Global Changes in Gene Expression of Barrett's Esophagus Compared to Normal Squamous Esophagus and Gastric Cardia Tissues
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{"title"=>"Global changes in gene expression of Barrett's esophagus compared to normal squamous esophagus and gastric cardia tissues", "type"=>"journal", "authors"=>[{"first_name"=>"Paula L.", "last_name"=>"Hyland", "scopus_author_id"=>"7004136309"}, {"first_name"=>"Nan", "last_name"=>"Hu", "scopus_author_id"=>"7202092916"}, {"first_name"=>"Melissa", "last_name"=>"Rotunno", "scopus_author_id"=>"24399869700"}, {"first_name"=>"Hua", "last_name"=>"Su", "scopus_author_id"=>"55727439800"}, {"first_name"=>"Chaoyu", "last_name"=>"Wang", "scopus_author_id"=>"55676494700"}, {"first_name"=>"Lemin", "last_name"=>"Wang", "scopus_author_id"=>"55677064900"}, {"first_name"=>"Ruth M.", "last_name"=>"Pfeiffer", "scopus_author_id"=>"56418948100"}, {"first_name"=>"Barbara", "last_name"=>"Gherman", "scopus_author_id"=>"56136644800"}, {"first_name"=>"Carol", "last_name"=>"Giffen", "scopus_author_id"=>"6701655220"}, {"first_name"=>"Cathy", "last_name"=>"Dykes", "scopus_author_id"=>"7003973859"}, {"first_name"=>"Sanford M.", "last_name"=>"Dawsey", "scopus_author_id"=>"7006254703"}, {"first_name"=>"Christian C.", "last_name"=>"Abnet", "scopus_author_id"=>"6701628811"}, {"first_name"=>"Kathryn M.", "last_name"=>"Johnson", "scopus_author_id"=>"56135034900"}, {"first_name"=>"Ruben D.", "last_name"=>"Acosta", "scopus_author_id"=>"57199405513"}, {"first_name"=>"Patrick E.", "last_name"=>"Young", "scopus_author_id"=>"26024508900"}, {"first_name"=>"Brooks D.", "last_name"=>"Cash", "scopus_author_id"=>"57189526947"}, {"first_name"=>"Philip R.", "last_name"=>"Taylor", "scopus_author_id"=>"56424546400"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"isbn"=>"1932-6203", "sgr"=>"84899583153", "pui"=>"372971546", "pmid"=>"24714516", "issn"=>"19326203", "scopus"=>"2-s2.0-84899583153", "doi"=>"10.1371/journal.pone.0093219"}, "id"=>"302f2995-2937-301d-a21f-6cc38a86cccd", "abstract"=>"BACKGROUND: Barrett's esophagus (BE) is a metaplastic precursor lesion of esophageal adenocarcinoma (EA), the most rapidly increasing cancer in western societies. While the prevalence of BE is increasing, the vast majority of EA occurs in patients with undiagnosed BE. Thus, we sought to identify genes that are altered in BE compared to the normal mucosa of the esophagus, and which may be potential biomarkers for the development or diagnosis of BE. DESIGN: We performed gene expression analysis using HG-U133A Affymetrix chips on fresh frozen tissue samples of Barrett's metaplasia and matched normal mucosa from squamous esophagus (NE) and gastric cardia (NC) in 40 BE patients. RESULTS: Using a cut off of 2-fold and P<1.12E-06 (0.05 with Bonferroni correction), we identified 1324 differentially-expressed genes comparing BE vs NE and 649 differentially-expressed genes comparing BE vs NC. Except for individual genes such as the SOXs and PROM1 that were dysregulated only in BE vs NE, we found a subset of genes (n = 205) whose expression was significantly altered in both BE vs NE and BE vs NC. These genes were overrepresented in different pathways, including TGF-β and Notch. CONCLUSION: Our findings provide additional data on the global transcriptome in BE tissues compared to matched NE and NC tissues which should promote further understanding of the functions and regulatory mechanisms of genes involved in BE development, as well as insight into novel genes that may be useful as potential biomarkers for the diagnosis of BE in the future.", "link"=>"http://www.mendeley.com/research/global-changes-gene-expression-barretts-esophagus-compared-normal-squamous-esophagus-gastric-cardia", "reader_count"=>16, "reader_count_by_academic_status"=>{"Researcher"=>4, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>3, "Other"=>3, "Student > Bachelor"=>1, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Researcher"=>4, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>3, "Other"=>3, "Student > Bachelor"=>1, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>4, "Medicine and Dentistry"=>9, "Chemistry"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>9}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}}, "reader_count_by_country"=>{"Hong Kong"=>1}, "group_count"=>2}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1454470"], "description"=>"<p>PCA was applied to each set of differentially-expressed probes to reduce the dimensionality of the microarray data with respect to individual samples. Phenotypic subgroups or tissues (BE, NE, and NC) can be differentiated from each other in BE patients, although there is some mixing of the phenotypes, particularly between BE and NC, which are more similar in terms of gene expression profiles. Color key: Blue = NC, Yellow = NE, Red = BE.</p>", "links"=>[], "tags"=>["Biochemistry", "biomarkers", "cell biology", "Molecular cell biology", "Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "gene expression", "genomics", "Molecular genetics", "Diagnostic medicine", "Gastroenterology and hepatology", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "Esophageal cancer", "Pathology and laboratory medicine", "Public and occupational health", "mathematics", "Statistics (mathematics)", "Biostatistics", "Bioassays and physiological analysis", "microarrays", "differentially-expressed", "probes", "matched", "nc", "tissues"], "article_id"=>990782, "categories"=>["Biological Sciences"], "users"=>["Paula L. Hyland", "Nan Hu", "Melissa Rotunno", "Hua Su", "Chaoyu Wang", "Lemin Wang", "Ruth M. Pfeiffer", "Barbara Gherman", "Carol Giffen", "Cathy Dykes", "Sanford M. Dawsey", "Christian C. Abnet", "Kathryn M. Johnson", "Ruben D. Acosta", "Patrick E. Young", "Brooks D. Cash", "Philip R. Taylor"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0093219.g001", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PCA_analyses_of_differentially_expressed_probes_2_fold_change_in_expression_and_P_/990782", "title"=>"PCA analyses of differentially-expressed probes (≥2 fold change in expression and <i>P</i><1.12E-06) between matched BE, NE, and NC tissues from BE patients.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-08 03:32:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1454491", "https://ndownloader.figshare.com/files/1454492", "https://ndownloader.figshare.com/files/1454493", "https://ndownloader.figshare.com/files/1454494", "https://ndownloader.figshare.com/files/1454495", "https://ndownloader.figshare.com/files/1454496", "https://ndownloader.figshare.com/files/1454497", "https://ndownloader.figshare.com/files/1454498"], "description"=>"<div><p>Background</p><p>Barrett's esophagus (BE) is a metaplastic precursor lesion of esophageal adenocarcinoma (EA), the most rapidly increasing cancer in western societies. While the prevalence of BE is increasing, the vast majority of EA occurs in patients with undiagnosed BE. Thus, we sought to identify genes that are altered in BE compared to the normal mucosa of the esophagus, and which may be potential biomarkers for the development or diagnosis of BE.</p><p>Design</p><p>We performed gene expression analysis using HG-U133A Affymetrix chips on fresh frozen tissue samples of Barrett's metaplasia and matched normal mucosa from squamous esophagus (NE) and gastric cardia (NC) in 40 BE patients.</p><p>Results</p><p>Using a cut off of 2-fold and <i>P</i><1.12E-06 (0.05 with Bonferroni correction), we identified 1324 differentially-expressed genes comparing BE vs NE and 649 differentially-expressed genes comparing BE vs NC. Except for individual genes such as the <i>SOXs</i> and <i>PROM1</i> that were dysregulated only in BE vs NE, we found a subset of genes (n = 205) whose expression was significantly altered in both BE vs NE and BE vs NC. These genes were overrepresented in different pathways, including TGF-β and Notch.</p><p>Conclusion</p><p>Our findings provide additional data on the global transcriptome in BE tissues compared to matched NE and NC tissues which should promote further understanding of the functions and regulatory mechanisms of genes involved in BE development, as well as insight into novel genes that may be useful as potential biomarkers for the diagnosis of BE in the future.