Comparative Genomics of Helicobacter pylori Strains of China Associated with Different Clinical Outcome
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{"title"=>"Comparative genomics of helicobacter pylori strains of china associated with different clinical outcome", "type"=>"journal", "authors"=>[{"first_name"=>"Yuanhai", "last_name"=>"You", "scopus_author_id"=>"25229226700"}, {"first_name"=>"Lihua", "last_name"=>"He", "scopus_author_id"=>"26643412800"}, {"first_name"=>"Maojun", "last_name"=>"Zhang", "scopus_author_id"=>"55704469900"}, {"first_name"=>"Jianying", "last_name"=>"Fu", "scopus_author_id"=>"55246668800"}, {"first_name"=>"Yixin", "last_name"=>"Gu", "scopus_author_id"=>"35388009800"}, {"first_name"=>"Binghua", "last_name"=>"Zhang", "scopus_author_id"=>"55502549900"}, {"first_name"=>"Xiaoxia", "last_name"=>"Tao", "scopus_author_id"=>"7202692309"}, {"first_name"=>"Jianzhong", "last_name"=>"Zhang", "scopus_author_id"=>"9939370800"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"22701658", "doi"=>"10.1371/journal.pone.0038528", "sgr"=>"84862025115", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "scopus"=>"2-s2.0-84862025115", "issn"=>"19326203", "pui"=>"364979176"}, "id"=>"cadae581-ff49-3706-a2ee-175361179934", "abstract"=>"In this study, a whole-genome CombiMatrix Custom oligonucleotide tiling microarray with 90,000 probes covering six sequenced Helicobacter pylori (H. pylori) genomes was designed. This microarray was used to compare the genomic profiles of eight unsequenced strains isolated from patients with different gastroduodenal diseases in Heilongjiang province of China. Since significant genomic variation was found among these strains, an additional 76 H. pylori strains associated with different clinical outcomes were isolated from various provinces of China. These strains were tested by polymerase chain reaction to demonstrate this distinction. We identified several highly variable regions in strains associated with gastritis, gastric ulceration, and gastric cancer. These regions are associated with genes involved in the bacterial type I, type II, and type III R-M systems. They were also associated with the virB gene, which lies on the well-studied cag pathogenic island. While previous studies have reported on the diverse genetic characterization of this pathogenic island, in this study, we find that it is conserved in all strains tested by microarray. Moreover, a number of genes involved in the type IV secretion system, which is related to horizontal DNA transfer between H. pylori strains, were identified in the comparative analysis of the strain-specific genes. These findings may provide insight into new biomarkers for the prediction of gastric diseases.", "link"=>"http://www.mendeley.com/research/comparative-genomics-helicobacter-pylori-strains-china-associated-different-clinical-outcome-2", "reader_count"=>20, "reader_count_by_academic_status"=>{"Researcher"=>6, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>5, "Student > Master"=>2, "Student > Bachelor"=>3, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Researcher"=>6, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>5, "Student > Master"=>2, "Student > Bachelor"=>3, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>10, "Medicine and Dentistry"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Chemistry"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>10}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"United States"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/628460"], "description"=>"<p>Large variable regions were labeled with colored rectangles. Predicted gastric cancer strain specific regions were labeled with a red rectangle. General genomic variations among all strains were labeled with a green rectangle. A blue rectangle represents diverse regions obtained from comparison of gastric cancer strains and superficial gastritis strains. Corresponding coding proteins were briefly labeled at the bottom of each rectangle. GC vs SG denotes comparison between the two strains of gastric cancer and the two strains of superficial gastritis.</p>", "links"=>[], "tags"=>["strains", "genes", "sequenced"], "article_id"=>298941, "categories"=>["Chemistry", "Infectious Diseases", "Cancer", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Yuanhai You", "Lihua He", "Maojun Zhang", "Jianying Fu", "Yixin Gu", "Binghua Zhang", "Xiaoxia Tao", "Jianzhong Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0038528.g004", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_eight_H_pylori_strains_based_on_strain_specific_genes_of_six_sequenced_strains_/298941", "title"=>"Comparison of eight <i>H. pylori</i> strains based on strain specific genes of six sequenced strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 04:18:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/628213"], "description"=>"<p>Large variable regions were labeled with colored rectangles. Predicted gastric cancer strain specific regions were labeled with a red rectangle. General genomic variation among all strains was labeled with a green rectangle. A blue rectangle represents diverse regions obtained from comparison of gastric cancer strains and superficial gastritis strains. Corresponding coding proteins were briefly labeled at the bottom of each rectangle. GC vs SG denotes comparison between the two strains of gastric cancer and the two strains of superficial gastritis. DR, different region.