Literature DB >> 24287335

Edgotype: a fundamental link between genotype and phenotype.

Nidhi Sahni1, Song Yi, Quan Zhong, Noor Jailkhani, Benoit Charloteaux, Michael E Cusick, Marc Vidal.   

Abstract

Classical 'one-gene/one-disease' models cannot fully reconcile with the increasingly appreciated prevalence of complicated genotype-to-phenotype associations in human disease. Genes and gene products function not in isolation but as components of intricate networks of macromolecules (DNA, RNA, or proteins) and metabolites linked through biochemical or physical interactions, represented in 'interactome' network models as 'nodes' and 'edges', respectively. Accordingly, mechanistic understanding of human disease will require understanding of how disease-causing mutations affect systems or interactome properties. The study of 'edgetics' uncovers specific loss or gain of interactions (edges) to interpret genotype-to-phenotype relationships. We review how distinct genetic variants, the genotype, lead to distinct phenotypic outcomes, the phenotype, through edgetic perturbations in interactome networks altogether representing the 'edgotype'.
Copyright © 2013 Elsevier Ltd. All rights reserved.

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Year:  2013        PMID: 24287335      PMCID: PMC3902775          DOI: 10.1016/j.gde.2013.11.002

Source DB:  PubMed          Journal:  Curr Opin Genet Dev        ISSN: 0959-437X            Impact factor:   5.578


  98 in total

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Authors:  Min Jie Alvin Tan; Elizabeth A White; Mathew E Sowa; J Wade Harper; Jon C Aster; Peter M Howley
Journal:  Proc Natl Acad Sci U S A       Date:  2012-04-30       Impact factor: 11.205

2.  Exome and whole-genome sequencing for gene discovery: the future is now!

Authors:  Jacek Majewski; David S Rosenblatt
Journal:  Hum Mutat       Date:  2012-04       Impact factor: 4.878

Review 3.  Protein networks in disease.

Authors:  Trey Ideker; Roded Sharan
Journal:  Genome Res       Date:  2008-04       Impact factor: 9.043

4.  Evidence for network evolution in an Arabidopsis interactome map.

Authors: 
Journal:  Science       Date:  2011-07-29       Impact factor: 47.728

Review 5.  Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease.

Authors:  David Botstein; Neil Risch
Journal:  Nat Genet       Date:  2003-03       Impact factor: 38.330

6.  Network modeling links breast cancer susceptibility and centrosome dysfunction.

Authors:  Miguel Angel Pujana; Jing-Dong J Han; Lea M Starita; Kristen N Stevens; Muneesh Tewari; Jin Sook Ahn; Gad Rennert; Víctor Moreno; Tomas Kirchhoff; Bert Gold; Volker Assmann; Wael M Elshamy; Jean-François Rual; Douglas Levine; Laura S Rozek; Rebecca S Gelman; Kristin C Gunsalus; Roger A Greenberg; Bijan Sobhian; Nicolas Bertin; Kavitha Venkatesan; Nono Ayivi-Guedehoussou; Xavier Solé; Pilar Hernández; Conxi Lázaro; Katherine L Nathanson; Barbara L Weber; Michael E Cusick; David E Hill; Kenneth Offit; David M Livingston; Stephen B Gruber; Jeffrey D Parvin; Marc Vidal
Journal:  Nat Genet       Date:  2007-10-07       Impact factor: 38.330

7.  Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network.

Authors:  Nicolas Simonis; Jean-François Rual; Anne-Ruxandra Carvunis; Murat Tasan; Irma Lemmens; Tomoko Hirozane-Kishikawa; Tong Hao; Julie M Sahalie; Kavitha Venkatesan; Fana Gebreab; Sebiha Cevik; Niels Klitgord; Changyu Fan; Pascal Braun; Ning Li; Nono Ayivi-Guedehoussou; Elizabeth Dann; Nicolas Bertin; David Szeto; Amélie Dricot; Muhammed A Yildirim; Chenwei Lin; Anne-Sophie de Smet; Huey-Ling Kao; Christophe Simon; Alex Smolyar; Jin Sook Ahn; Muneesh Tewari; Mike Boxem; Stuart Milstein; Haiyuan Yu; Matija Dreze; Jean Vandenhaute; Kristin C Gunsalus; Michael E Cusick; David E Hill; Jan Tavernier; Frederick P Roth; Marc Vidal
Journal:  Nat Methods       Date:  2009-01       Impact factor: 28.547

8.  Understanding the function-structure and function-mutation relationships of p53 tumor suppressor protein by high-resolution missense mutation analysis.

Authors:  Shunsuke Kato; Shuang-Yin Han; Wen Liu; Kazunori Otsuka; Hiroyuki Shibata; Ryunosuke Kanamaru; Chikashi Ishioka
Journal:  Proc Natl Acad Sci U S A       Date:  2003-06-25       Impact factor: 11.205

9.  A novel high-throughput (HTP) cloning strategy for site-directed designed chimeragenesis and mutation using the Gateway cloning system.