</p></div>", "links"=>[], "tags"=>["Biochemistry", "biomarkers", "cell biology", "Molecular cell biology", "Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "gene expression", "genomics", "Molecular genetics", "Diagnostic medicine", "Gastroenterology and hepatology", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "Esophageal cancer", "Pathology and laboratory medicine", "Public and occupational health", "mathematics", "Statistics (mathematics)", "Biostatistics", "Bioassays and physiological analysis", "microarrays", "esophagus", "compared", "squamous", "gastric", "cardia"], "article_id"=>990793, "categories"=>["Biological Sciences"], "users"=>["Paula L. Hyland", "Nan Hu", "Melissa Rotunno", "Hua Su", "Chaoyu Wang", "Lemin Wang", "Ruth M. Pfeiffer", "Barbara Gherman", "Carol Giffen", "Cathy Dykes", "Sanford M. Dawsey", "Christian C. Abnet", "Kathryn M. Johnson", "Ruben D. Acosta", "Patrick E. Young", "Brooks D. Cash", "Philip R. Taylor"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0093219.s001", "https://dx.doi.org/10.1371/journal.pone.0093219.s002", "https://dx.doi.org/10.1371/journal.pone.0093219.s003", "https://dx.doi.org/10.1371/journal.pone.0093219.s004", "https://dx.doi.org/10.1371/journal.pone.0093219.s005", "https://dx.doi.org/10.1371/journal.pone.0093219.s006", "https://dx.doi.org/10.1371/journal.pone.0093219.s007", "https://dx.doi.org/10.1371/journal.pone.0093219.s008"], "stats"=>{"downloads"=>16, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Global_Changes_in_Gene_Expression_of_Barrett_s_Esophagus_Compared_to_Normal_Squamous_Esophagus_and_Gastric_Cardia_Tissues_/990793", "title"=>"Global Changes in Gene Expression of Barrett's Esophagus Compared to Normal Squamous Esophagus and Gastric Cardia Tissues", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-04-08 03:32:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1454489"], "description"=>"<p>NOTE: Genes are listed in descending order by <i>P</i>-value. For genes with >1<sup>a</sup> or >2<sup>b</sup> probesets differentially expressed at <i>P</i><1.12E-06 only the most significant probeset for the gene is shown.</p>", "links"=>[], "tags"=>["Biochemistry", "biomarkers", "cell biology", "Molecular cell biology", "Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "gene expression", "genomics", "Molecular genetics", "Diagnostic medicine", "Gastroenterology and hepatology", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "Esophageal cancer", "Pathology and laboratory medicine", "Public and occupational health", "mathematics", "Statistics (mathematics)", "Biostatistics", "Bioassays and physiological analysis", "microarrays", "50", "differentially", "genes", "nc"], "article_id"=>990791, "categories"=>["Biological Sciences"], "users"=>["Paula L. Hyland", "Nan Hu", "Melissa Rotunno", "Hua Su", "Chaoyu Wang", "Lemin Wang", "Ruth M. Pfeiffer", "Barbara Gherman", "Carol Giffen", "Cathy Dykes", "Sanford M. Dawsey", "Christian C. Abnet", "Kathryn M. Johnson", "Ruben D. Acosta", "Patrick E. Young", "Brooks D. Cash", "Philip R. Taylor"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0093219.t003", "stats"=>{"downloads"=>6, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_showing_top_50_differentially_expressed_genes_in_BE_vs_NC_the_complete_list_is_reported_in_Table_S5_/990791", "title"=>"Summary showing top 50 differentially expressed genes in BE vs NC (the complete list is reported in Table S5).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-08 03:32:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1454488"], "description"=>"<p>NOTE: Genes are listed in descending order by <i>P</i>-value. For genes with >1<sup>a</sup> or >2<sup>b</sup> probesets differentially expressed at <i>P</i><1.12E-06 only the most significant probeset for the gene is shown.