ArticleProceedings of the National Academy of Sciences of the United States of America2013
Pathway-based personalized analysis of cancer.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 183 papers, 2 of them syntheses that pooled it.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
183 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Prediction of Acquired Taxane Resistance Using a Personalized Pathway-Based Machine Learning Method.Cancer research and treatment · 2019Pooled it
- Unveiling the Link Between Inflammation and Adaptive Immunity in Breast Cancer.Frontiers in immunology · 2019Pooled it
- Toward Personalized Computer Simulation of Breast Cancer Treatment: A Multiscale Pharmacokinetic and Pharmacodynamic Model Informed by Multitype Patient Data.Cancer research · 2019Trial
- Pathway potency in methylation altered network reveals lung cancer branching evolution and hallmarks.iScience · 2026Article
- Article
- Hyperpathway: visualizing organization of pathway-molecule enriched interactions in omics studies via hyperbolic bipartite network embedding.NPJ systems biology and applications · 2026Article
- GEDO: topology-based inference of gene module activity in Sjögren's disease.Briefings in bioinformatics · 2026Article
- Epigenetic remodeling via HDAC6 inhibition amplifies anti-tumoral immune responses in myeloid leukemia cells.Cell death & disease · 2026Article
- Cord blood DNA methylation and cell-type composition are not significantly associated with severe preeclampsia after cell-type and clinical covariate adjustment.GigaScience · 2026Article
- Chemoresistome mapping in individual breast cancer patients unravels diversity in dynamic transcriptional adaptation.Molecular oncology · 2025Article
- Precision Oncology: Current Landscape, Emerging Trends, Challenges, and Future Perspectives.Cells · 2025Review
- LaGrACE: estimating gene program dysregulation with latent regulatory network.Molecular systems biology · 2025Article
- Signalomics for molecular tumor boards and precision oncology of breast and gynecological cancers.Molecular systems biology · 2025Review
- Cell type proportions rather than DNA methylation in the cord blood show significant associations with severe preeclampsia.medRxiv : the preprint server for health sciences · 2025Article
- Longitudinal pathway analysis using structural information with case studies in early type 1 diabetes.Scientific reports · 2025Article
- Subtype-specific transcription factors affect polyamine metabolism and the tumor microenvironment in breast cancer.Cancer innovation · 2025Article
- Serum Lipidome and Metabolome Alterations in Obese Patients Undergoing Targeted Diet and Exercise Interventions: A Marker of Thyroid Function Recovery?International journal of endocrinology · 2025Article
- AEGAN-Pathifier: a data augmentation method to improve cancer classification for imbalanced gene expression data.BMC bioinformatics · 2024Article
- Distinct pathway activities are associated with prognosis and response to bortezomib-containing treatment in MCL1-M based molecular subtypes of multiple myeloma.Annals of hematology · 2024Article
- DeePathNet: A Transformer-Based Deep Learning Model Integrating Multiomic Data with Cancer Pathways.Cancer research communications · 2024Article
123 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We introduce Pathifier, an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene-level information into pathway-level information, generating a compact and biologically relevant representation of each sample. We demonstrate the algorithm's performance on three colorectal cancer datasets and two glioblastoma multiforme datasets and show that our multipathway-based representation is reproducible, preserves much of the original information, and allows inference of complex biologically significant information. We discovered several pathways that were significantly associated with survival of glioblastoma patients and two whose scores are predictive of survival in colorectal cancer: CXCR3-mediated signaling and oxidative phosphorylation. We also identified a subclass of proneural and neural glioblastoma with significantly better survival, and an EGF receptor-deregulated subclass of colon cancers.
Indexed as
Identifiers
What OpenQuestion holds
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 OpenQuestion graph.