Integrated Pathway Clusters with Coherent Biological Themes for Target Prioritisation
Events
Loading … Spinner

Mendeley | Further Information

{"title"=>"Integrated pathway clusters with coherent biological themes for target prioritisation", "type"=>"journal", "authors"=>[{"first_name"=>"Yi An", "last_name"=>"Chen", "scopus_author_id"=>"55895369000"}, {"first_name"=>"Lokesh P.", "last_name"=>"Tripathi", "scopus_author_id"=>"14525859300"}, {"first_name"=>"Benoit H.", "last_name"=>"Dessailly", "scopus_author_id"=>"16480149500"}, {"first_name"=>"Johan", "last_name"=>"Nyström-Persson", "scopus_author_id"=>"16233899800"}, {"first_name"=>"Shandar", "last_name"=>"Ahmad", "scopus_author_id"=>"7401993307"}, {"first_name"=>"Kenji", "last_name"=>"Mizuguchi", "scopus_author_id"=>"7101693768"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"24918583", "sgr"=>"84903397448", "doi"=>"10.1371/journal.pone.0099030", "scopus"=>"2-s2.0-84903397448", "pui"=>"373399025", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "issn"=>"19326203"}, "id"=>"2242ed7d-69d8-31cd-a3fd-f85df50e3fd8", "abstract"=>"Prioritising candidate genes for further experimental characterisation is an essential, yet challenging task in biomedical research. One way of achieving this goal is to identify specific biological themes that are enriched within the gene set of interest to obtain insights into the biological phenomena under study. Biological pathway data have been particularly useful in identifying functional associations of genes and/or gene sets. However, biological pathway information as compiled in varied repositories often differs in scope and content, preventing a more effective and comprehensive characterisation of gene sets. Here we describe a new approach to constructing biologically coherent gene sets from pathway data in major public repositories and employing them for functional analysis of large gene sets. We first revealed significant overlaps in gene content between different pathways and then defined a clustering method based on the shared gene content and the similarity of gene overlap patterns. We established the biological relevance of the constructed pathway clusters using independent quantitative measures and we finally demonstrated the effectiveness of the constructed pathway clusters in comparative functional enrichment analysis of gene sets associated with diverse human diseases gathered from the literature. The pathway clusters and gene mappings have been integrated into the TargetMine data warehouse and are likely to provide a concise, manageable and biologically relevant means of functional analysis of gene sets and to facilitate candidate gene prioritisation.", "link"=>"http://www.mendeley.com/research/integrated-pathway-clusters-coherent-biological-themes-target-prioritisation", "reader_count"=>18, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>8, "Student > Ph. D. Student"=>3, "Student > Master"=>2, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>8, "Student > Ph. D. Student"=>3, "Student > Master"=>2, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>6, "Nursing and Health Professions"=>1, "Agricultural and Biological Sciences"=>8, "Medicine and Dentistry"=>2, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>8}, "Computer Science"=>{"Computer Science"=>1}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}}, "reader_count_by_country"=>{"Canada"=>1, "Korea (South)"=>1}, "group_count"=>0}

Scopus | Further Information

{"@_fa"=>"true", "link"=>[{"@_fa"=>"true", "@ref"=>"self", "@href"=>"https://api.elsevier.com/content/abstract/scopus_id/84903397448"}, {"@_fa"=>"true", "@ref"=>"author-affiliation", "@href"=>"https://api.elsevier.com/content/abstract/scopus_id/84903397448?field=author,affiliation"}, {"@_fa"=>"true", "@ref"=>"scopus", "@href"=>"https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84903397448&origin=inward"}, {"@_fa"=>"true", "@ref"=>"scopus-citedby", "@href"=>"https://www.scopus.com/inward/citedby.uri?partnerID=HzOxMe3b&scp=84903397448&origin=inward"}], "prism:url"=>"https://api.elsevier.com/content/abstract/scopus_id/84903397448", "dc:identifier"=>"SCOPUS_ID:84903397448", "eid"=>"2-s2.0-84903397448", "dc:title"=>"Integrated pathway clusters with coherent biological themes for target prioritisation", "dc:creator"=>"Chen Y.", "prism:publicationName"=>"PLoS ONE", "prism:eIssn"=>"19326203", "prism:volume"=>"9", "prism:issueIdentifier"=>"6", "prism:pageRange"=>nil, "prism:coverDate"=>"2014-06-11", "prism:coverDisplayDate"=>"11 June 2014", "prism:doi"=>"10.1371/journal.pone.0099030", "citedby-count"=>"9", "affiliation"=>[{"@_fa"=>"true", "affilname"=>"National Institute of Biomedical Innovation", "affiliation-city"=>"Ibaraki", "affiliation-country"=>"Japan"}], "pubmed-id"=>"24918583", "prism:aggregationType"=>"Journal", "subtype"=>"ar", "subtypeDescription"=>"Article", "article-number"=>"e99030", "source-id"=>"10600153309", "openaccess"=>"1", "openaccessFlag"=>true}

