Viral Perturbations of Host Networks Reflect Disease Etiology
Publication Date
June 28, 2012
Journal
PLOS Computational Biology
Authors
Natali Gulbahce, Han Yan, Amélie Dricot, Megha Padi, et al
Volume
8
Issue
6
Pages
e1002531
DOI
http://doi.org/10.1371/journal.pcbi.1002531
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1002531
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/22761553
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3386155
Europe PMC
http://europepmc.org/abstract/MED/22761553
Web of Science
000305965300009
Scopus
84864053752
Mendeley
http://www.mendeley.com/research/viral-perturbations-host-networks-reflect-disease-etiology
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Mendeley | Further Information

{"title"=>"Viral perturbations of host networks reflect disease etiology", "type"=>"journal", "authors"=>[{"first_name"=>"Natali", "last_name"=>"Gulbahce", "scopus_author_id"=>"23501286700"}, {"first_name"=>"Han", "last_name"=>"Yan", "scopus_author_id"=>"35304260100"}, {"first_name"=>"Amélie", "last_name"=>"Dricot", "scopus_author_id"=>"6506916526"}, {"first_name"=>"Megha", "last_name"=>"Padi", "scopus_author_id"=>"23390325000"}, {"first_name"=>"Danielle", "last_name"=>"Byrdsong", "scopus_author_id"=>"55313643300"}, {"first_name"=>"Rachel", "last_name"=>"Franchi", "scopus_author_id"=>"55312914000"}, {"first_name"=>"Deok Sun", "last_name"=>"Lee", "scopus_author_id"=>"8572322600"}, {"first_name"=>"Orit", "last_name"=>"Rozenblatt-Rosen", "scopus_author_id"=>"6602637318"}, {"first_name"=>"Jessica C.", "last_name"=>"Mar", "scopus_author_id"=>"8300771200"}, {"first_name"=>"Michael A.", "last_name"=>"Calderwood", "scopus_author_id"=>"6602520462"}, {"first_name"=>"Amy", "last_name"=>"Baldwin", "scopus_author_id"=>"56869684300"}, {"first_name"=>"Bo", "last_name"=>"Zhao", "scopus_author_id"=>"8705324500"}, {"first_name"=>"Balaji", "last_name"=>"Santhanam", "scopus_author_id"=>"55192444500"}, {"first_name"=>"Pascal", "last_name"=>"Braun", "scopus_author_id"=>"7203026887"}, {"first_name"=>"Nicolas", "last_name"=>"Simonis", "scopus_author_id"=>"16508160200"}, {"first_name"=>"Kyung Won", "last_name"=>"Huh", "scopus_author_id"=>"35082064200"}, {"first_name"=>"Karin", "last_name"=>"Hellner", "scopus_author_id"=>"23966507900"}, {"first_name"=>"Miranda", "last_name"=>"Grace", "scopus_author_id"=>"7202436380"}, {"first_name"=>"Alyce", "last_name"=>"Chen", "scopus_author_id"=>"55313519400"}, {"first_name"=>"Renee", "last_name"=>"Rubio", "scopus_author_id"=>"14014396300"}, {"first_name"=>"Jarrod A.", "last_name"=>"Marto", "scopus_author_id"=>"6603720833"}, {"first_name"=>"Nicholas A.", "last_name"=>"Christakis", "scopus_author_id"=>"7005400323"}, {"first_name"=>"Elliott", "last_name"=>"Kieff", "scopus_author_id"=>"7102600215"}, {"first_name"=>"Frederick P.", "last_name"=>"Roth", "scopus_author_id"=>"7103020414"}, {"first_name"=>"Jennifer", "last_name"=>"Roecklein-Canfield", "scopus_author_id"=>"6505872107"}, {"first_name"=>"James A.", "last_name"=>"DeCaprio", "scopus_author_id"=>"7005976966"}, {"first_name"=>"Michael E.", "last_name"=>"Cusick", "scopus_author_id"=>"6603860369"}, {"first_name"=>"John", "last_name"=>"Quackenbush", "scopus_author_id"=>"7004974520"}, {"first_name"=>"David E.", "last_name"=>"Hill", "scopus_author_id"=>"56427360200"}, {"first_name"=>"Karl", "last_name"=>"Münger", "scopus_author_id"=>"7006292295"}, {"first_name"=>"Marc", "last_name"=>"Vidal", "scopus_author_id"=>"7202764997"}, {"first_name"=>"Albert László", "last_name"=>"Barabási", "scopus_author_id"=>"7006567633"}], "year"=>2012, "source"=>"PLoS Computational Biology", "identifiers"=>{"pmid"=>"22761553", "isbn"=>"1553-7358 (Electronic)\\r1553-734X (Linking)", "sgr"=>"84864053752", "doi"=>"10.1371/journal.pcbi.1002531", "issn"=>"1553734X", "scopus"=>"2-s2.0-84864053752", "pui"=>"365284153"}, "id"=>"f77632f8-5edc-381d-bb47-ff97c021b175", "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.", "link"=>"http://www.mendeley.com/research/viral-perturbations-host-networks-reflect-disease-etiology", "reader_count"=>128, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>17, "Researcher"=>42, "Student > Doctoral Student"=>7, "Student > Ph. D. Student"=>27, "Student > Postgraduate"=>7, "Student > Master"=>11, "Other"=>5, "Student > Bachelor"=>5, "Lecturer"=>1, "Professor"=>5}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>17, "Researcher"=>42, "Student > Doctoral Student"=>7, "Student > Ph. D. Student"=>27, "Student > Postgraduate"=>7, "Student > Master"=>11, "Other"=>5, "Student > Bachelor"=>5, "Lecturer"=>1, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Agricultural and Biological Sciences"=>65, "Philosophy"=>1, "Business, Management and Accounting"=>1, "Computer Science"=>12, "Energy"=>1, "Engineering"=>3, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>16, "Mathematics"=>3, "Medicine and Dentistry"=>10, "Physics and Astronomy"=>9, "Social Sciences"=>1, "Immunology and Microbiology"=>3}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>10}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>9}, "Mathematics"=>{"Mathematics"=>3}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>1}, "Engineering"=>{"Engineering"=>3}, "Energy"=>{"Energy"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>65}, "Computer Science"=>{"Computer Science"=>12}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>16}, "Philosophy"=>{"Philosophy"=>1}}, "reader_count_by_country"=>{"United States"=>6, "Japan"=>2, "United Kingdom"=>1, "Malaysia"=>1, "Spain"=>1, "India"=>1, "Canada"=>2, "Austria"=>1, "Norway"=>1, "Brazil"=>1, "Italy"=>3, "Slovenia"=>1, "France"=>4, "Germany"=>2}, "group_count"=>9}

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/616902"], "description"=>"<p><b>A,C</b>, The neighborhoods of viral targets in the host interactome, along with their disease associations, represent “viral disease networks”. Diseases associated with genes in the neighborhood of EBV (A) or HPV16 (C) targets that are not yet characterized with viral implications are shown as grey nodes. Node size is proportional to the degree of a node (number of neighbors it has) in the viral disease network. <b>B,D</b>, Diseases associated with genes in the neighborhoods of randomly generated viral targets of EBV (B) or HPV16 (D) are significantly sparser than the neighborhoods of actual viral targets. <b>E</b>, Benchmarking the prioritization using relative risk with virally infected patients showed that the higher-ranked diseases in the prioritization are more often associated with viral infection. <b>F</b>, Differentially expressed genes in E6 or E7 induced IMR90 and HFK cell populations with their associated diseases. If a gene is regulated by a specific viral protein target, it is also almost always differentially expressed in the cell population where that specific viral protein is induced. For example, <i>EDN1</i> is regulated by FOS, an E7 target, and EDN1 is differentially expressed in E7 induced cell populations. Large grey nodes: diseases with high relative risk among HPV patients.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology"], "article_id"=>287360, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Natali Gulbahce", "Han Yan", "Amélie Dricot", "Megha Padi", "Danielle Byrdsong", "Rachel Franchi", "Deok-Sun Lee", "Orit Rozenblatt-Rosen", "Jessica C. Mar", "Michael A. Calderwood", "Amy Baldwin", "Bo Zhao", "Balaji Santhanam", "Pascal Braun", "Nicolas Simonis", "Kyung-Won Huh", "Karin Hellner", "Miranda Grace", "Alyce Chen", "Renee Rubio", "Jarrod A. Marto", "Nicholas A. Christakis", "Elliott Kieff", "Frederick P. Roth", "Jennifer Roecklein-Canfield", "James A. DeCaprio", "Michael E. Cusick", "John Quackenbush", "David E. Hill", "Karl Münger", "Marc Vidal", "Albert-László Barabási"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002531.g003", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Viral_disease_networks_/287360", "title"=>"Viral disease networks.