The Identification of Pathway Markers in Intracranial Aneurysm Using Genome-Wide Association Data from Two Different Populations
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{"title"=>"The Identification of Pathway Markers in Intracranial Aneurysm Using Genome-Wide Association Data from Two Different Populations", "type"=>"journal", "authors"=>[{"first_name"=>"Burcu", "last_name"=>"Bakir-Gungor", "scopus_author_id"=>"25932029800"}, {"first_name"=>"Osman Ugur", "last_name"=>"Sezerman", "scopus_author_id"=>"15124634800"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84874587780", "pui"=>"368465839", "doi"=>"10.1371/journal.pone.0057022", "isbn"=>"1932-6203", "sgr"=>"84874587780", "pmid"=>"23483893"}, "id"=>"fd034cf7-6537-391c-8135-b2efbd0790dd", "abstract"=>"The identification of significant individual factors causing complex diseases is challenging in genome-wide association studies (GWAS) since each factor has only a modest effect on the disease development mechanism. In this study, we hypothesize that the biological pathways that are targeted by these individual factors show higher conservation within and across populations. To test this hypothesis, we searched for the disease related pathways on two intracranial aneurysm GWAS in European and Japanese case-control cohorts. Even though there were a few significantly conserved SNPs within and between populations, seven of the top ten affected pathways were found significant in both populations. The probability of random occurrence of such an event is 2.44E-36. We therefore claim that even though each individual has a unique combination of factors involved in the mechanism of disease development, most targeted pathways that need to be altered by these factors are, for the most part, the same. These pathways can serve as disease markers. Individuals, for example, can be scanned for factors affecting the genes in marker pathways. Hence, individual factors of disease development can be determined; and this knowledge can be exploited for drug development and personalized therapeutic applications. Here, we discuss the potential avenues of pathway markers in medicine and their translation to preventive and individualized health care.", "link"=>"http://www.mendeley.com/research/identification-pathway-markers-intracranial-aneurysm-using-genomewide-association-data-two-different-2", "reader_count"=>17, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>3, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>6, "Student > Master"=>3, "Student > Bachelor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>3, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>6, "Student > Master"=>3, "Student > Bachelor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>1, "Mathematics"=>1, "Medicine and Dentistry"=>6, "Agricultural and Biological Sciences"=>4, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Psychology"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>6}, "Psychology"=>{"Psychology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>4}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>2}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"United States"=>1}, "group_count"=>8}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/978602"], "description"=>"<p>The set of genes shown in blue includes genes that are found by EU GWAS; yellow includes genes that are found by JP GWAS; red includes genes that are found both by EU and JP GWAS.</p>", "links"=>[], "tags"=>["pathway", "mapk"], "article_id"=>645550, "categories"=>["Biological Sciences", "Genetics", "Neuroscience"], "users"=>["Burcu Bakir-Gungor", "Osman Ugur Sezerman"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0057022.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_KEGG_pathway_for_MAPK_signaling_/645550", "title"=>"KEGG pathway for MAPK signaling.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-07 08:51:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/978609"], "description"=>"<p>The shade of red color in genes indicates the number of targeted SNPs in JP population per base pair of the gene. Red refers to the highest targeted gene, whereas white refers to a gene product, not targeted by the SNPs. Blue border indicates that the gene is found to be differentially expressed.</p>", "links"=>[], "tags"=>["pathway", "tgf-beta"], "article_id"=>645556, "categories"=>["Biological Sciences", "Genetics", "Neuroscience"], "users"=>["Burcu Bakir-Gungor", "Osman Ugur Sezerman"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0057022.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_KEGG_pathway_map_for_TGF_beta_signaling_pathway_/645556", "title"=>"KEGG pathway map for TGF-beta signaling pathway.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-07 08:51:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/978611"], "description"=>"<p>The set of genes shown in blue includes genes that are found by EU GWAS; yellow includes genes that are found by JP GWAS; red includes genes that are found both by EU and JP GWAS.