Facebook

  • {"url"=>"http%3A%2F%2Fjournals.plos.org%2Fplosone%2Farticle%3Fid%3D10.1371%252Fjournal.pone.0099030", "share_count"=>0, "like_count"=>0, "comment_count"=>0, "click_count"=>0, "total_count"=>0}

Counter

  • {"month"=>"6", "year"=>"2014", "pdf_views"=>"45", "xml_views"=>"17", "html_views"=>"294"}
  • {"month"=>"7", "year"=>"2014", "pdf_views"=>"15", "xml_views"=>"0", "html_views"=>"70"}
  • {"month"=>"8", "year"=>"2014", "pdf_views"=>"6", "xml_views"=>"2", "html_views"=>"45"}
  • {"month"=>"9", "year"=>"2014", "pdf_views"=>"2", "xml_views"=>"1", "html_views"=>"46"}
  • {"month"=>"10", "year"=>"2014", "pdf_views"=>"8", "xml_views"=>"1", "html_views"=>"76"}
  • {"month"=>"11", "year"=>"2014", "pdf_views"=>"11", "xml_views"=>"1", "html_views"=>"88"}
  • {"month"=>"12", "year"=>"2014", "pdf_views"=>"6", "xml_views"=>"0", "html_views"=>"59"}
  • {"month"=>"1", "year"=>"2015", "pdf_views"=>"8", "xml_views"=>"1", "html_views"=>"41"}
  • {"month"=>"2", "year"=>"2015", "pdf_views"=>"5", "xml_views"=>"0", "html_views"=>"37"}
  • {"month"=>"3", "year"=>"2015", "pdf_views"=>"2", "xml_views"=>"0", "html_views"=>"33"}
  • {"month"=>"4", "year"=>"2015", "pdf_views"=>"10", "xml_views"=>"1", "html_views"=>"51"}
  • {"month"=>"5", "year"=>"2015", "pdf_views"=>"9", "xml_views"=>"0", "html_views"=>"55"}
  • {"month"=>"6", "year"=>"2015", "pdf_views"=>"8", "xml_views"=>"1", "html_views"=>"49"}
  • {"month"=>"7", "year"=>"2015", "pdf_views"=>"2", "xml_views"=>"0", "html_views"=>"30"}
  • {"month"=>"8", "year"=>"2015", "pdf_views"=>"4", "xml_views"=>"2", "html_views"=>"41"}
  • {"month"=>"9", "year"=>"2015", "pdf_views"=>"7", "xml_views"=>"1", "html_views"=>"55"}
  • {"month"=>"10", "year"=>"2015", "pdf_views"=>"2", "xml_views"=>"0", "html_views"=>"75"}
  • {"month"=>"11", "year"=>"2015", "pdf_views"=>"5", "xml_views"=>"0", "html_views"=>"69"}
  • {"month"=>"12", "year"=>"2015", "pdf_views"=>"2", "xml_views"=>"0", "html_views"=>"73"}
  • {"month"=>"1", "year"=>"2016", "pdf_views"=>"7", "xml_views"=>"0", "html_views"=>"100"}
  • {"month"=>"2", "year"=>"2016", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"38"}
  • {"month"=>"3", "year"=>"2016", "pdf_views"=>"2", "xml_views"=>"0", "html_views"=>"84"}
  • {"month"=>"4", "year"=>"2016", "pdf_views"=>"6", "xml_views"=>"0", "html_views"=>"28"}
  • {"month"=>"5", "year"=>"2016", "pdf_views"=>"5", "xml_views"=>"0", "html_views"=>"26"}
  • {"month"=>"6", "year"=>"2016", "pdf_views"=>"5", "xml_views"=>"0", "html_views"=>"20"}
  • {"month"=>"7", "year"=>"2016", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"13"}
  • {"month"=>"8", "year"=>"2016", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"17"}
  • {"month"=>"9", "year"=>"2016", "pdf_views"=>"8", "xml_views"=>"0", "html_views"=>"27"}
  • {"month"=>"10", "year"=>"2016", "pdf_views"=>"13", "xml_views"=>"0", "html_views"=>"28"}
  • {"month"=>"11", "year"=>"2016", "pdf_views"=>"1", "xml_views"=>"0", "html_views"=>"27"}
  • {"month"=>"12", "year"=>"2016", "pdf_views"=>"8", "xml_views"=>"0", "html_views"=>"22"}