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-28 02:02:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/616762"], "description"=>"<p><b>A,B</b>, The number of virally implicated diseases in the neighborhoods was higher than randomly expected for EBV (A) and HPV16 (B). <b>C,D</b>, The number of differentially expressed genes in the neighborhood of viral targets of either EBV (C) or HPV16 (D) was significantly higher compared to that in the neighborhood of randomly sampled host genes. The total number of genes regulated by EBV and HPV targets is 109 and 122, respectively. Expression level was measured in tissues of two virally implicated diseases respectively, Burkitt's lymphoma (EBV) and cervical cancer (HPV), and compared to normal tissues. <b>E,F</b>, Known virally implicated diseases in the vicinity of viral targets for EBV (E) and HPV16 (F). Examples of paths that are known to correspond to disease mechanism are highlighted in grey and listed individually underneath.</p>", "links"=>[], "tags"=>["implicated", "diseases", "genes", "neighborhoods", "viral"], "article_id"=>287204, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Natali Gulbahce", "Han Yan", "Amélie Dricot", "Megha Padi", "Danielle Byrdsong", "Rachel Franchi", "Deok-Sun Lee", "Orit Rozenblatt-Rosen", "Jessica C. Mar", "Michael A. Calderwood", "Amy Baldwin", "Bo Zhao", "Balaji Santhanam", "Pascal Braun", "Nicolas Simonis", "Kyung-Won Huh", "Karin Hellner", "Miranda Grace", "Alyce Chen", "Renee Rubio", "Jarrod A. Marto", "Nicholas A. Christakis", "Elliott Kieff", "Frederick P. Roth", "Jennifer Roecklein-Canfield", "James A. DeCaprio", "Michael E. Cusick", "John Quackenbush", "David E. Hill", "Karl Münger", "Marc Vidal", "Albert-László Barabási"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002531.g002", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Virally_implicated_diseases_associated_with_genes_in_the_neighborhoods_of_viral_targets_/287204", "title"=>"Virally implicated diseases associated with genes in the neighborhoods of viral targets.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-28 02:00:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/617025"], "description"=>"<p><b>A</b>, EBV-implicated diseases. <b>B</b>, HPV16-implicated diseases. Mapped gene column lists the genes found in the neighborhood of viral targets. An asterisk (*) in the “mapped gene” column corresponds to diseases where no known genes are reportedly associated with the disease in OMIM database, and (-) corresponds to diseases where there are genes reportedly associated with the disease in OMIM database but are not identified with our approach. Diseases marked with (<sup>i</sup>) correspond to EBV-implicated diseases within the framework of B cell lymphoma.</p>", "links"=>[], "tags"=>["implicated"], "article_id"=>287482, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Natali Gulbahce", "Han Yan", "Amélie Dricot", "Megha Padi", "Danielle Byrdsong", "Rachel Franchi", "Deok-Sun Lee", "Orit Rozenblatt-Rosen", "Jessica C. Mar", "Michael A. Calderwood", "Amy Baldwin", "Bo Zhao", "Balaji Santhanam", "Pascal Braun", "Nicolas Simonis", "Kyung-Won Huh", "Karin Hellner", "Miranda Grace", "Alyce Chen", "Renee Rubio", "Jarrod A. Marto", "Nicholas A. Christakis", "Elliott Kieff", "Frederick P. Roth", "Jennifer Roecklein-Canfield", "James A. DeCaprio", "Michael E. Cusick", "John Quackenbush", "David E. Hill", "Karl Münger", "Marc Vidal", "Albert-László Barabási"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002531.t001", "stats"=>{"downloads"=>4, "page_views"=>32, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Virally_implicated_diseases_/287482", "title"=>"Virally implicated diseases.