ArticleMolecular oncology2015
Pathway-based personalized analysis of breast cancer expression data.
Article in Molecular oncology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 41 citations in OpenAlex.
- Chemoresistome mapping in individual breast cancer patients unravels diversity in dynamic transcriptional adaptation.Molecular oncology · 2025Article
- Integrating computational methods andHeliyon · 2024Article
- Benign breast tumors may arise on different immunological backgrounds.Molecular oncology · 2024Article
- Construct prognostic models of multiple myeloma with pathway information incorporated.PLoS computational biology · 2024Article
- PAGER-scFGA: unveiling cell functions and molecular mechanisms in cell trajectories through single-cell functional genomics analysis.Frontiers in bioinformatics · 2024Article
- Identification of a neural development gene expression signature in colon cancer stem cells reveals a role foriScience · 2022Article
- DEMA: a distance-bounded energy-field minimization algorithm to model and layout biomolecular networks with quantitative features.Bioinformatics (Oxford, England) · 2022Article
- PAGER Web APP: An Interactive, Online Gene Set and Network Interpretation Tool for Functional Genomics.Frontiers in genetics · 2022Article
- A systematic comparison of data- and knowledge-driven approaches to disease subtype discovery.Briefings in bioinformatics · 2021Article
- Pathway-Based Personalized Analysis of Pan-Cancer Transcriptomic Data.Biomedicines · 2021Article
- Pan-cancer analysis of pathway-based gene expression pattern at the individual level reveals biomarkers of clinical prognosis.Cell reports methods · 2021Article
- Highly accurate diagnosis of papillary thyroid carcinomas based on personalized pathways coupled with machine learning.Briefings in bioinformatics · 2021Article
- Molecular Subclassification Based on Crosstalk Analysis Improves Prediction of Prognosis in Colorectal Cancer.Frontiers in genetics · 2021Article
- Transcriptional profiling reveals a subset of human breast tumors that retain wt TP53 but display mutant p53-associated features.Molecular oncology · 2020Article
- Pathway-Based Drug-Repurposing Schemes in Cancer: The Role of Translational Bioinformatics.Frontiers in oncology · 2020Review
- PathTracer: High-sensitivity detection of differential pathway activity in tumours.Scientific reports · 2019Article
- Article
- Developing a 'personalome' for precision medicine: emerging methods that compute interpretable effect sizes from single-subject transcriptomes.Briefings in bioinformatics · 2019Review
- PIMKL: Pathway-Induced Multiple Kernel Learning.NPJ systems biology and applications · 2019Article
- The Emerging Potential for Network Analysis to Inform Precision Cancer Medicine.Journal of molecular biology · 2018Review
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
introductionMost analyses of high throughput cancer data represent tumors by "atomistic" single-gene properties. Pathifier, a recently introduced method, characterizes a tumor in terms of "coarse grained" pathway-based variables.
methodsWe applied Pathifier to study a very large dataset of 2000 breast cancer samples and 144 normal tissues. Pathifier uses known gene assignments to pathways and biological processes to calculate for each pathway and tumor a Pathway Deregulation Score (PDS). Individual samples are represented in terms of their PDSs calculated for several hundred pathways, and the samples of the data set are analyzed and stratified on the basis of their profiles over these "coarse grained", biologically meaningful variables.
resultsWe identified nine tumor subtypes; a new subclass (comprising about 7% of the samples) exhibits high deregulation in 38 PKA pathways, induced by overexpression of the gene PRKACB. Another interesting finding is that basal tumors break into two subclasses, with low and high deregulation of a cluster of immune system pathways. High deregulation corresponds to higher concentrations of Tumor Infiltrating Lymphocytes, and the patients of this basal subtype have better prognosis. The analysis used 1000 "discovery set" tumors; our results were highly reproducible on 1000 independent "validation" samples.
conclusionsThe coarse-grained variables that represent pathway deregulation provide a basis for relevant, novel and robust findings for breast cancer. Our analysis indicates that in breast cancer reliable prognostic signatures are most likely to be obtained by treating separately different subgroups of the patients.
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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 OpenQuestion graph.