</p>", "links"=>[], "tags"=>["strains", "p12"], "article_id"=>298699, "categories"=>["Chemistry", "Infectious Diseases", "Cancer", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Yuanhai You", "Lihua He", "Maojun Zhang", "Jianying Fu", "Yixin Gu", "Binghua Zhang", "Xiaoxia Tao", "Jianzhong Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0038528.g003", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_comparison_of_eight_H_pylori_strains_based_on_P12_reference_sequence_/298699", "title"=>"Genome comparison of eight <i>H. pylori</i> strains based on P12 reference sequence.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 04:16:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/627851"], "description"=>"<p>A. Comparison between HLJ005 and 26695. B. Comparison between HLJ038 and 26695. C. Comparison between HLJ038 and HLJ005. Green spots show inferred loss while orange dots show no changes in the original data. Red spots show inferred increase. Segment 1 on the X-axis: probes of 26695 strain specific genes. Segment 2: probes of G27 strain specific genes. Segment 3: probes of HPAG1 strain specific genes. Segment 4: probes of J99 strain specific genes. Segment 5: probes of P12 strain specific genes. Segment 6: probes of Shi470 strain specific genes.</p>", "links"=>[], "tags"=>["26695", "genes", "sequenced"], "article_id"=>298332, "categories"=>["Chemistry", "Infectious Diseases", "Cancer", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Yuanhai You", "Lihua He", "Maojun Zhang", "Jianying Fu", "Yixin Gu", "Binghua Zhang", "Xiaoxia Tao", "Jianzhong Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0038528.g001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_HLJ005_HLJ038_and_26695_based_on_strain_specific_genes_of_the_six_sequenced_genomes_/298332", "title"=>"Comparison of HLJ005, HLJ038, and 26695 based on strain specific genes of the six sequenced genomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 04:14:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/628068"], "description"=>"<p>A. Comparison between HLJ005 and 26695. B. Comparison between HLJ038 and 26695. C. Comparison between HLJ038 and HLJ005. Green spots show inferred loss while orange dots show no changes in the original data. Red spots show inferred increase. The red rectangle indicates the predicted 5.2 kb absent region both in gastric cancer strain HLJ038 and HLJ005 based on the 0–100 kb of the reference P12 chromosome.</p>", "links"=>[], "tags"=>["26695", "kb", "p12"], "article_id"=>298552, "categories"=>["Chemistry", "Infectious Diseases", "Cancer", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Yuanhai You", "Lihua He", "Maojun Zhang", "Jianying Fu", "Yixin Gu", "Binghua Zhang", "Xiaoxia Tao", "Jianzhong Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0038528.g002", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_HLJ005_HLJ038_and_26695_based_on_0_8211_100_kb_of_p12_genome_/298552", "title"=>"Comparison of HLJ005, HLJ038, and 26695 based on 0–100 kb of p12 genome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 04:15:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/628881"], "description"=>"<p>Note: GC, gastric cancer. GU, gastric ulcer. AG, atrophic gastritis, DU, duodenal ulcer, GDU, gastroduodenal ulcer. FD, functional dyspepsia. SG, non-atrophic gastritis.</p>", "links"=>[], "tags"=>["84", "strains"], "article_id"=>299364, "categories"=>["Chemistry", "Infectious Diseases", "Cancer", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Yuanhai You", "Lihua He", "Maojun Zhang", "Jianying Fu", "Yixin Gu", "Binghua Zhang", "Xiaoxia Tao", "Jianzhong Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0038528.t001", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characteristics_of_the_84_H_pylori_strains_studied_/299364", "title"=>"Characteristics of the 84 <i>H. pylori</i> strains studied.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 04:20:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/628830"], "description"=>"<p>Note: GC, gastric cancer. GU, gastric ulcer. AG, atrophic gastritis, DU, duodenal ulcer GDU, gastroduodenal ulcer, FD, functional dyspepsia, SG, non-atrophic gastritis.</p>", "links"=>[], "tags"=>["genetics and genomics", "Infectious diseases", "Computational biology", "oncology", "Evolutionary biology", "Gastroenterology and hepatology"], "article_id"=>299314, "categories"=>["Chemistry", "Infectious Diseases", "Cancer", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Yuanhai You", "Lihua He", "Maojun Zhang", "Jianying Fu", "Yixin Gu", "Binghua Zhang", "Xiaoxia Tao", "Jianzhong Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0038528.t005", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_hrg_A_in_different_diseases_/299314", "title"=>"Distribution of <i>hrg</i>A in different diseases.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 04:20:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/628906"], "description"=>"<p>General features of the sequenced <i>H. pylori</i> genomes selected for microarray probe design.</p>", "links"=>[], "tags"=>["sequenced", "genomes", "microarray", "probe"], "article_id"=>299391, "categories"=>["Chemistry", "Infectious Diseases", "Cancer", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Yuanhai You", "Lihua He", "Maojun Zhang", "Jianying Fu", "Yixin Gu", "Binghua Zhang", "Xiaoxia Tao", "Jianzhong Zhang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0038528.t002", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_General_features_of_the_sequenced_H_pylori_genomes_selected_for_microarray_probe_design_/299391", "title"=>"General features of the sequenced <i>H. pylori</i> genomes selected for microarray probe design.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 04:20:37"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"6", "full-text"=>"4", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"4", "full-text"=>"2", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}

