Whole Blood Gene Expression Profile Associated with Spontaneous Preterm Birth in Women with Threatened Preterm Labor
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{"title"=>"Whole blood gene expression profile associated with spontaneous preterm birth in women with threatened preterm labor.", "type"=>"journal", "authors"=>[{"first_name"=>"Yujing Jan", "last_name"=>"Heng"}, {"first_name"=>"Craig Edward", "last_name"=>"Pennell"}, {"first_name"=>"Hon Nian", "last_name"=>"Chua"}, {"first_name"=>"Jonathan Edward", "last_name"=>"Perkins"}, {"first_name"=>"Stephen James", "last_name"=>"Lye"}], "year"=>2014, "source"=>"PloS one", "identifiers"=>{"issn"=>"1932-6203", "pmid"=>"24828675", "doi"=>"10.1371/journal.pone.0096901"}, "id"=>"da3fcd89-e1e7-324a-a1f4-fefdf59a37ba", "abstract"=>"Threatened preterm labor (TPTL) is defined as persistent premature uterine contractions between 20 and 37 weeks of gestation and is the most common condition that requires hospitalization during pregnancy. Most of these TPTL women continue their pregnancies to term while only an estimated 5% will deliver a premature baby within ten days. The aim of this work was to study differential whole blood gene expression associated with spontaneous preterm birth (sPTB) within 48 hours of hospital admission. Peripheral blood was collected at point of hospital admission from 154 women with TPTL before any medical treatment. Microarrays were utilized to investigate differential whole blood gene expression between TPTL women who did (n = 48) or did not have a sPTB (n = 106) within 48 hours of admission. Total leukocyte and neutrophil counts were significantly higher (35% and 41% respectively) in women who had sPTB than women who did not deliver within 48 hours (p<0.001). Fetal fibronectin (fFN) test was performed on 62 women. There was no difference in the urine, vaginal and placental microbiology and histopathology reports between the two groups of women. There were 469 significant differentially expressed genes (FDR<0.05); 28 differentially expressed genes were chosen for microarray validation using qRT-PCR and 20 out of 28 genes were successfully validated (p<0.05). An optimal random forest classifier model to predict sPTB was achieved using the top nine differentially expressed genes coupled with peripheral clinical blood data (sensitivity 70.8%, specificity 75.5%). These differentially expressed genes may further elucidate the underlying mechanisms of sPTB and pave the way for future systems biology studies to predict sPTB.", "link"=>"http://www.mendeley.com/research/whole-blood-gene-expression-profile-associated-spontaneous-preterm-birth-women-threatened-preterm-la", "reader_count"=>35, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>7, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>2, "Other"=>2, "Student > Master"=>5, "Student > Bachelor"=>3, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>7, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>2, "Other"=>2, "Student > Master"=>5, "Student > Bachelor"=>3, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>4, "Materials Science"=>1, "Medicine and Dentistry"=>11, "Agricultural and Biological Sciences"=>14, "Design"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Chemistry"=>1, "Social Sciences"=>2}, "reader_count_by_subdiscipline"=>{"Design"=>{"Design"=>1}, "Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>11}, "Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>14}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"New Zealand"=>1, "Italy"=>1, "Spain"=>1, "India"=>1}, "group_count"=>5}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1497377"], "description"=>"<p>Predicting spontaneous preterm birth within 48(with and without peripheral clinical blood data) and comparing the predictive efficacies of fetal fibronectin and the random forest classifier models (top 9 genes, with or without peripheral clinical blood data and fFN) to predict spontaneous preterm birth within 48 hours in 62 women.</p>", "links"=>[], "tags"=>["Biochemistry", "biomarkers", "Computational biology", "Comparative genomics", "genetics", "genomics", "Diagnostic medicine", "Pathology and laboratory medicine", "Public and occupational health", "Global health", "women's health", "Maternal health", "birth", "Labor and delivery", "Preterm labor", "pregnancy", "Management of high-risk pregnancies", "Obstetrics and gynecology", "spontaneous", "preterm", "peripheral", "comparing", "predictive", "efficacies", "fetal", "fibronectin", "classifier", "48", "hours", "62"], "article_id"=>1026509, "categories"=>["Biological Sciences"], "users"=>["Yujing Jan Heng", "Craig Edward Pennell", "Hon Nian Chua", "Jonathan Edward Perkins", "Stephen James Lye"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0096901.t005", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Predicting_spontaneous_preterm_birth_within_48_with_and_without_peripheral_clinical_blood_data_and_comparing_the_predictive_efficacies_of_fetal_fibronectin_and_the_random_forest_classifier_models_top_9_genes_with_or_without_peripheral_clinical_blood_data/1026509", "title"=>"Predicting spontaneous preterm birth within 48(with and without peripheral clinical blood data) and comparing the predictive efficacies of fetal fibronectin and the random forest classifier models (top 9 genes, with or without peripheral clinical blood data and fFN) to predict spontaneous preterm birth within 48 hours in 62 women.