ArticlePatterns (New York, N.Y.)2021
Causal interactions from proteomic profiles: Molecular data meet pathway knowledge.
Article in Patterns (New York, N.Y.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers, 1 of them a synthesis 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
58 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Toward standardization and a concerted vision for platelet proteomics research: communication from the SSC of the ISTH.Journal of thrombosis and haemostasis : JTH · 2025Guideline
- Protein modification systems as cancer biomarkers and therapeutic targets.Precision clinical medicine · 2026Review
- Integrative Proteogenomic Characterization of Left-Sided and Right-Sided Colorectal Cancer.MedComm · 2026Article
- Decoding disease and therapy through multiomics integration and systems analysis.Briefings in bioinformatics · 2026Review
- Single-Cell Proteomic Technologies: Tools in the Quest for Principles.Annual review of biophysics · 2026Review
- Benchmarking EGF signaling pathway inference using phosphoproteomics and kinase-substrate interactions.Nature communications · 2026Article
- PU.1 inhibition sensitizes stem-monocytic AML to BCL2 blockade.bioRxiv : the preprint server for biology · 2026Article
- Phosphoproteomics of osimertinib-tolerant persister cells reveals targetable kinase-substrate signatures.Molecular systems biology · 2025Article
- Computational Approaches for Pathway-Centric Analysis of Protein Post-Translational Modifications.Proteomics · 2025Review
- Oncostatin M orchestrates collective epithelial migration via HIF1A activation.bioRxiv : the preprint server for biology · 2025Article
- Strategies to include prior knowledge in omics analysis with deep neural networks.Patterns (New York, N.Y.) · 2025Review
- Proteomic Profiling Towards a Better Understanding of Genetic Based Muscular Diseases: The Current Picture and a Look to the Future.Biomolecules · 2025Review
- Systems-level reconstruction of kinase phosphosignaling networks regulating endothelial barrier integrity using temporal data.NPJ systems biology and applications · 2024Article
- Systems-level reconstruction of kinase phosphosignaling networks regulating endothelial barrier integrity using temporal data.bioRxiv : the preprint server for biology · 2024Article
- DSCI: a database of synthetic biology components for innate immunity and cell engineering decision-making processes.Advanced biotechnology · 2024Article
- SignalingProfiler 2.0 a network-based approach to bridge multi-omics data to phenotypic hallmarks.NPJ systems biology and applications · 2024Article
- Unveiling hidden connections in omics data via pyPARAGON: an integrative hybrid approach for disease network construction.Briefings in bioinformatics · 2024Article
- Memory effects of prior subculture may impact the quality of multiomic perturbation profiles.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Prioritizing drug targets by perturbing biological network response functions.PLoS computational biology · 2024Article
- Platelet proteomics emerges from the womb: mass spectrometry insights into neonatal platelet biology.Journal of thrombosis and haemostasis : JTH · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
14 authors.
Funding
Abstract
We present a computational method to infer causal mechanisms in cell biology by analyzing changes in high-throughput proteomic profiles on the background of prior knowledge captured in biochemical reaction knowledge bases. The method mimics a biologist's traditional approach of explaining changes in data using prior knowledge but does this at the scale of hundreds of thousands of reactions. This is a specific example of how to automate scientific reasoning processes and illustrates the power of mapping from experimental data to prior knowledge via logic programming. The identified mechanisms can explain how experimental and physiological perturbations, propagating in a network of reactions, affect cellular responses and their phenotypic consequences. Causal pathway analysis is a powerful and flexible discovery tool for a wide range of cellular profiling data types and biological questions. The automated causation inference tool, as well as the source code, are freely available at http://causalpath.org.
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.