Authors:  Yasuhiro Suzuki; Naoko Kagawa; Toru Fujino; Tsuyoshi Sumiya; Taichi Andoh; Kumiko Ishikawa; Rie Kimura; Kiyokazu Kemmochi; Tsutomu Ohta; Shigeo Tanaka
Journal:  Nucleic Acids Res       Date:  2005-07-11       Impact factor: 16.971

10.  'Edgetic' perturbation of a C. elegans BCL2 ortholog.

Authors:  Matija Dreze; Benoit Charloteaux; Stuart Milstein; Pierre-Olivier Vidalain; Muhammed A Yildirim; Quan Zhong; Nenad Svrzikapa; Viviana Romero; Géraldine Laloux; Robert Brasseur; Jean Vandenhaute; Mike Boxem; Michael E Cusick; David E Hill; Marc Vidal
Journal:  Nat Methods       Date:  2009-10-25       Impact factor: 28.547

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  62 in total

Review 1.  Viewing protein fitness landscapes through a next-gen lens.

Authors:  Jeffrey I Boucher; Pamela Cote; Julia Flynn; Li Jiang; Aneth Laban; Parul Mishra; Benjamin P Roscoe; Daniel N A Bolon
Journal:  Genetics       Date:  2014-10       Impact factor: 4.562

2.  dSysMap: exploring the edgetic role of disease mutations.

Authors:  Roberto Mosca; Jofre Tenorio-Laranga; Roger Olivella; Victor Alcalde; Arnaud Céol; Montserrat Soler-López; Patrick Aloy
Journal:  Nat Methods       Date:  2015-03       Impact factor: 28.547

3.  RMut: R package for a Boolean sensitivity analysis against various types of mutations.

Authors:  Hung-Cuong Trinh; Yung-Keun Kwon
Journal:  PLoS One       Date:  2019-03-19       Impact factor: 3.240

4.  Regulome networks and mutational landscape in liver cancer: An informative path to precision medicine.

Authors:  Song Yi; Nidhi Sahni
Journal:  Hepatology       Date:  2017-06-07       Impact factor: 17.425

Review 5.  Functional variomics and network perturbation: connecting genotype to phenotype in cancer.

Authors:  Song Yi; Shengda Lin; Yongsheng Li; Wei Zhao; Gordon B Mills; Nidhi Sahni
Journal:  Nat Rev Genet       Date:  2017-03-27       Impact factor: 53.242

Review 6.  Gene Regulatory Network Perturbation by Genetic and Epigenetic Variation.

Authors:  Yongsheng Li; Daniel J McGrail; Juan Xu; Gordon B Mills; Nidhi Sahni; Song Yi
Journal:  Trends Biochem Sci       Date:  2018-06-22       Impact factor: 13.807

7.  The last enzyme of the de novo purine synthesis pathway 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase (ATIC) plays a central role in insulin signaling and the Golgi/endosomes protein network.

Authors:  Martial Boutchueng-Djidjou; Gabriel Collard-Simard; Suzanne Fortier; Sébastien S Hébert; Isabelle Kelly; Christian R Landry; Robert L Faure
Journal:  Mol Cell Proteomics       Date:  2015-02-16       Impact factor: 5.911

8.  Widespread macromolecular interaction perturbations in human genetic disorders.

Authors:  Nidhi Sahni; Song Yi; Mikko Taipale; Juan I Fuxman Bass; Jasmin Coulombe-Huntington; Fan Yang; Jian Peng; Jochen Weile; Georgios I Karras; Yang Wang; István A Kovács; Atanas Kamburov; Irina Krykbaeva; Mandy H Lam; George Tucker; Vikram Khurana; Amitabh Sharma; Yang-Yu Liu; Nozomu Yachie; Quan Zhong; Yun Shen; Alexandre Palagi; Adriana San-Miguel; Changyu Fan; Dawit Balcha; Amelie Dricot; Daniel M Jordan; Jennifer M Walsh; Akash A Shah; Xinping Yang; Ani K Stoyanova; Alex Leighton; Michael A Calderwood; Yves Jacob; Michael E Cusick; Kourosh Salehi-Ashtiani; Luke J Whitesell; Shamil Sunyaev; Bonnie Berger; Albert-László Barabási; Benoit Charloteaux; David E Hill; Tong Hao; Frederick P Roth; Yu Xia; Albertha J M Walhout; Susan Lindquist; Marc Vidal
Journal:  Cell       Date:  2015-04-23       Impact factor: 41.582

9.  Systems biology and the analysis of genetic variation.

Authors:  Shamil R Sunyaev; Frederick P Roth
Journal:  Curr Opin Genet Dev       Date:  2013-11-28       Impact factor: 5.578

Review 10.  Genetics of Combined Pituitary Hormone Deficiency: Roadmap into the Genome Era.

Authors:  Qing Fang; Akima S George; Michelle L Brinkmeier; Amanda H Mortensen; Peter Gergics; Leonard Y M Cheung; Alexandre Z Daly; Adnan Ajmal; María Ines Pérez Millán; A Bilge Ozel; Jacob O Kitzman; Ryan E Mills; Jun Z Li; Sally A Camper
Journal:  Endocr Rev       Date:  2016-11-09       Impact factor: 19.871

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