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-05-14 02:50:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1497376"], "description"=>"<p>Elevated gene expressions are indicated in green; down-regulated gene expressions are indicated in red. The colors on the top bars represent women who had a spontaneous preterm birth within 48 hours (red), preterm delivery between 2 to 7 days (green), preterm delivery between 7 days and within 37 weeks of gestation (blue) and women who delivered at term (yellow).</p>", "links"=>[], "tags"=>["Biochemistry", "biomarkers", "Computational biology", "Comparative genomics", "genetics", "genomics", "Diagnostic medicine", "Pathology and laboratory medicine", "Public and occupational health", "Global health", "women's health", "Maternal health", "birth", "Labor and delivery", "Preterm labor", "pregnancy", "Management of high-risk pregnancies", "Obstetrics and gynecology", "50", "differentially", "genes", "displays", "hierarchical", "consistency"], "article_id"=>1026508, "categories"=>["Biological Sciences"], "users"=>["Yujing Jan Heng", "Craig Edward Pennell", "Hon Nian Chua", "Jonathan Edward Perkins", "Stephen James Lye"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0096901.g005", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_This_heat_map_of_the_top_50_differentially_expressed_genes_highest_fold_changes_displays_the_hierarchical_clustering_consistency_and_regulation_of_the_gene_expression_levels_/1026508", "title"=>"This heat map of the top 50 differentially expressed genes (highest fold changes) displays the hierarchical clustering, consistency and regulation of the gene expression levels.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-05-14 02:50:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1497358"], "description"=>"<p>GO Slim terms of (A) cellular components, (B) molecular functions and (C) biological process that are representative of the 469 significantly expressed genes.</p>", "links"=>[], "tags"=>["Biochemistry", "biomarkers", "Computational biology", "Comparative genomics", "genetics", "genomics", "Diagnostic medicine", "Pathology and laboratory medicine", "Public and occupational health", "Global health", "women's health", "Maternal health", "birth", "Labor and delivery", "Preterm labor", "pregnancy", "Management of high-risk pregnancies", "Obstetrics and gynecology", "slim", "cellular", "molecular", "functions", "469"], "article_id"=>1026490, "categories"=>["Biological Sciences"], "users"=>["Yujing Jan Heng", "Craig Edward Pennell", "Hon Nian Chua", "Jonathan Edward Perkins", "Stephen James Lye"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0096901.g002", "stats"=>{"downloads"=>2, "page_views"=>29, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GO_Slim_terms_of_A_cellular_components_B_molecular_functions_and_C_biological_process_that_are_representative_of_the_469_significantly_expressed_genes_/1026490", "title"=>"GO Slim terms of (A) cellular components, (B) molecular functions and (C) biological process that are representative of the 469 significantly expressed genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-05-14 02:50:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1497367"], "description"=>"<p>(<b>A</b>) Models using the top nine genes, with and without peripheral clinical blood data in 154 women. (<b>B</b>) Models developed using the top nine genes, fetal fibronectin (fFN) and clinical blood data in 62 women. The lines for nine genes only and nine genes with fFN are superimposed.</p>", "links"=>[], "tags"=>["Biochemistry", "biomarkers", "Computational biology", "Comparative genomics", "genetics", "genomics", "Diagnostic medicine", "Pathology and laboratory medicine", "Public and occupational health", "Global health", "women's health", "Maternal health", "birth", "Labor and delivery", "Preterm labor", "pregnancy", "Management of high-risk pregnancies", "Obstetrics and gynecology", "curves", "displaying", "performances", "classifier"], "article_id"=>1026499, "categories"=>["Biological Sciences"], "users"=>["Yujing Jan Heng", "Craig Edward Pennell", "Hon Nian Chua", "Jonathan Edward Perkins", "Stephen James Lye"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0096901.g004", "stats"=>{"downloads"=>2, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Receiver_operator_characteristics_curves_displaying_the_performances_of_the_random_forest_classifier_models_/1026499", "title"=>"Receiver operator characteristics curves displaying the performances of the random forest classifier models.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-05-14 02:50:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1497365"], "description"=>"<p>Each cluster is indicated by a different color and their representative GO slim term(s). Edges of “->” indicate activating/catalyzing; “-|” for inhibition; “-” for functional interactions extracted from complexes or inputs and “- - -” for predicted functional interactions.