ArticleNucleic acids research2012
An integer linear programming approach for finding deregulated subgraphs in regulatory networks.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 260 citations in OpenAlex.
- De novo identification of maximally deregulated subnetworks based on multi-omics data with DeRegNet.BMC bioinformatics · 2022Article
- GeneTrail: A Framework for the Analysis of High-Throughput Profiles.Frontiers in molecular biosciences · 2021Article
- A Cancer Gene Module Mining Method Based on Bio-Network of Multi-Omics Gene Groups.Frontiers in oncology · 2020Article
- pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks.Frontiers in genetics · 2019Article
- Constraints on signaling network logic reveal functional subgraphs on Multiple Myeloma OMIC data.BMC systems biology · 2018Article
- Network module identification-A widespread theoretical bias and best practices.Methods (San Diego, Calif.) · 2018Article
- Network-based analysis of omics data: the LEAN method.Bioinformatics (Oxford, England) · 2017Article
- On the performance of de novo pathway enrichment.NPJ systems biology and applications · 2017Article
- Mathematical and Computational Modeling in Complex Biological Systems.BioMed research international · 2017Review
- Unraveling novel TF-miRNA regulatory crosstalk in metastasis of Soft Tissue Sarcoma.Scientific reports · 2015Article
- Diversified Control Paths: A Significant Way Disease Genes Perturb the Human Regulatory Network.PloS one · 2015Article
- Revealing molecular mechanisms by integrating high-dimensional functional screens with protein interaction data.PLoS computational biology · 2014Article
- Systematic permutation testing in GWAS pathway analyses: identification of genetic networks in dilated cardiomyopathy and ulcerative colitis.BMC genomics · 2014Article
- Anti-triangle centrality-based community detection in complex networks.IET systems biology · 2014Article
- WMAXC: a weighted maximum clique method for identifying condition-specific sub-network.PloS one · 2014Article
- BiNA: a visual analytics tool for biological network data.PloS one · 2014Article
- Integrative approaches for finding modular structure in biological networks.Nature reviews. Genetics · 2013Review
- Article
- An integrative network algorithm identifies age-associated differential methylation interactome hotspots targeting stem-cell differentiation pathways.Scientific reports · 2013Article
Corrections and comments
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Authors and funding
15 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Deregulation of cell signaling pathways plays a crucial role in the development of tumors. The identification of such pathways requires effective analysis tools that facilitate the interpretation of expression differences. Here, we present a novel and highly efficient method for identifying deregulated subnetworks in a regulatory network. Given a score for each node that measures the degree of deregulation of the corresponding gene or protein, the algorithm computes the heaviest connected subnetwork of a specified size reachable from a designated root node. This root node can be interpreted as a molecular key player responsible for the observed deregulation. To demonstrate the potential of our approach, we analyzed three gene expression data sets. In one scenario, we compared expression profiles of non-malignant primary mammary epithelial cells derived from BRCA1 mutation carriers and of epithelial cells without BRCA1 mutation. Our results suggest that oxidative stress plays an important role in epithelial cells of BRCA1 mutation carriers and that the activation of stress proteins may result in avoidance of apoptosis leading to an increased overall survival of cells with genetic alterations. In summary, our approach opens new avenues for the elucidation of pathogenic mechanisms and for the detection of molecular key players.
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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.