Using Information Interaction to Discover Epistatic Effects in Complex Diseases
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{"title"=>"Using Information Interaction to Discover Epistatic Effects in Complex Diseases", "type"=>"journal", "authors"=>[{"first_name"=>"Orlando", "last_name"=>"Anunciação", "scopus_author_id"=>"37121440000"}, {"first_name"=>"Susana", "last_name"=>"Vinga", "scopus_author_id"=>"55893670600"}, {"first_name"=>"Arlindo L.", "last_name"=>"Oliveira", "scopus_author_id"=>"7201929537"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"24194833", "sgr"=>"84886052456", "doi"=>"10.1371/journal.pone.0076300", "scopus"=>"2-s2.0-84886052456", "pui"=>"370091171", "issn"=>"19326203"}, "id"=>"b1fc847f-1903-3410-bcc3-64500a6a74b1", "abstract"=>"It is widely agreed that complex diseases are typically caused by the joint effects of multiple instead of a single genetic variation. These genetic variations may show stronger effects when considered together than when considered individually, a phenomenon known as epistasis or multilocus interaction. In this work, we explore the applicability of information interaction to discover pairwise epistatic effects related with complex diseases. We start by showing that traditional approaches such as classification methods or greedy feature selection methods (such as the Fleuret method) do not perform well on this problem. We then compare our information interaction method with BEAM and SNPHarvester in artificial datasets simulating epistatic interactions and show that our method is more powerful to detect pairwise epistatic interactions than its competitors. We show results of the application of information interaction method to the WTCCC breast cancer dataset. Our results are validated using permutation tests. We were able to find 89 statistically significant pairwise interactions with a p-value lower than 10(-3). Even though many recent algorithms have been designed to find epistasis with low marginals, we observed that all (except one) of the SNPs involved in statistically significant interactions have moderate or high marginals. We also report that the interactions found in this work were not present in gene-gene interaction network STRING.", "link"=>"http://www.mendeley.com/research/using-information-interaction-discover-epistatic-effects-complex-diseases-3", "reader_count"=>13, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>4, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>1, "Student > Master"=>1, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>4, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>1, "Student > Master"=>1, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>2, "Mathematics"=>1, "Medicine and Dentistry"=>1, "Agricultural and Biological Sciences"=>4, "Neuroscience"=>1, "Computer Science"=>4}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Neuroscience"=>{"Neuroscience"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>4}, "Computer Science"=>{"Computer Science"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Mathematics"=>{"Mathematics"=>1}}, "reader_count_by_country"=>{"Portugal"=>1, "Germany"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/1255548"], "description"=>"<p>Graph representing the gene-gene interactions found with information interaction method on the WTCCC Breast Cancer dataset.</p>", "links"=>[], "tags"=>["gene-gene", "interactions", "wtccc", "cancer"], "article_id"=>830587, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["Orlando Anunciação", "Susana Vinga", "Arlindo L. Oliveira"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0076300.g007", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Graph_representing_the_gene_gene_interactions_found_with_information_interaction_method_on_the_WTCCC_Breast_Cancer_dataset_/830587", "title"=>"Graph representing the gene-gene interactions found with information interaction method on the WTCCC Breast Cancer dataset.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-23 02:48:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1255542"], "description"=>"<p> is on the horizontal axis and Information Interaction is on the vertical axis. The 5 interacting pairs are very explicit, with information interaction values above 0.19.</p>", "links"=>[], "tags"=>["pairs", "snps"], "article_id"=>830581, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["Orlando Anunciação", "Susana Vinga", "Arlindo L. Oliveira"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0076300.g002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Information_Interaction_values_for_all_pairs_of_SNPs_in_artificial_dataset_/830581", "title"=>"Information Interaction values for all pairs of SNPs in artificial dataset.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-23 02:48:02"}
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  • {"files"=>["https://ndownloader.figshare.com/files/1255550"], "description"=>"<p>SNPs and their respective genes discovered with both IIM and MIM, only with IIM and only with MIM. Between parenthesis we have the number of SNPs in the respective category.</p>", "links"=>[], "tags"=>["respective", "genes", "discovered", "iim", "parenthesis", "snps"], "article_id"=>830589, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["Orlando Anunciação", "Susana Vinga", "Arlindo L. Oliveira"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0076300.t004", "stats"=>{"downloads"=>4, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SNPs_and_their_respective_genes_discovered_with_both_IIM_and_MIM_only_with_IIM_and_only_with_MIM_Between_parenthesis_we_have_the_number_of_SNPs_in_the_respective_category_/830589", "title"=>"SNPs and their respective genes discovered with both IIM and MIM, only with IIM and only with MIM. Between parenthesis we have the number of SNPs in the respective category.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-10-23 02:48:02"}