  • {"month"=>"1", "year"=>"2017", "pdf_views"=>"8", "xml_views"=>"1", "html_views"=>"34"}
  • {"month"=>"2", "year"=>"2017", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"34"}
  • {"month"=>"3", "year"=>"2017", "pdf_views"=>"7", "xml_views"=>"0", "html_views"=>"29"}
  • {"month"=>"4", "year"=>"2017", "pdf_views"=>"7", "xml_views"=>"0", "html_views"=>"24"}
  • {"month"=>"5", "year"=>"2017", "pdf_views"=>"2", "xml_views"=>"0", "html_views"=>"27"}
  • {"month"=>"6", "year"=>"2017", "pdf_views"=>"1", "xml_views"=>"0", "html_views"=>"33"}
  • {"month"=>"7", "year"=>"2017", "pdf_views"=>"7", "xml_views"=>"1", "html_views"=>"25"}
  • {"month"=>"8", "year"=>"2017", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"22"}
  • {"month"=>"9", "year"=>"2017", "pdf_views"=>"2", "xml_views"=>"1", "html_views"=>"27"}
  • {"month"=>"10", "year"=>"2017", "pdf_views"=>"3", "xml_views"=>"2", "html_views"=>"38"}
  • {"month"=>"11", "year"=>"2017", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"76"}
  • {"month"=>"12", "year"=>"2017", "pdf_views"=>"3", "xml_views"=>"2", "html_views"=>"36"}
  • {"month"=>"1", "year"=>"2018", "pdf_views"=>"4", "xml_views"=>"1", "html_views"=>"22"}
  • {"month"=>"2", "year"=>"2018", "pdf_views"=>"1", "xml_views"=>"0", "html_views"=>"6"}
  • {"month"=>"3", "year"=>"2018", "pdf_views"=>"12", "xml_views"=>"2", "html_views"=>"30"}
  • {"month"=>"4", "year"=>"2018", "pdf_views"=>"5", "xml_views"=>"1", "html_views"=>"19"}
  • {"month"=>"5", "year"=>"2018", "pdf_views"=>"10", "xml_views"=>"0", "html_views"=>"29"}
  • {"month"=>"6", "year"=>"2018", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"18"}
  • {"month"=>"7", "year"=>"2018", "pdf_views"=>"5", "xml_views"=>"3", "html_views"=>"20"}
  • {"month"=>"8", "year"=>"2018", "pdf_views"=>"6", "xml_views"=>"1", "html_views"=>"14"}
  • {"month"=>"9", "year"=>"2018", "pdf_views"=>"2", "xml_views"=>"0", "html_views"=>"11"}
  • {"month"=>"10", "year"=>"2018", "pdf_views"=>"6", "xml_views"=>"1", "html_views"=>"18"}
  • {"month"=>"11", "year"=>"2018", "pdf_views"=>"9", "xml_views"=>"0", "html_views"=>"21"}
  • {"month"=>"12", "year"=>"2018", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"7"}
  • {"month"=>"1", "year"=>"2019", "pdf_views"=>"2", "xml_views"=>"0", "html_views"=>"6"}
  • {"month"=>"2", "year"=>"2019", "pdf_views"=>"8", "xml_views"=>"0", "html_views"=>"9"}
  • {"month"=>"3", "year"=>"2019", "pdf_views"=>"12", "xml_views"=>"0", "html_views"=>"13"}
  • {"month"=>"4", "year"=>"2019", "pdf_views"=>"10", "xml_views"=>"0", "html_views"=>"13"}
  • {"month"=>"5", "year"=>"2019", "pdf_views"=>"9", "xml_views"=>"0", "html_views"=>"14"}
  • {"month"=>"6", "year"=>"2019", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"21"}
  • {"month"=>"7", "year"=>"2019", "pdf_views"=>"6", "xml_views"=>"0", "html_views"=>"11"}
  • {"month"=>"8", "year"=>"2019", "pdf_views"=>"26", "xml_views"=>"0", "html_views"=>"43"}
  • {"month"=>"9", "year"=>"2019", "pdf_views"=>"6", "xml_views"=>"0", "html_views"=>"9"}

Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1529928"], "description"=>"<p>A) Dendrogram generated by using a matrix of gene overlap indices for all pairwise pathway comparisons. Specific pathway clusters no27 (red) and no15 (blue) are highlighted. B) Cluster no27 “Metabolism of lipids and lipoproteins” included eight pathways, all associated with lipid metabolism. C) Cluster no15 “Glycolysis/Gluconeogenesis | Lysine degradation | Valine, leucine and isoleucine degradation” consisted of ten pathways, most of which were associated with amino acid metabolism.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "Protein interactions", "proteomics", "Computational biology", "Biological data management", "Comparative genomics", "genetics", "genomics", "Functional genomics", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Sequence analysis", "systems biology", "clusters", "functionally", "pathways", "overlap"], "article_id"=>1053293, "categories"=>["Biological Sciences"], "users"=>["Yi-An Chen", "Lokesh P. Tripathi", "Benoît H. Dessailly", "Johan Nyström-Persson", "Shandar Ahmad", "Kenji Mizuguchi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099030.g003", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hierarchical_clusters_of_functionally_related_pathways_based_on_gene_overlap_profiles_/1053293", "title"=>"Hierarchical clusters of functionally related pathways based on gene overlap profiles.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-11 02:43:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1529927"], "description"=>"<p>A) Pathway data are compiled in varied repositories, which differ appreciably in scope and content and B) there exists significant redundancy within pathway definitions among different databases. C) An outline of our approach to integrating pathway data from KEGG, Reactome and NCI-PID databases.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "Protein interactions", "proteomics", "Computational biology", "Biological data management", "Comparative genomics", "genetics", "genomics", "Functional genomics", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Sequence analysis", "systems biology", "challenges", "encountered", "integrating", "pathway"], "article_id"=>1053292, "categories"=>["Biological Sciences"], "users"=>["Yi-An Chen", "Lokesh P. Tripathi", "Benoît H. Dessailly", "Johan Nyström-Persson", "Shandar Ahmad", "Kenji Mizuguchi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099030.g002", "stats"=>{"downloads"=>3, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overcoming_the_challenges_encountered_in_integrating_diverse_pathway_data_/1053292", "title"=>"Overcoming the challenges encountered in integrating diverse pathway data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-11 02:43:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1529924"], "description"=>"<p>Benefits of using an integrated pathway repository for GSFE analysis.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "Protein interactions", "proteomics", "Computational biology", "Biological data management", "Comparative genomics", "genetics", "genomics", "Functional genomics", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Sequence analysis", "systems biology", "pathway", "repository", "gsfe"], "article_id"=>1053289, "categories"=>["Biological Sciences"], "users"=>["Yi-An Chen", "Lokesh P. Tripathi", "Benoît H. Dessailly", "Johan Nyström-Persson", "Shandar Ahmad", "Kenji Mizuguchi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099030.g001", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Benefits_of_using_an_integrated_pathway_repository_for_GSFE_analysis_/1053289", "title"=>"Benefits of using an integrated pathway repository for GSFE analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-11 02:43:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1529936"], "description"=>"<p><i>Purity</i> and <i>edit distance</i> scores at different <i>PD</i> cutoffs (0.6, 0.65 and 0.75) are included for comparison.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "Protein interactions", "proteomics", "Computational biology", "Biological data management", "Comparative genomics", "genetics", "genomics", "Functional genomics", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Sequence analysis", "systems biology", "scores", "ipcs", "benchmarked", "kegg", "pathway", "sub-types", "higher", "randomised"], "article_id"=>1053301, "categories"=>["Biological Sciences"], "users"=>["Yi-An Chen", "Lokesh P. Tripathi", "Benoît H. Dessailly", "Johan Nyström-Persson", "Shandar Ahmad", "Kenji Mizuguchi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099030.t003", "stats"=>{"downloads"=>7, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Purity_and_Edit_distance_scores_for_the_IPCs_PD_0_7_when_benchmarked_against_the_KEGG_pathway_sub_types_either_at_the_top_level_Main_class_or_the_second_level_Sub_class_were_much_higher_than_those_of_the_randomised_dendrograms_/1053301", "title"=>"<i>Purity</i> and <i>Edit distance</i> scores for the IPCs (<i>PD</i> = 0.7) when benchmarked against the KEGG pathway sub-types either at the top level (Main class) or the second level (Sub class) were much higher than those of the randomised dendrograms.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-11 02:43:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1529935"], "description"=>"<p>The number of human genes and pathways from different databases, which were consolidated into clusters of related pathways.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "Protein interactions", "proteomics", "Computational biology", "Biological data management", "Comparative genomics", "genetics", "genomics", "Functional genomics", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Sequence analysis", "systems biology", "genes", "pathways", "consolidated", "clusters"], "article_id"=>1053300, "categories"=>["Biological Sciences"], "users"=>["Yi-An Chen", "Lokesh P. Tripathi", "Benoît H. Dessailly", "Johan Nyström-Persson", "Shandar Ahmad", "Kenji Mizuguchi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099030.t001", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_number_of_human_genes_and_pathways_from_different_databases_which_were_consolidated_into_clusters_of_related_pathways_/1053300", "title"=>"The number of human genes and pathways from different databases, which were consolidated into clusters of related pathways.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-11 02:43:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1529930"], "description"=>"<p>Functional similarity (<i>FS</i>) scores within a pathway cluster (Intra-cluster) were much higher than scores across pathway clusters (Inter-cluster).