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My personal mutanome: a computational genomic medicine platform for searching network perturbing alleles linking genotype to phenotype

Yadi Zhou, Junfei Zhao, Jiansong Fang, William Martin, Lang Li, Ruth Nussinov, Timothy A. Chan, Charis Eng, Feixiong Cheng
2021 Genome Biology  
MPM contains 490,245 mutations from over 10,800 tumor exomes across 33 cancer types in The Cancer Genome Atlas mapped to 94,563 structure-resolved/predicted protein-protein interaction interfaces ("edgetic  ...  We present a comprehensive database, My Personal Mutanome (MPM), for accelerating the development of precision cancer medicine protocols.  ...  Hardis Chair of Cancer Genomic Medicine at the Cleveland Clinic, and an ACS Clinical Research Professor. Review history The review history is available as Additional file 2.  ... 
doi:10.1186/s13059-021-02269-3 pmid:33514395 pmcid:PMC7845113 fatcat:5ybr723hl5aifniswgtbaufjfa

OncoOmics approaches to reveal essential genes in breast cancer: a panoramic view from pathogenesis to precision medicine [article]

Andres Lopez-Cortes, Cesar Paz-y-Mino, Santiago Guerrero, Alejandro Cabrera-Andrade, Stephen J. Barigye, Cristian R. Munteanu, Humberto Gonzalez-Diaz, Alejandro Pazos, Yunierkis Perez-Castillo, Eduardo Tejera
2019 bioRxiv   pre-print
previously prioritized genes by the Consensus Strategy, the Pan-Cancer Atlas, the Pharmacogenomics Knowledgebase and the Cancer Genome Interpreter, in order to reveal essential genes to accelerate the  ...  Therefore, the main objective of this study was to analyze genetic alterations, signaling pathways, protein-protein interaction networks, protein expression, dependency maps and enrichment maps in 230  ...  Cytoscape: a software environment for integrated models of networks. Genome Res. 13, 2498-504 (2003). Ivanov, A. A. et al. The OncoPPi Portal: an integrative resource to explore and Li, Z. et al.  ... 
doi:10.1101/638866 fatcat:jvxapgsmjvdk5gurdtsjt4vlnm

Prediction of druggable proteins using machine learning and functional enrichment analysis: a focus on cancer-related proteins and RNA-binding proteins [article]

Andres Lopez-Cortes, Alejandro Cabrera-Andrade, Carlos M Cruz-Segundo, Julian Dorado, Alejandro Pazos, Humberto Gonzales-Diaz, Cesar Paz-y-Mino, Yunierkis Perez-Castillo, Eduardo Tejera, Cristian R. Munteanu
2019 bioRxiv   pre-print
The druggable proteome can be defined as the percentage of proteins that have the capacity to bind an antibody or small molecule with adequate chemical properties and affinity.  ...  Conclusions: This powerful model predicts several druggable proteins which should be deeply studied to find better therapeutic targets and thus improve clinical trials.  ...  Ivanov AA, Revennaugh B, Rusnak L, et al (2018) The OncoPPi Portal: an integrative 491 resource to explore and prioritize protein-protein interactions for cancer target discovery. 492 Bioinformatics 34  ... 
doi:10.1101/825513 fatcat:qnw6hfb5eng3dkhjg77zviqjpe

MEDICI: Mining Essentiality Data to Identify Critical Interactions for Cancer Drug Target Discovery and Development

Sahar Harati, Lee A. D. Cooper, Josue D. Moran, Felipe O. Giuste, Yuhong Du, Andrei A. Ivanov, Margaret A. Johns, Fadlo R. Khuri, Haian Fu, Carlos S. Moreno, Esmaeil Ebrahimie
2017 PLoS ONE  
Protein-protein interactions (PPIs) mediate the transmission and regulation of oncogenic signals that are essential to cellular proliferation and survival, and thus represent potential targets for anti-cancer  ...  The ability to computationally predict or infer PPI essentiality would help prioritize PPIs for drug discovery and help advance understanding of cancer biology.  ...  All datasets used in the analysis are available for download at the Cancer Target Discovery and Development (CTD2) Data Portal (https://ctd2.nci.nih.gov/ dataPortal/).  ... 
doi:10.1371/journal.pone.0170339 pmid:28118365 pmcid:PMC5261804 fatcat:4sqiqulucra2xn6lvi5x6rpvtm