Network-Based Data Integration for Selecting Candidate Virulence Associated Proteins in the Cereal Infecting Fungus Fusarium graminearum
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{"title"=>"Network-Based Data Integration for Selecting Candidate Virulence Associated Proteins in the Cereal Infecting Fungus Fusarium graminearum", "type"=>"journal", "authors"=>[{"first_name"=>"Artem", "last_name"=>"Lysenko", "scopus_author_id"=>"35105526200"}, {"first_name"=>"Martin", "last_name"=>"Urban", "scopus_author_id"=>"9234200800"}, {"first_name"=>"Laura", "last_name"=>"Bennett", "scopus_author_id"=>"36647323800"}, {"first_name"=>"Sophia", "last_name"=>"Tsoka", "scopus_author_id"=>"6603414724"}, {"first_name"=>"Elzbieta", "last_name"=>"Janowska-Sejda", "scopus_author_id"=>"55785280500"}, {"first_name"=>"Chris J.", "last_name"=>"Rawlings", "scopus_author_id"=>"7102250077"}, {"first_name"=>"Kim E.", "last_name"=>"Hammond-Kosack", "scopus_author_id"=>"6603832654"}, {"first_name"=>"Mansoor", "last_name"=>"Saqi", "scopus_author_id"=>"6701736348"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"369260728", "sgr"=>"84879824141", "issn"=>"19326203", "pmid"=>"23861834", "scopus"=>"2-s2.0-84879824141", "doi"=>"10.1371/journal.pone.0067926", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"55794ad5-19d2-33c8-8996-1d3959292418", "abstract"=>"The identification of virulence genes in plant pathogenic fungi is important for understanding the infection process, host range and for developing control strategies. The analysis of already verified virulence genes in phytopathogenic fungi in the context of integrated functional networks can give clues about the underlying mechanisms and pathways directly or indirectly linked to fungal pathogenicity and can suggest new candidates for further experimental investigation, using a 'guilt by association' approach. Here we study 133 genes in the globally important Ascomycete fungus Fusarium graminearum that have been experimentally tested for their involvement in virulence. An integrated network that combines information from gene co-expression, predicted protein-protein interactions and sequence similarity was employed and, using 100 genes known to be required for virulence, we found a total of 215 new proteins potentially associated with virulence of which 29 are annotated as hypothetical proteins. The majority of these potential virulence genes are located in chromosomal regions known to have a low recombination frequency. We have also explored the taxonomic diversity of these candidates and found 25 sequences, which are likely to be fungal specific. We discuss the biological relevance of a few of the potentially novel virulence associated genes in detail. The analysis of already verified virulence genes in phytopathogenic fungi in the context of integrated functional networks can give clues about the underlying mechanisms and pathways directly or indirectly linked to fungal pathogenicity and can suggest new candidates for further experimental investigation, using a 'guilt by association' approach.", "link"=>"http://www.mendeley.com/research/networkbased-data-integration-selecting-candidate-virulence-associated-proteins-cereal-infecting-fun", "reader_count"=>32, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>9, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>6, "Student > Postgraduate"=>2, "Other"=>2, "Student > Master"=>5, "Student > Bachelor"=>3, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>9, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>6, "Student > Postgraduate"=>2, "Other"=>2, "Student > Master"=>5, "Student > Bachelor"=>3, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Nursing and Health Professions"=>1, "Agricultural and Biological Sciences"=>26, "Computer Science"=>2}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>26}, "Computer Science"=>{"Computer Science"=>2}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Italy"=>1, "Israel"=>1, "India"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1111230"], "description"=>"<p>Each row provides the information for one sequence. The left hand three columns (SEQ, PPI, COEX) indicate the network in which the prediction could be made (black). For the bottom 15 rows only the integrated network provides the prediction. The right hand heatmap shows the proportional distribution of all BLAST hits from the 215 predictions to the NCBI nr database (white – lowest, red - highest) across the taxonomical levels. All hits were counted once, at the lowest possible level of taxonomical specificity. The grey colour shows cases where there were no hits at a particular taxonomic level. See <b><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067926#pone.0067926.s008\" target=\"_blank\">Table S2</a></b> for the detailed results for each individual FGSG protein.