</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "Protein interactions", "proteomics", "Computational biology", "Biological data management", "Comparative genomics", "genetics", "genomics", "Functional genomics", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Sequence analysis", "systems biology", "scores", "pathway", "higher", "clusters"], "article_id"=>1053295, "categories"=>["Biological Sciences"], "users"=>["Yi-An Chen", "Lokesh P. Tripathi", "Benoît H. Dessailly", "Johan Nyström-Persson", "Shandar Ahmad", "Kenji Mizuguchi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099030.g004", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Functional_similarity_FS_scores_within_a_pathway_cluster_Intra_cluster_were_much_higher_than_scores_across_pathway_clusters_Inter_cluster_/1053295", "title"=>"Functional similarity (<i>FS</i>) scores within a pathway cluster (Intra-cluster) were much higher than scores across pathway clusters (Inter-cluster).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-11 02:43:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1529944", "https://ndownloader.figshare.com/files/1529945", "https://ndownloader.figshare.com/files/1529946", "https://ndownloader.figshare.com/files/1529947", "https://ndownloader.figshare.com/files/1529948"], "description"=>"<div><p>Prioritising candidate genes for further experimental characterisation is an essential, yet challenging task in biomedical research. One way of achieving this goal is to identify specific biological themes that are enriched within the gene set of interest to obtain insights into the biological phenomena under study. Biological pathway data have been particularly useful in identifying functional associations of genes and/or gene sets. However, biological pathway information as compiled in varied repositories often differs in scope and content, preventing a more effective and comprehensive characterisation of gene sets. Here we describe a new approach to constructing biologically coherent gene sets from pathway data in major public repositories and employing them for functional analysis of large gene sets. We first revealed significant overlaps in gene content between different pathways and then defined a clustering method based on the shared gene content and the similarity of gene overlap patterns. We established the biological relevance of the constructed pathway clusters using independent quantitative measures and we finally demonstrated the effectiveness of the constructed pathway clusters in comparative functional enrichment analysis of gene sets associated with diverse human diseases gathered from the literature. The pathway clusters and gene mappings have been integrated into the TargetMine data warehouse and are likely to provide a concise, manageable and biologically relevant means of functional analysis of gene sets and to facilitate candidate gene prioritisation.</p></div>", "links"=>[], "tags"=>["Biochemistry", "proteins", "Protein interactions", "proteomics", "Computational biology", "Biological data management", "Comparative genomics", "genetics", "genomics", "Functional genomics", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Sequence analysis", "systems biology", "pathway", "clusters", "coherent", "themes"], "article_id"=>1053305, "categories"=>["Biological Sciences"], "users"=>["Yi-An Chen", "Lokesh P. Tripathi", "Benoît H. Dessailly", "Johan Nyström-Persson", "Shandar Ahmad", "Kenji Mizuguchi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0099030.s001", "https://dx.doi.org/10.1371/journal.pone.0099030.s002", "https://dx.doi.org/10.1371/journal.pone.0099030.s003", "https://dx.doi.org/10.1371/journal.pone.0099030.s004", "https://dx.doi.org/10.1371/journal.pone.0099030.s005"], "stats"=>{"downloads"=>52, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Integrated_Pathway_Clusters_with_Coherent_Biological_Themes_for_Target_Prioritisation_/1053305", "title"=>"Integrated Pathway Clusters with Coherent Biological Themes for Target Prioritisation", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-06-11 02:43:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1529940"], "description"=>"<p>Pathway pairs within (intra-database) and across (intra-database) pathway datasets, with <i>OI<sub>i,j</sub></i> >0.8.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "Protein interactions", "proteomics", "Computational biology", "Biological data management", "Comparative genomics", "genetics", "genomics", "Functional genomics", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Sequence analysis", "systems biology", "pairs", "pathway"], "article_id"=>1053303, "categories"=>["Biological Sciences"], "users"=>["Yi-An Chen", "Lokesh P. Tripathi", "Benoît H. Dessailly", "Johan Nyström-Persson", "Shandar Ahmad", "Kenji Mizuguchi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099030.t002", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pathway_pairs_within_intra_database_and_across_intra_database_pathway_datasets_with_OI_i_j_0_8_/1053303", "title"=>"Pathway pairs within (intra-database) and across (intra-database) pathway datasets, with <i>OI<sub>i,j</sub></i> >0.8.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-11 02:43:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1529934"], "description"=>"<p>The online user interface allows the users to query and visualise integrated pathway clusters and perform GSFE analysis with the supplied list of genes.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "Protein interactions", "proteomics", "Computational biology", "Biological data management", "Comparative genomics", "genetics", "genomics", "Functional genomics", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Sequence analysis", "systems biology", "interface", "allows", "users", "query", "visualise", "pathway", "clusters", "gsfe", "supplied"], "article_id"=>1053299, "categories"=>["Biological Sciences"], "users"=>["Yi-An Chen", "Lokesh P. Tripathi", "Benoît H. Dessailly", "Johan Nyström-Persson", "Shandar Ahmad", "Kenji Mizuguchi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099030.g005", "stats"=>{"downloads"=>0, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_online_user_interface_allows_the_users_to_query_and_visualise_integrated_pathway_clusters_and_perform_GSFE_analysis_with_the_supplied_list_of_genes_/1053299", "title"=>"The online user interface allows the users to query and visualise integrated pathway clusters and perform GSFE analysis with the supplied list of genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-11 02:43:26"}