</p>", "links"=>[], "tags"=>["pathway", "calcium"], "article_id"=>645558, "categories"=>["Biological Sciences", "Genetics", "Neuroscience"], "users"=>["Burcu Bakir-Gungor", "Osman Ugur Sezerman"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0057022.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_KEGG_pathway_for_calcium_signaling_/645558", "title"=>"KEGG pathway for calcium signaling.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-07 08:52:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/978615"], "description"=>"<p>In steps (i) to (v), a gene-wise Pw-value for association with disease was computed by integrating functional information. In step (vi), Pw-values were loaded as two separate attributes of the genes in a PPI network. In step (vii), active sub-networks of interacting gene products that were also associated with the disease, are identified. In step (viii), genes in an identified active sub-network were tested whether they are part of functionally important KEGG pathways. Lastly, step (ix) integrates the functional enrichments of the generated sub-networks.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "neurological disorders"], "article_id"=>645560, "categories"=>["Biological Sciences", "Genetics", "Neuroscience"], "users"=>["Burcu Bakir-Gungor", "Osman Ugur Sezerman"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0057022.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Outline_of_our_assessment_process_/645560", "title"=>"Outline of our assessment process.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-07 08:52:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/978622", "https://ndownloader.figshare.com/files/978623", "https://ndownloader.figshare.com/files/978624", "https://ndownloader.figshare.com/files/978625", "https://ndownloader.figshare.com/files/978630"], "description"=>"<div><p>The identification of significant individual factors causing complex diseases is challenging in genome-wide association studies (GWAS) since each factor has only a modest effect on the disease development mechanism. In this study, we hypothesize that the biological pathways that are targeted by these individual factors show higher conservation within and across populations. To test this hypothesis, we searched for the disease related pathways on two intracranial aneurysm GWAS in European and Japanese case–control cohorts. Even though there were a few significantly conserved SNPs within and between populations, seven of the top ten affected pathways were found significant in both populations. The probability of random occurrence of such an event is 2.44E−36. We therefore claim that even though each individual has a unique combination of factors involved in the mechanism of disease development, most targeted pathways that need to be altered by these factors are, for the most part, the same. These pathways can serve as disease markers. Individuals, for example, can be scanned for factors affecting the genes in marker pathways. Hence, individual factors of disease development can be determined; and this knowledge can be exploited for drug development and personalized therapeutic applications. Here, we discuss the potential avenues of pathway markers in medicine and their translation to preventive and individualized health care.</p> </div>", "links"=>[], "tags"=>["pathway", "markers", "intracranial", "aneurysm", "genome-wide", "populations"], "article_id"=>645567, "categories"=>["Biological Sciences", "Genetics", "Neuroscience"], "users"=>["Burcu Bakir-Gungor", "Osman Ugur Sezerman"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0057022.s001", "https://dx.doi.org/10.1371/journal.pone.0057022.s002", "https://dx.doi.org/10.1371/journal.pone.0057022.s003", "https://dx.doi.org/10.1371/journal.pone.0057022.s004", "https://dx.doi.org/10.1371/journal.pone.0057022.s005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Identification_of_Pathway_Markers_in_Intracranial_Aneurysm_Using_Genome_Wide_Association_Data_from_Two_Different_Populations__/645567", "title"=>"The Identification of Pathway Markers in Intracranial Aneurysm Using Genome-Wide Association Data from Two Different Populations", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-03-07 08:53:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1006301"], "description"=>"<p>7 commonly identified out of the top 10 affected pathways in both populations are shown in bold. 12 commonly identified pathways out of the top 20 are shown in italic.</p>", "links"=>[], "tags"=>["20", "over-represented", "eu", "jp"], "article_id"=>666927, "categories"=>["Biological Sciences", "Genetics", "Neuroscience"], "users"=>["Burcu Bakir-Gungor", "Osman Ugur Sezerman"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0057022.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_top_20_over_represented_pathways_identified_for_both_EU_and_JP_populations_/666927", "title"=>"The top 20 over-represented pathways, identified for both EU and JP populations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-06 01:55:27"}

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