Viral Perturbations of Host Networks Reflect Disease Etiology
Natali Gulbahce,Han Yan,Amélie Dricot,Megha Padi,Danielle Byrdsong,Rachel Franchi,Deok-Sun Lee,Deok-Sun Lee,Orit Rozenblatt-Rosen,Jessica C. Mar,Michael A. Calderwood,Amy Baldwin,Amy Baldwin,Bo Zhao,Balaji Santhanam,Pascal Braun,Nicolas Simonis,Nicolas Simonis,Kyung-Won Huh,Kyung-Won Huh,Karin Hellner,Miranda Grace,Alyce A. Chen,Renee Rubio,Jarrod A. Marto,Nicholas A. Christakis,Elliott Kieff,Frederick P. Roth,Jennifer Roecklein-Canfield,Jennifer Roecklein-Canfield,James A. DeCaprio,Michael E. Cusick,John Quackenbush,David E. Hill,Karl Münger,Marc Vidal,Albert-László Barabási,Albert-László Barabási +37 more
TLDR
In this article, the authors examined whether viral perturbations of host interactome may underlie such virally implicated disease relationships, using as models two different human viruses, Epstein-Barr virus (EBV) and human papillomavirus (HPV).Abstract:
Many human diseases, arising from mutations of disease susceptibility genes (genetic diseases), are also associated with viral infections (virally implicated diseases), either in a directly causal manner or by indirect associations. Here we examine whether viral perturbations of host interactome may underlie such virally implicated disease relationships. Using as models two different human viruses, Epstein-Barr virus (EBV) and human papillomavirus (HPV), we find that host targets of viral proteins reside in network proximity to products of disease susceptibility genes. Expression changes in virally implicated disease tissues and comorbidity patterns cluster significantly in the network vicinity of viral targets. The topological proximity found between cellular targets of viral proteins and disease genes was exploited to uncover a novel pathway linking HPV to Fanconi anemia.read more
Citations
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Network Medicine: A Network-Based Approach to Human Disease
TL;DR: Advances in this direction are essential for identifying new disease genes, for uncovering the biological significance of disease-associated mutations identified by genome-wide association studies and full-genome sequencing, and for identifying drug targets and biomarkers for complex diseases.
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The BioGRID interaction database: 2015 update
Andrew Chatr-aryamontri,Bobby-Joe Breitkreutz,Rose Oughtred,Lorrie Boucher,Sven Heinicke,Daici Chen,Chris Stark,Ashton Breitkreutz,Nadine Kolas,Lara O'Donnell,Teresa Reguly,Julie Nixon,Lindsay Ramage,Andrew G. Winter,Adnane Sellam,Christie S. Chang,Jodi E. Hirschman,Chandra L. Theesfeld,Jennifer M. Rust,Michael S. Livstone,Kara Dolinski,Mike Tyers +21 more
TL;DR: The BioGRID architecture has been improved to support a broader range of interaction and post-translational modification types, to allow the representation of more complex multi-gene/protein interactions, to account for cellular phenotypes through structured ontologies, to expedite curation through semi-automated text-mining approaches, and to enhance curation quality control.
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A “candidate-interactome” aggregate analysis of genome-wide association data in multiple sclerosis
Rosella Mechelli,Renato Umeton,Claudia Policano,Viviana Annibali,Giulia Coarelli,Vito A. G. Ricigliano,Danila Vittori,Arianna Fornasiero,Maria Chiara Buscarinu,Silvia Romano,Marco Salvetti,Giovanni Ristori +11 more
TL;DR: The interaction between genotype and Epstein Barr virus emerges as relevant for multiple sclerosis etiology, and also other viruses have a similar potential, though probably less relevant in epidemiological terms.
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Human symptoms–disease network
TL;DR: It is found that the symptom-based similarity of two diseases correlates strongly with the number of shared genetic associations and the extent to which their associated proteins interact.
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Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins
Orit Rozenblatt-Rosen,Rahul C. Deo,Rahul C. Deo,Megha Padi,Guillaume Adelmant,Michael A. Calderwood,Thomas Rolland,Miranda Grace,Miranda Grace,Amélie Dricot,Manor Askenazi,Maria Tavares,Sam Pevzner,Sam Pevzner,Fieda Abderazzaq,Danielle Byrdsong,Anne-Ruxandra Carvunis,Alyce A. Chen,Alyce A. Chen,Jingwei Cheng,Jingwei Cheng,Mick Correll,Melissa Duarte,Melissa Duarte,Changyu Fan,Mariet C.W. Feltkamp,Scott B. Ficarro,Rachel Franchi,Rachel Franchi,Brijesh K. Garg,Natali Gulbahce,Tong Hao,Amy M. Holthaus,Amy M. Holthaus,Robert James,Anna Korkhin,Anna Korkhin,Larisa Litovchick,Larisa Litovchick,Jessica C. Mar,Theodore R. Pak,Sabrina Rabello,Renee Rubio,Yun Shen,Saurav Singh,Jennifer M. Spangle,Jennifer M. Spangle,Murat Tasan,Murat Tasan,Shelly Wanamaker,Shelly Wanamaker,James T. Webber,Jennifer Roecklein-Canfield,Jennifer Roecklein-Canfield,Eric Johannsen,Eric Johannsen,Albert-László Barabási,Rameen Beroukhim,Rameen Beroukhim,Rameen Beroukhim,Elliott Kieff,Elliott Kieff,Michael E. Cusick,David E. Hill,Karl Münger,Karl Münger,Jarrod A. Marto,John Quackenbush,Frederick P. Roth,James A. DeCaprio,James A. DeCaprio,Marc Vidal +71 more
TL;DR: It is shown that systematic analyses of host targets of viral proteins can identify cancer genes with a success rate on a par with their identification through functional genomics and large-scale cataloguing of tumour mutations, to increase the specificity of cancer gene identification.
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