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-06-28 02:04:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/616547"], "description"=>"<p><b>A</b>, Viral proteins (virome) interact with host proteins (viral targets) in the host interactome, which in turn are linked to various human diseases (phenome) through mutations in particular disease susceptibility genes (variome). <b>B</b>, Determining topological proximity between viral targets and genes associated with virally implicated diseases by measuring the shortest path lengths between them. For each disease, the minimum number of hops of interactions needed to connect any of its associated genes to any viral targets is designated as the shortest path. <b>C,D</b>, The average shortest path for either EBV (C) or HPV16 (D) was significantly shorter than random expectation.</p>", "links"=>[], "tags"=>["viral", "proteome", "virally", "implicated", "diseases"], "article_id"=>286995, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Natali Gulbahce", "Han Yan", "Amélie Dricot", "Megha Padi", "Danielle Byrdsong", "Rachel Franchi", "Deok-Sun Lee", "Orit Rozenblatt-Rosen", "Jessica C. Mar", "Michael A. Calderwood", "Amy Baldwin", "Bo Zhao", "Balaji Santhanam", "Pascal Braun", "Nicolas Simonis", "Kyung-Won Huh", "Karin Hellner", "Miranda Grace", "Alyce Chen", "Renee Rubio", "Jarrod A. Marto", "Nicholas A. Christakis", "Elliott Kieff", "Frederick P. Roth", "Jennifer Roecklein-Canfield", "James A. DeCaprio", "Michael E. Cusick", "John Quackenbush", "David E. Hill", "Karl Münger", "Marc Vidal", "Albert-László Barabási"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002531.g001", "stats"=>{"downloads"=>0, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Linking_a_viral_proteome_to_virally_implicated_diseases_through_the_host_interactome_/286995", "title"=>"Linking a viral proteome to virally implicated diseases through the host interactome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-28 01:56:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/321196", "https://ndownloader.figshare.com/files/321219", "https://ndownloader.figshare.com/files/321243", "https://ndownloader.figshare.com/files/321265", "https://ndownloader.figshare.com/files/321282"], "description"=>"<div><p>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.</p> </div>", "links"=>[], "tags"=>["viral", "perturbations", "networks", "etiology"], "article_id"=>123388, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Natali Gulbahce", "Han Yan", "Amélie Dricot", "Megha Padi", "Danielle Byrdsong", "Rachel Franchi", "Deok-Sun Lee", "Orit Rozenblatt-Rosen", "Jessica C. Mar", "Michael A. Calderwood", "Amy Baldwin", "Bo Zhao", "Balaji Santhanam", "Pascal Braun", "Nicolas Simonis", "Kyung-Won Huh", "Karin Hellner", "Miranda Grace", "Alyce Chen", "Renee Rubio", "Jarrod A. Marto", "Nicholas A. Christakis", "Elliott Kieff", "Frederick P. Roth", "Jennifer Roecklein-Canfield", "James A. DeCaprio", "Michael E. Cusick", "John Quackenbush", "David E. Hill", "Karl Münger", "Marc Vidal", "Albert-László Barabási"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1002531.s001", "https://dx.doi.org/10.1371/journal.pcbi.1002531.s002", "https://dx.doi.org/10.1371/journal.pcbi.1002531.s003", "https://dx.doi.org/10.1371/journal.pcbi.1002531.s004", "https://dx.doi.org/10.1371/journal.pcbi.1002531.s005"], "stats"=>{"downloads"=>4, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Viral_Perturbations_of_Host_Networks_Reflect_Disease_Etiology/123388", "title"=>"Viral Perturbations of Host Networks Reflect Disease Etiology", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-06-28 00:56:28"}

PMC Usage Stats | Further Information

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Relative Metric

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