</p>", "links"=>[], "tags"=>["biotechnology", "Genetic engineering", "Genetically modified organisms", "Computational biology", "genomics", "Genome analysis tools", "Gene prediction", "Comparative genomics", "Functional genomics", "Genome databases", "Molecular genetics", "Gene identification and analysis", "genetics", "Gene function", "microbiology", "Mycology", "fungi", "Host-pathogen interaction", "Model organisms", "Yeast and fungal models", "displaying", "taxonomic", "virulence"], "article_id"=>739568, "categories"=>["Biological Sciences"], "users"=>["Artem Lysenko", "Martin Urban", "Laura Bennett", "Sophia Tsoka", "Elzbieta Janowska-Sejda", "Chris J. Rawlings", "Kim E. Hammond-Kosack", "Mansoor Saqi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0067926.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Heat_map_displaying_the_taxonomic_distribution_for_each_of_the_predicted_virulence_associated_proteins_/739568", "title"=>"Heat map displaying the taxonomic distribution for each of the predicted virulence associated proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-04 01:50:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1111231"], "description"=>"<p>The neighbourhood of FGSG_06878 (prediction -large white triangle) and these 8 seed proteins to which it is linked, visualised with Ondex <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067926#pone.0067926-Kohler1\" target=\"_blank\">[16]</a>. The magenta coloured edges predicted PPI information, blue edges predicted co-expression information and the green coloured edges predict sequence similarity information.</p>", "links"=>[], "tags"=>["biotechnology", "Genetic engineering", "Genetically modified organisms", "Computational biology", "genomics", "Genome analysis tools", "Gene prediction", "Comparative genomics", "Functional genomics", "Genome databases", "Molecular genetics", "Gene identification and analysis", "genetics", "Gene function", "microbiology", "Mycology", "fungi", "Host-pathogen interaction", "Model organisms", "Yeast and fungal models", "neighbourhood", "virulence"], "article_id"=>739569, "categories"=>["Biological Sciences"], "users"=>["Artem Lysenko", "Martin Urban", "Laura Bennett", "Sophia Tsoka", "Elzbieta Janowska-Sejda", "Chris J. Rawlings", "Kim E. Hammond-Kosack", "Mansoor Saqi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0067926.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_local_neighbourhood_for_the_predicted_virulence_gene_FGSG_06878_/739569", "title"=>"The local neighbourhood for the predicted virulence gene FGSG_06878.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-04 01:50:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1111232"], "description"=>"<p>The immediate neighbourhood in the integrated network within which the predicted virulence associated protein FGSG_00559 resides (large white triangle). Shown are the types of links between the predictions and the seeds. Magenta coloured edges predicted PPI information and blue edges predicted co-expression information. The various node colours of the seeds as shown in the legend indicate the experimentally determined outcomes. There are 3 additional virulence predictions in this neighbourhood (small white triangles).</p>", "links"=>[], "tags"=>["biotechnology", "Genetic engineering", "Genetically modified organisms", "Computational biology", "genomics", "Genome analysis tools", "Gene prediction", "Comparative genomics", "Functional genomics", "Genome databases", "Molecular genetics", "Gene identification and analysis", "genetics", "Gene function", "microbiology", "Mycology", "fungi", "Host-pathogen interaction", "Model organisms", "Yeast and fungal models", "neighbourhood", "virulence"], "article_id"=>739570, "categories"=>["Biological Sciences"], "users"=>["Artem Lysenko", "Martin Urban", "Laura Bennett", "Sophia Tsoka", "Elzbieta Janowska-Sejda", "Chris J. Rawlings", "Kim E. Hammond-Kosack", "Mansoor Saqi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0067926.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_local_neighbourhood_for_the_predicted_virulence_gene_FGSG_00559_/739570", "title"=>"The local neighbourhood for the predicted virulence gene FGSG_00559.