ArticleOncotarget2017
High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes.
Article in Oncotarget, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers, 1 of them a synthesis that pooled it.
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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
49 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Hepatic steatosis and steatohepatitis: a functional meta-analysis of sex-based differences in transcriptomic studies.Biology of sex differences · 2021Pooled it
- Bottlenecks in advancing and applying multiomic data integration-common data resources as rate-limiting drivers-the high-impact use case of atherosclerotic cardiovascular disease.Briefings in bioinformatics · 2025Review
- RSEA: A Web Server for Pathway Enrichment Analysis of Metabolic Reaction Sets.Biotechnology and bioengineering · 2025Article
- CanSeer: a translational methodology for developing personalized cancer models and therapeutics.Scientific reports · 2025Article
- Strategy for drug repurposing in fibroadipogenic replacement during muscle wasting: application to duchenne muscular dystrophy.Frontiers in cell and developmental biology · 2025Article
- Pathway metrics accurately stratify T cells to their cells states.BioData mining · 2024Article
- drexml: A command line tool and Python package for drug repurposing.Computational and structural biotechnology journal · 2024Article
- Comparative profiling of whole-cell and exosome samples reveals protein signatures that stratify breast cancer subtypes.Cellular and molecular life sciences : CMLS · 2024Article
- Interferon and B-cell Signatures Inform Precision Medicine in Lupus Nephritis.Kidney international reports · 2024Article
- NetActivity enhances transcriptional signals by combining gene expression into robust gene set activity scores through interpretable autoencoders.Nucleic acids research · 2024Article
- The mechanistic functional landscape of retinitis pigmentosa: a machine learning-driven approach to therapeutic target discovery.Journal of translational medicine · 2024Article
- Single cell RNA sequencing of human FAPs reveals different functional stages in Duchenne muscular dystrophy.Frontiers in cell and developmental biology · 2024Article
- Functional Profiling of Soft Tissue Sarcoma Using Mechanistic Models.International journal of molecular sciences · 2023Article
- Crosstalk between Metabolite Production and Signaling Activity in Breast Cancer.International journal of molecular sciences · 2023Article
- SigPrimedNet: A Signaling-Informed Neural Network for scRNA-seq Annotation of Known and Unknown Cell Types.Biology · 2023Article
- Short- and long-term effects of radiation exposure at low dose and low dose rate in normal human VH10 fibroblasts.Frontiers in public health · 2023Article
- Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches.Frontiers in immunology · 2023Article
- An SPM-Enriched Marine Oil Supplement Shifted Microglia Polarization toward M2, Ameliorating Retinal Degeneration inAntioxidants (Basel, Switzerland) · 2022Article
- Article
- Endoglin and MMP14 Contribute to Ewing Sarcoma Spreading by Modulation of Cell-Matrix Interactions.International journal of molecular sciences · 2022Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding the aspects of the cell functionality that account for disease or drug action mechanisms is a main challenge for precision medicine. Here we propose a new method that models cell signaling using biological knowledge on signal transduction. The method recodes individual gene expression values (and/or gene mutations) into accurate measurements of changes in the activity of signaling circuits, which ultimately constitute high-throughput estimations of cell functionalities caused by gene activity within the pathway. Moreover, such estimations can be obtained either at cohort-level, in case/control comparisons, or personalized for individual patients. The accuracy of the method is demonstrated in an extensive analysis involving 5640 patients from 12 different cancer types. Circuit activity measurements not only have a high diagnostic value but also can be related to relevant disease outcomes such as survival, and can be used to assess therapeutic interventions.
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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 OpenQuestion graph.