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  • {"files"=>["https://ndownloader.figshare.com/files/1255546"], "description"=>"<p>Accumulated number of pairwise interactions detected with Information Interaction in WTCCC Breast Cancer Dataset with and .</p>", "links"=>[], "tags"=>["pairwise", "interactions", "wtccc", "cancer", "dataset"], "article_id"=>830585, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["Orlando Anunciação", "Susana Vinga", "Arlindo L. Oliveira"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0076300.g006", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Accumulated_number_of_pairwise_interactions_detected_with_Information_Interaction_in_WTCCC_Breast_Cancer_Dataset_with_and_/830585", "title"=>"Accumulated number of pairwise interactions detected with Information Interaction in WTCCC Breast Cancer Dataset with and .", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-23 02:48:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1255544"], "description"=>"<p>Comparison of Information Interaction Search with 10 permutations for threshold selection with SNP Harvester and BEAM in terms of Power.</p>", "links"=>[], "tags"=>["10", "permutations", "snp", "harvester"], "article_id"=>830583, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["Orlando Anunciação", "Susana Vinga", "Arlindo L. Oliveira"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0076300.g004", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_Information_Interaction_Search_with_10_permutations_for_threshold_selection_with_SNP_Harvester_and_BEAM_in_terms_of_Power_/830583", "title"=>"Comparison of Information Interaction Search with 10 permutations for threshold selection with SNP Harvester and BEAM in terms of Power.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-23 02:48:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1255545"], "description"=>"<p>SNP Harvester false positives were obtained by inspecting SNP Harvester results files that are available in <a href=\"http://bioinformatics.ust.hk/SNPHarvester.html\" target=\"_blank\">http://bioinformatics.ust.hk/SNPHarvester.html</a>.</p>", "links"=>[], "tags"=>["ii", "snp", "harvester"], "article_id"=>830584, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["Orlando Anunciação", "Susana Vinga", "Arlindo L. Oliveira"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0076300.g005", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_II_Method_and_SNP_Harvester_in_terms_of_False_Positives_/830584", "title"=>"Comparison of II Method and SNP Harvester in terms of False Positives.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-23 02:48:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1255543"], "description"=>"<p>In this dataset, two pairwise interactions seem evident, but the other three are difficult to detect.</p>", "links"=>[], "tags"=>["pairwise", "interactions"], "article_id"=>830582, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["Orlando Anunciação", "Susana Vinga", "Arlindo L. Oliveira"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0076300.g003", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_In_this_dataset_two_pairwise_interactions_seem_evident_but_the_other_three_are_difficult_to_detect_/830582", "title"=>"In this dataset, two pairwise interactions seem evident, but the other three are difficult to detect.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-23 02:48:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1255552"], "description"=>"<p>Number of SNPs detected in the WTCCC Breast Cancer dataset with Mutual Information Method and a threshold .</p>", "links"=>[], "tags"=>["snps", "wtccc", "cancer", "dataset"], "article_id"=>830591, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["Orlando Anunciação", "Susana Vinga", "Arlindo L. Oliveira"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0076300.t003", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_SNPs_detected_in_the_WTCCC_Breast_Cancer_dataset_with_Mutual_Information_Method_and_a_threshold_/830591", "title"=>"Number of SNPs detected in the WTCCC Breast Cancer dataset with Mutual Information Method and a threshold .", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-10-23 02:48:02"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"6", "full-text"=>"3", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}

Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Computational biology", "average_usage"=>[295, 511, 651, 775, 882, 992, 1100, 1201, 1304, 1400, 1486, 1570, 1650]}, {"subject_area"=>"/Biology and life sciences/Neuroscience", "average_usage"=>[261, 444, 554, 655, 748, 834, 923, 1004, 1089, 1170, 1244, 1315, 1380]}, {"subject_area"=>"/Computer and information sciences/Artificial intelligence", "average_usage"=>[271, 413, 528, 633, 737, 815, 890, 970, 1042, 1119, 1222, 1287, 1315]}, {"subject_area"=>"/Engineering and technology", "average_usage"=>[254, 440, 558, 675, 785, 883, 972, 1061, 1154, 1248, 1336, 1414, 1489]}, {"subject_area"=>"/Medicine and health sciences/Oncology", "average_usage"=>[249, 468, 599, 718, 820, 920, 1008, 1093, 1181, 1281, 1357, 1444, 1517]}, {"subject_area"=>"/Physical sciences", "average_usage"=>[254, 431, 547, 651, 748, 842, 932, 1017, 1098, 1178, 1259, 1336, 1404]}, {"subject_area"=>"/Physical sciences/Mathematics", "average_usage"=>[259, 431, 541, 639, 727, 816, 898, 980, 1061, 1136, 1214, 1294, 1356]}]}
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