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-04 01:50:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1111233"], "description"=>"<p>Gene IDs are: FGSG_03543 <i>(TRI14)</i>, FGSG_10397 <i>(CLM1)</i>, FGSG_17598 (related to O-methyl sterigmatocystin oxidoreductase), FGSG_03535 <i>(TRI4)</i>, FGSG_03534 <i>(TRI3)</i>, FGSG_16251 <i>(TRI6)</i>, FGSG_03540 <i>(TRI11).</i></p>", "links"=>[], "tags"=>["biotechnology", "Genetic engineering", "Genetically modified organisms", "Computational biology", "genomics", "Genome analysis tools", "Gene prediction", "Comparative genomics", "Functional genomics", "Genome databases", "Molecular genetics", "Gene identification and analysis", "genetics", "Gene function", "microbiology", "Mycology", "fungi", "Host-pathogen interaction", "Model organisms", "Yeast and fungal models", "neighbourhood", "virulence", "fgsg_00071"], "article_id"=>739571, "categories"=>["Biological Sciences"], "users"=>["Artem Lysenko", "Martin Urban", "Laura Bennett", "Sophia Tsoka", "Elzbieta Janowska-Sejda", "Chris J. Rawlings", "Kim E. Hammond-Kosack", "Mansoor Saqi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0067926.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_local_neighbourhood_for_the_predicted_virulence_gene_FGSG_00071_TRI1_/739571", "title"=>"The local neighbourhood for the predicted virulence gene FGSG_00071 <i>(TRI1)</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-04 01:50:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1111234"], "description"=>"<p>Although connected to the two seed proteins FGSG_09614 <i>(GPA2)</i> and FGSG_04104 <i>(GPB1),</i> experimental evidence in barley suggests that the two predictions 05535 and 09988 are dispensable for pathogenicity <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067926#pone.0067926-Yu1\" target=\"_blank\">[36]</a>. Genetic redundancy is suggested to explain this fact. (FGSG_05698: probable <i>CPC2</i> protein, FGSG_09870: probable <i>CPC2</i> protein; FGSG_09271: probable <i>SEC13</i> - protein transport protein; FGSG_10251: probable <i>LST8</i> protein; FGSG_04618: related to vegetatible incompatibility protein <i>HET-E-1</i>; FGSG_16028: probable U5 snRNP-specific 40 kD protein (novel WD-40 repeat protein); FGSG_05038: probable nuclear migration protein.</p>", "links"=>[], "tags"=>["biotechnology", "Genetic engineering", "Genetically modified organisms", "Computational biology", "genomics", "Genome analysis tools", "Gene prediction", "Comparative genomics", "Functional genomics", "Genome databases", "Molecular genetics", "Gene identification and analysis", "genetics", "Gene function", "microbiology", "Mycology", "fungi", "Host-pathogen interaction", "Model organisms", "Yeast and fungal models", "neighbourhood", "fgsg_05535"], "article_id"=>739572, "categories"=>["Biological Sciences"], "users"=>["Artem Lysenko", "Martin Urban", "Laura Bennett", "Sophia Tsoka", "Elzbieta Janowska-Sejda", "Chris J. Rawlings", "Kim E. Hammond-Kosack", "Mansoor Saqi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0067926.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_neighbourhood_of_FGSG_05535_and_FGSG_09988_/739572", "title"=>"The neighbourhood of FGSG_05535 and FGSG_09988.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-04 01:50:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1111235"], "description"=>"<p>The predicted virulence genes are shown as black vertical bars in track 1 for each chromosome. The verified virulence seeds (red bars) are depicted in track 2. Recombination frequency across the chromosomes is depicted in track 3 using a colour gradient (white (0.0) lowest to crimson (>8 cM highest). The various colours in track 3 for each chromosome indicate the frequence of recombination (cM/27 kb), i. e. # clBeige 1 clKhaki 2 clGold 3 clGoldenRod 4 clTomato 8 clCrimson. The numbers between the colours are boundary values in cM/27 kb. Beige represents the lowest and crimson the highest recombination frequency <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067926#pone.0067926-Gale1\" target=\"_blank\">[47]</a>. (Image generated using OmniMapFree <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067926#pone.0067926-Antoniw1\" target=\"_blank\">[27]</a>).</p>", "links"=>[], "tags"=>["biotechnology", "Genetic engineering", "Genetically modified organisms", "Computational biology", "genomics", "Genome analysis tools", "Gene prediction", "Comparative genomics", "Functional genomics", "Genome databases", "Molecular genetics", "Gene identification and analysis", "genetics", "Gene function", "microbiology", "Mycology", "fungi", "Host-pathogen interaction", "Model organisms", "Yeast and fungal models", "predictions", "chromosomes"], "article_id"=>739573, "categories"=>["Biological Sciences"], "users"=>["Artem Lysenko", "Martin Urban", "Laura Bennett", "Sophia Tsoka", "Elzbieta Janowska-Sejda", "Chris J. Rawlings", "Kim E. Hammond-Kosack", "Mansoor Saqi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0067926.