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HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery
2014
Computer applications in the biosciences : CABIOS
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HyperModules is a network search algorithm that finds frequently mutated gene modules with significant clinical or phenotypic signatures from biomolecular interaction networks. ...
Correlating disease mutations with clinical and phenotypic information such as drug response or patient survival is an important goal of personalized cancer genomics and a first step in biomarker discovery ...
ACKNOWLEDGEMENTS The authors thank Jason Montojo and Harold Rodriguez for Cytoscape help. Conflict of Interest: none declared. ...
doi:10.1093/bioinformatics/btu172
pmid:24713437
pmcid:PMC4103591
fatcat:howfy3q5x5blrnd6pmdmjefzyq
Biological Networks for Cancer Candidate Biomarkers Discovery
2016
Cancer Informatics
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A variety of genomic alterations, such as point mutations, copy number variations, and gene rearrangements, contribute ...
identify significant mutated gene modules as potential multivariate biomarkers for cancer. ...
Based on gene mutation information, biomolecular interaction networks, and patient clinical information, Leung et al. 15 developed a Cytoscape plug-in called HyperModules to clinically and phenotypically ...
doi:10.4137/cin.s39458
pmid:27625573
pmcid:PMC5012434
fatcat:zuqt2qdd7bejvfsex5dipfmbgy
Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer
2016
Genome Medicine
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Integrated mutation analysis of clinical information and protein interaction networks suggests that many PTM-specific mutations associate with decreased patient survival. ...
Gene-focused analysis with the ActiveDriver method reveals significant co-occurrences of acetylation and ubiquitination PTMs and mutation hotspots in known oncoproteins (TP53, AKT1, IDH1) and highlights ...
Acknowledgements We gratefully acknowledge the contributions from TCGA Research Network and its TCGA Pan-Cancer Analysis Working Group. ...
doi:10.1186/s13073-016-0311-2
pmid:27175787
pmcid:PMC4864925
fatcat:lihgz2o7k5fjxjihqbqcuqgwbu
Pathway and network analysis of cancer genomes
2015
Nature Methods
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HyperModules was applied to the kinase-signaling network in ovarian cancer and revealed network modules with mutations in phosphorylation sites and kinase domains that significantly correlated with patient ...
The HyperModules method 47 identifies subnetworks with cancer mutations that are maximally correlated with clinical characteristics such as patient survival, tumor stage or relapse. ...
competinG Financial interests The authors declare no competing financial interests. reprints and permissions information is available online at http://www.nature. com/reprints/index.html. ...
doi:10.1038/nmeth.3440
pmid:26125594
pmcid:PMC4717906
fatcat:qxeg5bsmufdubboiqdp2bfn2eu
Computational methods and opportunities for phosphorylation network medicine
2014
Translational Cancer Research
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Kinase inhibitors are being regularly used in clinics for cancer treatment. ...
With the increasing understanding of the complexity and redundancy of cell signaling, there is a growing recognition that targeting the entire network or system could be a necessary and advantageous strategy ...
Special thanks to the phosphoproteomics research group at the Moffitt Cancer Center: Eric Haura, John Koomen, Uwe Rix, and Keiran Smalley. We also thank Alvaro ...
pmid:25530950
pmcid:PMC4271781
fatcat:bbfxl2kggzcvfowfn6fmlvrqnu