PMC Usage Stats | Further Information

  • {"unique-ip"=>"11", "full-text"=>"9", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"10"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"2"}
  • {"unique-ip"=>"3", "full-text"=>"1", "pdf"=>"1", "abstract"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"11"}
  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"12"}
  • {"unique-ip"=>"8", "full-text"=>"11", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"1"}
  • {"unique-ip"=>"9", "full-text"=>"5", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"2", "year"=>"2015", "month"=>"11"}
  • {"unique-ip"=>"7", "full-text"=>"5", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"12"}
  • {"unique-ip"=>"5", "full-text"=>"2", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"1"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"3"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"4"}
  • {"unique-ip"=>"1", "full-text"=>"2", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"5"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"6"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"7"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"8"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"9"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"10"}
  • {"unique-ip"=>"4", "full-text"=>"2", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"11"}
  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"12"}
  • {"unique-ip"=>"6", "full-text"=>"1", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"1"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"2"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"3"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"4"}
  • {"unique-ip"=>"28", "full-text"=>"11", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"5", "cited-by"=>"1", "year"=>"2017", "month"=>"5"}
  • {"unique-ip"=>"6", "full-text"=>"3", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"6"}
  • {"unique-ip"=>"3", "full-text"=>"4", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"7"}
  • {"unique-ip"=>"2", "full-text"=>"1", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"8"}
  • {"unique-ip"=>"1", "full-text"=>"0", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"9"}
  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"11"}
  • {"unique-ip"=>"1", "full-text"=>"2", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"1"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}
  • {"unique-ip"=>"3", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"1"}
  • {"unique-ip"=>"2", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"5", "full-text"=>"3", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"4"}
  • {"unique-ip"=>"7", "full-text"=>"7", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"9", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"5"}
  • {"unique-ip"=>"1", "full-text"=>"0", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
  • {"unique-ip"=>"8", "full-text"=>"5", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"8", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"6", "full-text"=>"6", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"12", "full-text"=>"8", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"3", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"9", "full-text"=>"12", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"3", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"12", "full-text"=>"5", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"5", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"9", "full-text"=>"8", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}

Relative Metric

{"start_date"=>"2014-01-01T00:00:00Z", "end_date"=>"2014-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[291]}, {"subject_area"=>"/Biology and life sciences/Molecular biology", "average_usage"=>[292, 461]}, {"subject_area"=>"/Computer and information sciences", "average_usage"=>[327, 511]}, {"subject_area"=>"/Medicine and health sciences/Oncology", "average_usage"=>[266]}]}
Loading … Spinner
There are currently no alerts