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Position_of_the_predictions_in_relation_to_the_4_chromosomes_of_Fusarium_graminearum_/739573", "title"=>"Position of the predictions in relation to the 4 chromosomes of <i>Fusarium graminearum</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-04 01:50:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1111236"], "description"=>"<p>The number of seeds to which each predicted virulence node is connected, in the four networks is shown. A node linked to 2 or more seed nodes is termed a prediction. Some predictions have links to multiple seeds.</p>", "links"=>[], "tags"=>["biotechnology", "Genetic engineering", "Genetically modified organisms", "Computational biology", "genomics", "Genome analysis tools", "Gene prediction", "Comparative genomics", "Functional genomics", "Genome databases", "Molecular genetics", "Gene identification and analysis", "genetics", "Gene function", "microbiology", "Mycology", "fungi", "Host-pathogen interaction", "Model organisms", "Yeast and fungal models", "virulence", "nodes", "numbers", "connected"], "article_id"=>739574, "categories"=>["Biological Sciences"], "users"=>["Artem Lysenko", "Martin Urban", "Laura Bennett", "Sophia Tsoka", "Elzbieta Janowska-Sejda", "Chris J. Rawlings", "Kim E. Hammond-Kosack", "Mansoor Saqi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0067926.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Predicting_virulence_nodes_based_on_the_seed_numbers_connected_within_the_local_neighbourhood_/739574", "title"=>"Predicting virulence nodes based on the seed numbers connected within the local neighbourhood.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-04 01:50:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1111237"], "description"=>"<p>The probability that a verified virulence (VV)seed is connected to at least 2 others by chance.</p>", "links"=>[], "tags"=>["biotechnology", "Genetic engineering", "Genetically modified organisms", "Computational biology", "genomics", "Genome analysis tools", "Gene prediction", "Comparative genomics", "Functional genomics", "Genome databases", "Molecular genetics", "Gene identification and analysis", "genetics", "Gene function", "microbiology", "Mycology", "fungi", "Host-pathogen interaction", "Model organisms", "Yeast and fungal models", "probability", "verified", "virulence", "connected"], "article_id"=>739575, "categories"=>["Biological Sciences"], "users"=>["Artem Lysenko", "Martin Urban", "Laura Bennett", "Sophia Tsoka", "Elzbieta Janowska-Sejda", "Chris J. Rawlings", "Kim E. Hammond-Kosack", "Mansoor Saqi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0067926.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_probability_that_a_verified_virulence_VV_seed_is_connected_to_at_least_2_others_by_chance_/739575", "title"=>"The probability that a verified virulence (VV)seed is connected to at least 2 others by chance.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-04 01:50:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1111238"], "description"=>"<p>Global properties of the three constituent networks and the integrated network. The sequence similarity network excludes nodes with no edges (‘orphan’ proteins with no sequence similarity matches). Column 4 is the number of verified virulence (VV) seeds involved in the predictions, using the rule that a node must be connected to at least 2 seeds to be a prediction (in brackets are the corresponding numbers if we require connection to at least 3 seeds); Column 8 gives the number of predictions (in brackets are the corresponding prediction counts if we require a more stringent rule i. e. a node must be connected to at least 3 seeds to be a prediction).</p>", "links"=>[], "tags"=>["biotechnology", "Genetic engineering", "Genetically modified organisms", "Computational biology", "genomics", "Genome analysis tools", "Gene prediction", "Comparative genomics", "Functional genomics", "Genome databases", "Molecular genetics", "Gene identification and analysis", "genetics", "Gene function", "microbiology", "Mycology", "fungi", "Host-pathogen interaction", "Model organisms", "Yeast and fungal models"], "article_id"=>739576, "categories"=>["Biological Sciences"], "users"=>["Artem Lysenko", "Martin Urban", "Laura Bennett", "Sophia Tsoka", "Elzbieta Janowska-Sejda", "Chris J. Rawlings", "Kim E. Hammond-Kosack", "Mansoor Saqi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0067926.