</p>", "links"=>[], "tags"=>["Biochemistry", "biomarkers", "cell biology", "Molecular cell biology", "Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "gene expression", "genomics", "Molecular genetics", "Diagnostic medicine", "Gastroenterology and hepatology", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "Esophageal cancer", "Pathology and laboratory medicine", "Public and occupational health", "mathematics", "Statistics (mathematics)", "Biostatistics", "Bioassays and physiological analysis", "microarrays", "50", "differentially", "genes", "ne"], "article_id"=>990790, "categories"=>["Biological Sciences"], "users"=>["Paula L. Hyland", "Nan Hu", "Melissa Rotunno", "Hua Su", "Chaoyu Wang", "Lemin Wang", "Ruth M. Pfeiffer", "Barbara Gherman", "Carol Giffen", "Cathy Dykes", "Sanford M. Dawsey", "Christian C. Abnet", "Kathryn M. Johnson", "Ruben D. Acosta", "Patrick E. Young", "Brooks D. Cash", "Philip R. Taylor"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0093219.t002", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_showing_top_50_differentially_expressed_genes_in_BE_vs_NE_the_complete_list_is_reported_in_Table_S4_/990790", "title"=>"Summary showing top 50 differentially expressed genes in BE vs NE (the complete list is reported in Table S4).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-08 03:32:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1454487"], "description"=>"<p>Persons scoring ≥3 on a scale of 0–13 on the gastroesophageal reflux disease (GERD) questionnaire were considered to have GERD. Tobacco use refers to smoked cigarettes: Yes>6 months ever smoked, No<6 months ever smoked. Alcohol use refers to ever drank alcohol: No/Yes (where NoAbbreviations: Body mass index, BMI; gastroesophageal reflux disease, GERD.</p>", "links"=>[], "tags"=>["Biochemistry", "biomarkers", "cell biology", "Molecular cell biology", "Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "gene expression", "genomics", "Molecular genetics", "Diagnostic medicine", "Gastroenterology and hepatology", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "Esophageal cancer", "Pathology and laboratory medicine", "Public and occupational health", "mathematics", "Statistics (mathematics)", "Biostatistics", "Bioassays and physiological analysis", "microarrays"], "article_id"=>990789, "categories"=>["Biological Sciences"], "users"=>["Paula L. Hyland", "Nan Hu", "Melissa Rotunno", "Hua Su", "Chaoyu Wang", "Lemin Wang", "Ruth M. Pfeiffer", "Barbara Gherman", "Carol Giffen", "Cathy Dykes", "Sanford M. Dawsey", "Christian C. Abnet", "Kathryn M. Johnson", "Ruben D. Acosta", "Patrick E. Young", "Brooks D. Cash", "Philip R. Taylor"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0093219.t001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characteristics_of_study_population_/990789", "title"=>"Characteristics of study population.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-08 03:32:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1454486"], "description"=>"<p>Two hundred and five overlapping genes were identified between BE vs. NE and BE vs. NC tissues after Bonferroni correction (<i>P</i><1.12-E06) and with a 2-fold or greater differential expression. Diagram illustrates the TGF-β1 signaling pathway in BE vs NE and BE vs NC comparative groups. The direction and/or magnitude of expression is inverse for thirty two genes in the TGF-β1 network between the comparative groups. Genes include: <i>SERPINB2, TMOD3, EPHA2, KRT15, ADCY7, SST, FMOD, CD36, CA9, ALCAM, IL1RN, TIMP2, CAST, MITF, SPRR1A, BHLHE40, MCL1, IL13RA1, ACPP, SRD5A1, NR2F2, ALDH1A1, DST, TJP1, CD9, TGFA, MUC4, PMAIP1, ZFP36, CCNG2, IL18</i> and <i>CHGA</i>. Data source: Signaling Pathways, Ariadne Pathways. Primary red and blue colors and shading indicate the direction and degree of differential expression with pink to red indicating degrees of increasing upregulation and light blue to darker blue indicating increasing downregulation. Grey indicates a gene product that is part of the pathway, but is absent in the experimental list tested. Abbreviations: BE, Barrett's; NE, normal squamous epithelium; NC, normal gastric cardia epithelium.