract
introductionExtensive research is directed to uncover new biomarkers capable to stratify breast cancer patients into clinically relevant cohorts. However, the overall performance ranking of such marker candidates compared to other genes is virtually absent. Here, we present the ranking of all survival related genes in chemotherapy treated basal and estrogen positive/HER2 negative breast cancer.
methodsWe searched the GEO repository to uncover transcriptomic datasets with available follow-up and clinical data. After quality control and normalization, samples entered an integrated database. Molecular subtypes were designated using gene expression data. Relapse-free survival analysis was performed using Cox proportional hazards regression. False discovery rate was computed to combat multiple hypothesis testing. Kaplan-Meier plots were drawn to visualize the best performing genes.
resultsThe entire database includes 7,830 unique samples from 55 independent datasets. Of those with available relapse-free survival time, 3,382 samples were estrogen receptor-positive and 696 were basal. In chemotherapy treated ER positive/ERBB2 negative patients the significant prognostic biomarker genes achieved hazard rates between 1.76 and 3.33 with a p value below 5.8E-04. The significant prognostic genes in adjuvant chemotherapy treated basal breast cancer samples reached hazard rates between 1.88 and 3.61 with a p value below 7.2E-04. Our integrated platform was extended enabling the validation of future biomarker candidates.
conclusionsA reference ranking for all genes in two chemotherapy treated breast cancer cohorts is presented. The results help to neglect those with unlikely clinical significance and to focus future research on the most promising candidates.
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