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_the_global_properties_of_the_four_predicted_networks_/739576", "title"=>"Comparison of the global properties of the four predicted networks.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-04 01:50:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1111239"], "description"=>"&<p>recovered from forward genetic screens.</p>", "links"=>[], "tags"=>["biotechnology", "Genetic engineering", "Genetically modified organisms", "Computational biology", "genomics", "Genome analysis tools", "Gene prediction", "Comparative genomics", "Functional genomics", "Genome databases", "Molecular genetics", "Gene identification and analysis", "genetics", "Gene function", "microbiology", "Mycology", "fungi", "Host-pathogen interaction", "Model organisms", "Yeast and fungal models", "verified", "virulence", "seeds"], "article_id"=>739577, "categories"=>["Biological Sciences"], "users"=>["Artem Lysenko", "Martin Urban", "Laura Bennett", "Sophia Tsoka", "Elzbieta Janowska-Sejda", "Chris J. Rawlings", "Kim E. Hammond-Kosack", "Mansoor Saqi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0067926.t006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Funcat_analysis_of_the_verified_virulence_seeds_and_candidate_virulence_associated_proteins_/739577", "title"=>"Funcat analysis of the verified virulence seeds and candidate virulence associated proteins.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-04 01:50:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1111240"], "description"=>"<p>This prediction FGSG_06878 was confirmed to be a virulence protein in the recent paper of [21-Wang et al.]. Note that prediction FGSG_06878 is linked to seed FGSG_06385 by both predicted PPI and sequence similarity information. In planta phenotypes are rv, reduced virulence, a quantitative reduction in disease causing ability and the more stringent lp, indicating loss of pathogenicity where disease establishment is aborted.</p>", "links"=>[], "tags"=>["biotechnology", "Genetic engineering", "Genetically modified organisms", "Computational biology", "genomics", "Genome analysis tools", "Gene prediction", "Comparative genomics", "Functional genomics", "Genome databases", "Molecular genetics", "Gene identification and analysis", "genetics", "Gene function", "microbiology", "Mycology", "fungi", "Host-pathogen interaction", "Model organisms", "Yeast and fungal models", "fgsg_06878", "virulence", "links"], "article_id"=>739578, "categories"=>["Biological Sciences"], "users"=>["Artem Lysenko", "Martin Urban", "Laura Bennett", "Sophia Tsoka", "Elzbieta Janowska-Sejda", "Chris J. Rawlings", "Kim E. Hammond-Kosack", "Mansoor Saqi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0067926.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_prediction_of_FGSG_06878_as_a_virulence_factor_with_links_to_8_seeds_/739578", "title"=>"The prediction of FGSG_06878 as a virulence factor with links to 8 seeds.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-04 01:50:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1111241"], "description"=>"<p>Counts of the different phenotypes according to the study by Wang and collegues <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067926#pone.0067926-Wang1\" target=\"_blank\">[26]</a> that were found among the predictions derived using four different networks.</p>", "links"=>[], "tags"=>["biotechnology", "Genetic engineering", "Genetically modified organisms", "Computational biology", "genomics", "Genome analysis tools", "Gene prediction", "Comparative genomics", "Functional genomics", "Genome databases", "Molecular genetics", "Gene identification and analysis", "genetics", "Gene function", "microbiology", "Mycology", "fungi", "Host-pathogen interaction", "Model organisms", "Yeast and fungal models", "phenotypes", "seeds"], "article_id"=>739579, "categories"=>["Biological Sciences"], "users"=>["Artem Lysenko", "Martin Urban", "Laura Bennett", "Sophia Tsoka", "Elzbieta Janowska-Sejda", "Chris J. Rawlings", "Kim E. Hammond-Kosack", "Mansoor Saqi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0067926.t005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_the_distribution_of_known_phenotypes_of_the_seeds_within_the_four_predicted_networks_/739579", "title"=>"Comparison of the distribution of known phenotypes of the seeds within the four predicted networks.