Relative Metric

{"start_date"=>"2012-01-01T00:00:00Z", "end_date"=>"2012-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[322, 550, 671, 773, 864, 955, 1048, 1135, 1223, 1308, 1387, 1465, 1534, 1602, 1673, 1744, 1813, 1885, 1955, 2026, 2093, 2160, 2228, 2290, 2349]}, {"subject_area"=>"/Biology and life sciences/Computational biology", "average_usage"=>[375, 629, 760, 889, 1000, 1110, 1203, 1298, 1399, 1492, 1603, 1699, 1774, 1855, 1918, 1998, 2062, 2152, 2227, 2312, 2378, 2461, 2528, 2600, 2664]}, {"subject_area"=>"/Biology and life sciences/Microbiology", "average_usage"=>[339, 580, 709, 814, 907, 1003, 1095, 1190, 1286, 1375, 1466, 1546, 1622, 1694, 1765, 1830, 1902, 1978, 2054, 2122, 2194, 2269, 2330, 2388, 2460]}, {"subject_area"=>"/Biology and life sciences/Molecular biology", "average_usage"=>[324, 551, 679, 782, 879, 971, 1064, 1154, 1245, 1328, 1406, 1476, 1541, 1617, 1683, 1754, 1818, 1893, 1962, 2025, 2092, 2164, 2227, 2294, 2355]}, {"subject_area"=>"/Medicine and health sciences", "average_usage"=>[312, 547, 668, 769, 861, 953, 1046, 1135, 1224, 1307, 1388, 1464, 1536, 1606, 1676, 1744, 1812, 1882, 1954, 2020, 2089, 2155, 2218, 2282, 2344]}, {"subject_area"=>"/Medicine and health sciences/Gastroenterology and hepatology", "average_usage"=>[300, 551, 690, 799, 882, 973, 1070, 1148, 1253, 1340, 1421, 1524, 1599, 1666, 1752, 1833, 1893, 1990, 2051, 2110, 2181, 2243, 2303, 2369, 2434]}]}

F1000Prime | Further Information

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Net::HTTPTooManyRequests

Source
Scopus
Time
2019-08-27 21:07:16 UTC
Target URL
https://api.elsevier.com/content/search/index:SCOPUS?query=DOI(10.1371%2Fjournal.pone.0038528)
Trace

/app/models/concerns/networkable.rb:21:in `get_result'
/app/models/source.rb:165:in `get_data'
/app/models/retrieval_status.rb:47:in `perform_get_data'
/app/jobs/source_job.rb:52:in `block (2 levels) in perform'
/app/jobs/source_job.rb:51:in `block in perform'
/app/jobs/source_job.rb:35:in `each'
/app/jobs/source_job.rb:35:in `perform'