ArticleBioinformatics (Oxford, England)2015
MEMCover: integrated analysis of mutual exclusivity and functional network reveals dysregulated pathways across multiple cancer types.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Variant-Specific Landscape of Mutual Exclusivity Among BRAF, EGFR, and KRAS Oncogenes Reveals Overlap With Functionally Antagonistic Mutant Pairs.International journal of cancer · 2026Article
- Context-dependent synthetic lethality - an emerging precision therapeutic approach.Nature reviews. Cancer · 2026Review
- AutoFocus: a hierarchical framework to explore multi-omic disease associations spanning multiple scales of biomolecular interaction.Communications biology · 2024Article
- A latent variable model for evaluating mutual exclusivity and co-occurrence between driver mutations in cancer.bioRxiv : the preprint server for biology · 2024Article
- Identifying Cancer Driver Pathways Based on the Mouth Brooding Fish Algorithm.Entropy (Basel, Switzerland) · 2023Article
- Endocrine Disrupting Chemicals Influence Hub Genes Associated with Aggressive Prostate Cancer.International journal of molecular sciences · 2023Article
- Statistical tests for intra-tumour clonal co-occurrence and exclusivity.PLoS computational biology · 2021Article
- Identification of Common Driver Gene Modules and Associations between Cancers through Integrated Network Analysis.Global challenges (Hoboken, NJ) · 2021Article
- Analysis, identification and visualization of subgroups in genomics.Briefings in bioinformatics · 2021Review
- A forward selection algorithm to identify mutually exclusive alterations in cancer studies.Journal of human genetics · 2021Article
- Performance Assessment of the Network Reconstruction Approaches on Various Interactomes.Frontiers in molecular biosciences · 2021Article
- A Network-Centric Framework for the Evaluation of Mutual Exclusivity Tests on Cancer Drivers.Frontiers in genetics · 2021Article
- DriveWays: a method for identifying possibly overlapping driver pathways in cancer.Scientific reports · 2020Article
- Identifying Drug Sensitivity Subnetworks with NETPHIX.iScience · 2020Article
- Network-based approaches elucidate differences within APOBEC and clock-like signatures in breast cancer.Genome medicine · 2020Article
- Modelling cancer progression using Mutual Hazard Networks.Bioinformatics (Oxford, England) · 2020Article
- An Effective Graph Clustering Method to Identify Cancer Driver Modules.Frontiers in bioengineering and biotechnology · 2020Article
- Identification of the PTEN-ARID4B-PI3K pathway reveals the dependency on ARID4B by PTEN-deficient prostate cancer.Nature communications · 2019Article
- Review
- Adaptively Weighted and Robust Mathematical Programming for the Discovery of Driver Gene Sets in Cancers.Scientific reports · 2019Article
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Authors and funding
4 authors.
Funding
Abstract
motivationThe data gathered by the Pan-Cancer initiative has created an unprecedented opportunity for illuminating common features across different cancer types. However, separating tissue-specific features from across cancer signatures has proven to be challenging. One of the often-observed properties of the mutational landscape of cancer is the mutual exclusivity of cancer driving mutations. Even though studies based on individual cancer types suggested that mutually exclusive pairs often share the same functional pathway, the relationship between across cancer mutual exclusivity and functional connectivity has not been previously investigated.
resultsWe introduce a classification of mutual exclusivity into three basic classes: within tissue type exclusivity, across tissue type exclusivity and between tissue type exclusivity. We then combined across-cancer mutual exclusivity with interactions data to uncover pan-cancer dysregulated pathways. Our new method, Mutual Exclusivity Module Cover (MEMCover) not only identified previously known Pan-Cancer dysregulated subnetworks but also novel subnetworks whose across cancer role has not been appreciated well before. In addition, we demonstrate the existence of mutual exclusivity hubs, putatively corresponding to cancer drivers with strong growth advantages. Finally, we show that while mutually exclusive pairs within or across cancer types are predominantly functionally interacting, the pairs in between cancer mutual exclusivity class are more often disconnected in functional networks.
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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.