ReviewFrontiers in physiology2013
Methods and approaches in the topology-based analysis of biological pathways.
Review in Frontiers in physiology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 113 papers.
What it found
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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.
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Who cites it
113 citing papers in PubMed.
- Pathway mapping of leukocyte transcriptome in influenza patients reveals distinct pathogenic mechanisms associated with progression to severe infection.BMC medical genomics · 2020Trial
- The physiological drivers of commercial broiler chicken performance uncovered with transcriptomics analyses and a novel pathway activation method.Poultry science · 2026Article
- Aortic Single-Cell Transcriptome Analysis Reveals ApoE-Isoform-Specific Influences on Vascular Disease.International journal of molecular sciences · 2026Article
- Cell line-specific gene network enrichment analysis for interpreting continuous phenotypes.Briefings in bioinformatics · 2026Article
- A practical guide to functional enrichment analysis.Frontiers in bioinformatics · 2026Article
- Deciphering tuberculosis pathway mechanisms via graph neural networks and multimodal deep learning: a comprehensive AI-driven framework for precision medicine.Frontiers in pharmacology · 2026Article
- Cytokine-Cytokine Receptor Interaction and Endocytosis are Common Pathways for Symptom Burden and Sickness Behavior Symptoms in Oncology Patients Undergoing Chemotherapy.Cancer medicine · 2025Article
- Reconciling multiple connectivity-based systems biology methods for drug repurposing.Briefings in bioinformatics · 2025Review
- Perturbations in the neuroactive ligand-receptor interaction and renin angiotensin system pathways are associated with cancer-related cognitive impairment.Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer · 2025Article
- Self-reported cancer-related cognitive impairment is associated with perturbed neurotransmission pathways.Journal of neural transmission (Vienna, Austria : 1996) · 2025Article
- Estimating Enzyme Expression and Metabolic Pathway Activity inJournal of computational biology : a journal of computational molecular cell biology · 2025Article
- Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry.ACS measurement science au · 2024Review
- Article
- RCPA: An Open-Source R Package for Data Processing, Differential Analysis, Consensus Pathway Analysis, and Visualization.Current protocols · 2024Article
- Adult Human, but Not Rodent, Spermatogonial Stem Cells Retain States with a Foetal-like Signature.Cells · 2024Article
- Perturbations in inflammatory pathways are associated with shortness of breath profiles in oncology patients receiving chemotherapy.Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer · 2024Article
- Combination of computational new approach methodologies for enhancing evidence of biological pathway conservation across species.The Science of the total environment · 2024Article
- Gene set correlation enrichment analysis for interpreting and annotating gene expression profiles.Nucleic acids research · 2024Article
- Robustness evaluations of pathway activity inference methods on gene expression data.BMC bioinformatics · 2024Article
- Control Theory and Systems Biology: Potential Applications in Neurodegeneration and Search for Therapeutic Targets.International journal of molecular sciences · 2023Review
53 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
The goal of pathway analysis is to identify the pathways significantly impacted in a given phenotype. Many current methods are based on algorithms that consider pathways as simple gene lists, dramatically under-utilizing the knowledge that such pathways are meant to capture. During the past few years, a plethora of methods claiming to incorporate various aspects of the pathway topology have been proposed. These topology-based methods, sometimes referred to as "third generation," have the potential to better model the phenomena described by pathways. Although there is now a large variety of approaches used for this purpose, no review is currently available to offer guidance for potential users and developers. This review covers 22 such topology-based pathway analysis methods published in the last decade. We compare these methods based on: type of pathways analyzed (e.g., signaling or metabolic), input (subset of genes, all genes, fold changes, gene p-values, etc.), mathematical models, pathway scoring approaches, output (one or more pathway scores, p-values, etc.) and implementation (web-based, standalone, etc.). We identify and discuss challenges, arising both in methodology and in pathway representation, including inconsistent terminology, different data formats, lack of meaningful benchmarks, and the lack of tissue and condition specificity.
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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.