Literature DB >> 33514395

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

Yadi Zhou1, Junfei Zhao2,3, Jiansong Fang1, William Martin1, Lang Li4, Ruth Nussinov5,6, Timothy A Chan1,7,8,9,10, Charis Eng1,8,9,10,11, Feixiong Cheng12,13,14.   

Abstract

Massive genome sequencing data have inspired new challenges in personalized treatments and facilitated oncological drug discovery. We present a comprehensive database, My Personal Mutanome (MPM), for accelerating the development of precision cancer medicine protocols. 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") and 311,022 functional sites ("nodetic"), including ligand-protein binding sites and 8 types of protein posttranslational modifications. In total, 8884 survival results and 1,271,132 drug responses are obtained for these mapped interactions. MPM is available at https://mutanome.lerner.ccf.org .

Entities:  

Keywords:  Edgetic; Mutanome; Nodetic; Precision cancer medicine; Protein-protein interaction; Somatic mutations

Mesh:

Year:  2021        PMID: 33514395      PMCID: PMC7845113          DOI: 10.1186/s13059-021-02269-3

Source DB:  PubMed          Journal:  Genome Biol        ISSN: 1474-7596            Impact factor:   13.583


  61 in total

1.  Association Between Specific Mutations in KRAS Codon 12 and Colorectal Liver Metastasis.

Authors:  Georgios Antonios Margonis; Yuhree Kim; Gaya Spolverato; Aslam Ejaz; Rohan Gupta; David Cosgrove; Robert Anders; Georgios Karagkounis; Michael A Choti; Timothy M Pawlik
Journal:  JAMA Surg       Date:  2015-08       Impact factor: 14.766

2.  Effect of KRAS oncogene substitutions on protein behavior: implications for signaling and clinical outcome.

Authors:  Nathan T Ihle; Lauren A Byers; Edward S Kim; Pierre Saintigny; J Jack Lee; George R Blumenschein; Anne Tsao; Suyu Liu; Jill E Larsen; Jing Wang; Lixia Diao; Kevin R Coombes; Lu Chen; Shuxing Zhang; Mena F Abdelmelek; Ximing Tang; Vassiliki Papadimitrakopoulou; John D Minna; Scott M Lippman; Waun K Hong; Roy S Herbst; Ignacio I Wistuba; John V Heymach; Garth Powis
Journal:  J Natl Cancer Inst       Date:  2012-01-13       Impact factor: 13.506

3.  Comprehensive Characterization of Cancer Driver Genes and Mutations.

Authors:  Matthew H Bailey; Collin Tokheim; Eduard Porta-Pardo; Sohini Sengupta; Denis Bertrand; Amila Weerasinghe; Antonio Colaprico; Michael C Wendl; Jaegil Kim; Brendan Reardon; Patrick Kwok-Shing Ng; Kang Jin Jeong; Song Cao; Zixing Wang; Jianjiong Gao; Qingsong Gao; Fang Wang; Eric Minwei Liu; Loris Mularoni; Carlota Rubio-Perez; Niranjan Nagarajan; Isidro Cortés-Ciriano; Daniel Cui Zhou; Wen-Wei Liang; Julian M Hess; Venkata D Yellapantula; David Tamborero; Abel Gonzalez-Perez; Chayaporn Suphavilai; Jia Yu Ko; Ekta Khurana; Peter J Park; Eliezer M Van Allen; Han Liang; Michael S Lawrence; Adam Godzik; Nuria Lopez-Bigas; Josh Stuart; David Wheeler; Gad Getz; Ken Chen; Alexander J Lazar; Gordon B Mills; Rachel Karchin; Li Ding
Journal:  Cell       Date:  2018-04-05       Impact factor: 41.582

Review 4.  Mapping the protein-protein and genetic interactions of cancer to guide precision medicine.

Authors:  Mehdi Bouhaddou; Manon Eckhardt; Zun Zar Chi Naing; Minkyu Kim; Trey Ideker; Nevan J Krogan
Journal:  Curr Opin Genet Dev       Date:  2019-07-06       Impact factor: 5.578

Review 5.  Personal Mutanomes Meet Modern Oncology Drug Discovery and Precision Health.

Authors:  Feixiong Cheng; Han Liang; Atul J Butte; Charis Eng; Ruth Nussinov
Journal:  Pharmacol Rev       Date:  2018-12-13       Impact factor: 25.468

6.  Oncogenic mutations of the PIK3CA gene in head and neck squamous cell carcinomas.

Authors:  Avaniyapuram Kannan Murugan; Nguyen Thi Hong; Yasuhisa Fukui; Arasambattu Kannan Munirajan; Nobuo Tsuchida
Journal:  Int J Oncol       Date:  2008-01       Impact factor: 5.650

7.  Phospho.ELM: a database of phosphorylation sites--update 2011.

Authors:  Holger Dinkel; Claudia Chica; Allegra Via; Cathryn M Gould; Lars J Jensen; Toby J Gibson; Francesca Diella
Journal:  Nucleic Acids Res       Date:  2010-11-09       Impact factor: 16.971

8.  Oncogenic PI3K/AKT promotes the step-wise evolution of combination BRAF/MEK inhibitor resistance in melanoma.

Authors:  Mal Irvine; Ashleigh Stewart; Bernadette Pedersen; Suzanah Boyd; Richard Kefford; Helen Rizos
Journal:  Oncogenesis       Date:  2018-09-20       Impact factor: 7.485

9.  Network-based prediction of drug combinations.

Authors:  Feixiong Cheng; István A Kovács; Albert-László Barabási
Journal:  Nat Commun       Date:  2019-03-13       Impact factor: 14.919

Review 10.  Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers.

Authors:  Ruth Nussinov; Hyunbum Jang; Chung-Jung Tsai; Feixiong Cheng
Journal:  PLoS Comput Biol       Date:  2019-03-28       Impact factor: 4.475

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  5 in total

Review 1.  Interpretable artificial intelligence and exascale molecular dynamics simulations to reveal kinetics: Applications to Alzheimer's disease.

Authors:  William Martin; Gloria Sheynkman; Felice C Lightstone; Ruth Nussinov; Feixiong Cheng
Journal:  Curr Opin Struct Biol       Date:  2021-10-07       Impact factor: 6.809

Review 2.  Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs.

Authors:  Ruth Nussinov; Mingzhen Zhang; Ryan Maloney; Yonglan Liu; Chung-Jung Tsai; Hyunbum Jang
Journal:  J Mol Biol       Date:  2022-04-01       Impact factor: 6.151

3.  A full-proteome, interaction-specific characterization of mutational hotspots across human cancers.

Authors:  Siwei Chen; Yuan Liu; Yingying Zhang; Shayne D Wierbowski; Steven M Lipkin; Xiaomu Wei; Haiyuan Yu
Journal:  Genome Res       Date:  2021-12-28       Impact factor: 9.438

4.  Network-based protein-protein interaction prediction method maps perturbations of cancer interactome.

Authors:  Jiajun Qiu; Kui Chen; Chunlong Zhong; Sihao Zhu; Xiao Ma
Journal:  PLoS Genet       Date:  2021-11-02       Impact factor: 5.917

Review 5.  Mechanism of activation and the rewired network: New drug design concepts.

Authors:  Ruth Nussinov; Mingzhen Zhang; Ryan Maloney; Chung-Jung Tsai; Bengi Ruken Yavuz; Nurcan Tuncbag; Hyunbum Jang
Journal:  Med Res Rev       Date:  2021-10-25       Impact factor: 12.388

  5 in total

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