</p>", "links"=>[], "tags"=>["Biochemistry", "biomarkers", "cell biology", "Molecular cell biology", "Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "gene expression", "genomics", "Molecular genetics", "Diagnostic medicine", "Gastroenterology and hepatology", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "Esophageal cancer", "Pathology and laboratory medicine", "Public and occupational health", "mathematics", "Statistics (mathematics)", "Biostatistics", "Bioassays and physiological analysis", "microarrays", "differentially", "genes", "ne", "nc"], "article_id"=>990788, "categories"=>["Biological Sciences"], "users"=>["Paula L. Hyland", "Nan Hu", "Melissa Rotunno", "Hua Su", "Chaoyu Wang", "Lemin Wang", "Ruth M. Pfeiffer", "Barbara Gherman", "Carol Giffen", "Cathy Dykes", "Sanford M. Dawsey", "Christian C. Abnet", "Kathryn M. Johnson", "Ruben D. Acosta", "Patrick E. Young", "Brooks D. Cash", "Philip R. Taylor"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0093219.g003", "stats"=>{"downloads"=>2, "page_views"=>25, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pathway_based_analyses_of_common_differentially_expressed_genes_in_BE_vs_NE_and_BE_vs_NC_comparisons_/990788", "title"=>"Pathway-based analyses of common differentially expressed genes in BE vs NE and BE vs NC comparisons.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-08 03:32:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1454481"], "description"=>"<p><b>A.</b> The left Venn diagram represents the total number of genes with significant differential expression between BE and NE (≥2 fc and <i>P</i><1.12E-06), whereas the right Venn diagram represents the total number with genes significant differential expression between BE and NC (≥2 fc and <i>P</i><1.12E-06). The overlap between the two differentially-expressed sets contained 205 genes used for functional classification and pathway-based analyses. <b>B.</b> Enrichment of the 205 genes in known biological processes (GO, Ariadne Genomics, MD). The columns entitled: ‘Total no of genes in process’ and ‘Number of genes involved in process (% overlap)’ refer to the total number of genes currently known in each process according to the database (Pathway Studio 9.00), and the % overlap of the 205 genes with the total gene number in each process, respectively. Enrichment of the 205 genes identified in each process relative to the whole gene set is also shown. The largest proportion of genes (7.3%) out of the 205 genes were involved in response to drugs and cell adhesion; however, relative to the overall number of genes in the identified process, cellular response to insulin showed the greatest enrichment.</p>", "links"=>[], "tags"=>["Biochemistry", "biomarkers", "cell biology", "Molecular cell biology", "Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "gene expression", "genomics", "Molecular genetics", "Diagnostic medicine", "Gastroenterology and hepatology", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "Esophageal cancer", "Pathology and laboratory medicine", "Public and occupational health", "mathematics", "Statistics (mathematics)", "Biostatistics", "Bioassays and physiological analysis", "microarrays", "differential", "fc", "ne", "nc", "enrichment"], "article_id"=>990783, "categories"=>["Biological Sciences"], "users"=>["Paula L. Hyland", "Nan Hu", "Melissa Rotunno", "Hua Su", "Chaoyu Wang", "Lemin Wang", "Ruth M. Pfeiffer", "Barbara Gherman", "Carol Giffen", "Cathy Dykes", "Sanford M. Dawsey", "Christian C. Abnet", "Kathryn M. Johnson", "Ruben D. Acosta", "Patrick E. Young", "Brooks D. Cash", "Philip R. Taylor"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0093219.g002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Paired_analyses_of_significant_differential_gene_expression_2_fc_and_P_/990783", "title"=>"Paired analyses of significant differential gene expression (≥2 fc and <i>P</i><1.12E-06) in BE vs NE and BE vs NC and enrichment in known biological processes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-08 03:32:57"}

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Relative Metric

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