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-04 01:50:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1111242", "https://ndownloader.figshare.com/files/1111244", "https://ndownloader.figshare.com/files/1111245", "https://ndownloader.figshare.com/files/1111246", "https://ndownloader.figshare.com/files/1111247", "https://ndownloader.figshare.com/files/1111248", "https://ndownloader.figshare.com/files/1111249", "https://ndownloader.figshare.com/files/1111250", "https://ndownloader.figshare.com/files/1111251", "https://ndownloader.figshare.com/files/1111252", "https://ndownloader.figshare.com/files/1111253", "https://ndownloader.figshare.com/files/1111254", "https://ndownloader.figshare.com/files/1111255", "https://ndownloader.figshare.com/files/1111256", "https://ndownloader.figshare.com/files/1111257"], "description"=>"<div><p>The identification of virulence genes in plant pathogenic fungi is important for understanding the infection process, host range and for developing control strategies. The analysis of already verified virulence genes in phytopathogenic fungi in the context of integrated functional networks can give clues about the underlying mechanisms and pathways directly or indirectly linked to fungal pathogenicity and can suggest new candidates for further experimental investigation, using a ‘guilt by association’ approach. Here we study 133 genes in the globally important Ascomycete fungus <i>Fusarium graminearum</i> that have been experimentally tested for their involvement in virulence. An integrated network that combines information from gene co-expression, predicted protein-protein interactions and sequence similarity was employed and, using 100 genes known to be required for virulence, we found a total of 215 new proteins potentially associated with virulence of which 29 are annotated as hypothetical proteins. The majority of these potential virulence genes are located in chromosomal regions known to have a low recombination frequency. We have also explored the taxonomic diversity of these candidates and found 25 sequences, which are likely to be fungal specific. We discuss the biological relevance of a few of the potentially novel virulence associated genes in detail. The analysis of already verified virulence genes in phytopathogenic fungi in the context of integrated functional networks can give clues about the underlying mechanisms and pathways directly or indirectly linked to fungal pathogenicity and can suggest new candidates for further experimental investigation, using a ‘guilt by association’ approach.</p></div>", "links"=>[], "tags"=>["biotechnology", "Genetic engineering", "Genetically modified organisms", "Computational biology", "genomics", "Genome analysis tools", "Gene prediction", "Comparative genomics", "Functional genomics", "Genome databases", "Molecular genetics", "Gene identification and analysis", "genetics", "Gene function", "microbiology", "Mycology", "fungi", "Host-pathogen interaction", "Model organisms", "Yeast and fungal models", "network-based", "selecting", "virulence", "proteins", "cereal", "infecting", "fungus"], "article_id"=>739580, "categories"=>["Biological Sciences"], "users"=>["Artem Lysenko", "Martin Urban", "Laura Bennett", "Sophia Tsoka", "Elzbieta Janowska-Sejda", "Chris J. Rawlings", "Kim E. Hammond-Kosack", "Mansoor Saqi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0067926.s001", "https://dx.doi.org/10.1371/journal.pone.0067926.s002", "https://dx.doi.org/10.1371/journal.pone.0067926.s003", "https://dx.doi.org/10.1371/journal.pone.0067926.s004", "https://dx.doi.org/10.1371/journal.pone.0067926.s005", "https://dx.doi.org/10.1371/journal.pone.0067926.s006", "https://dx.doi.org/10.1371/journal.pone.0067926.s007", "https://dx.doi.org/10.1371/journal.pone.0067926.s008", "https://dx.doi.org/10.1371/journal.pone.0067926.s009", "https://dx.doi.org/10.1371/journal.pone.0067926.s010", "https://dx.doi.org/10.1371/journal.pone.0067926.s011", "https://dx.doi.org/10.1371/journal.pone.0067926.s012", "https://dx.doi.org/10.1371/journal.pone.0067926.s013", "https://dx.doi.org/10.1371/journal.pone.0067926.s014", "https://dx.doi.org/10.1371/journal.pone.0067926.s015"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Network_Based_Data_Integration_for_Selecting_Candidate_Virulence_Associated_Proteins_in_the_Cereal_Infecting_Fungus_Fusarium_graminearum_/739580", "title"=>"Network-Based Data Integration for Selecting Candidate Virulence Associated Proteins in the Cereal Infecting Fungus <i>Fusarium graminearum</i>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-07-04 01:50:37"}

PMC Usage Stats | Further Information

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