</p>", "links"=>[], "tags"=>["Biochemistry", "biomarkers", "Computational biology", "Comparative genomics", "genetics", "genomics", "Diagnostic medicine", "Pathology and laboratory medicine", "Public and occupational health", "Global health", "women's health", "Maternal health", "birth", "Labor and delivery", "Preterm labor", "pregnancy", "Management of high-risk pregnancies", "Obstetrics and gynecology", "469", "genes", "revealed", "clusters", "consisting"], "article_id"=>1026498, "categories"=>["Biological Sciences"], "users"=>["Yujing Jan Heng", "Craig Edward Pennell", "Hon Nian Chua", "Jonathan Edward Perkins", "Stephen James Lye"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0096901.g003", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reactome_Functional_Interaction_analysis_of_469_significant_genes_revealed_eight_clusters_consisting_of_at_least_five_of_genes_/1026498", "title"=>"Reactome Functional Interaction analysis of 469 significant genes revealed eight clusters consisting of at least five of genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-05-14 02:50:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1497379"], "description"=>"<p>∧Peripheral blood data (total leukocytes, neutrophils, lymphocytes, monocytes counts and hemoglobin) were obtained from 125 women (<48 hours delivery n = 45, >48 hours delivery n = 80). *Significantly different between preterm delivery within 48 hours (n = 48) and no preterm delivery within 48 hours (n = 106).</p>", "links"=>[], "tags"=>["Biochemistry", "biomarkers", "Computational biology", "Comparative genomics", "genetics", "genomics", "Diagnostic medicine", "Pathology and laboratory medicine", "Public and occupational health", "Global health", "women's health", "Maternal health", "birth", "Labor and delivery", "Preterm labor", "pregnancy", "Management of high-risk pregnancies", "Obstetrics and gynecology", "demographics", "154"], "article_id"=>1026511, "categories"=>["Biological Sciences"], "users"=>["Yujing Jan Heng", "Craig Edward Pennell", "Hon Nian Chua", "Jonathan Edward Perkins", "Stephen James Lye"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0096901.t001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Clinical_demographics_of_the_154_study_participants_/1026511", "title"=>"Clinical demographics of the 154 study participants.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-05-14 02:50:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1497380"], "description"=>"<p>Top twenty significantly expressed genes (FDR<0.05, <i>Limma</i>) ranked by fold change.</p>", "links"=>[], "tags"=>["Biochemistry", "biomarkers", "Computational biology", "Comparative genomics", "genetics", "genomics", "Diagnostic medicine", "Pathology and laboratory medicine", "Public and occupational health", "Global health", "women's health", "Maternal health", "birth", "Labor and delivery", "Preterm labor", "pregnancy", "Management of high-risk pregnancies", "Obstetrics and gynecology", "genes", "ranked"], "article_id"=>1026512, "categories"=>["Biological Sciences"], "users"=>["Yujing Jan Heng", "Craig Edward Pennell", "Hon Nian Chua", "Jonathan Edward Perkins", "Stephen James Lye"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0096901.t003", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Top_twenty_significantly_expressed_genes_FDR_Limma_ranked_by_fold_change_/1026512", "title"=>"Top twenty significantly expressed genes (FDR<0.05, <i>Limma</i>) ranked by fold change.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-05-14 02:50:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1497378"], "description"=>"<p>Functional enrichment analysis of a total of 1333 genes (FDR<0.1, <i>Limma</i>) resulted in 31 enriched GO terms with odds ratio of >2 (adjusted <i>p</i><0.05).</p>", "links"=>[], "tags"=>["Biochemistry", "biomarkers", "Computational biology", "Comparative genomics", "genetics", "genomics", "Diagnostic medicine", "Pathology and laboratory medicine", "Public and occupational health", "Global health", "women's health", "Maternal health", "birth", "Labor and delivery", "Preterm labor", "pregnancy", "Management of high-risk pregnancies", "Obstetrics and gynecology", "enrichment", "1333", "genes", "resulted", "31", "enriched"], "article_id"=>1026510, "categories"=>["Biological Sciences"], "users"=>["Yujing Jan Heng", "Craig Edward Pennell", "Hon Nian Chua", "Jonathan Edward Perkins", "Stephen James Lye"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0096901.t004", "stats"=>{"downloads"=>5, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Functional_enrichment_analysis_of_a_total_of_1333_genes_FDR_Limma_resulted_in_31_enriched_GO_terms_with_odds_ratio_of_2_adjusted_p_/1026510", "title"=>"Functional enrichment analysis of a total of 1333 genes (FDR<0.1, <i>Limma</i>) resulted in 31 enriched GO terms with odds ratio of >2 (adjusted <i>p</i><0.05).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-05-14 02:50:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1497355"], "description"=>"<p>The dot plots (mean and standard deviations) of gestational age at presentation of women who did or did not have a spontaneous preterm birth (sPTB) within 48 hours of hospital admission in the microarray (A) and qRT-PCR (B) study, respectively.</p>", "links"=>[], "tags"=>["Biochemistry", "biomarkers", "Computational biology", "Comparative genomics", "genetics", "genomics", "Diagnostic medicine", "Pathology and laboratory medicine", "Public and occupational health", "Global health", "women's health", "Maternal health", "birth", "Labor and delivery", "Preterm labor", "pregnancy", "Management of high-risk pregnancies", "Obstetrics and gynecology", "gestational", "women", "did", "spontaneous", "preterm", "48", "hours", "microarray", "qrt-pcr"], "article_id"=>1026487, "categories"=>["Biological Sciences"], "users"=>["Yujing Jan Heng", "Craig Edward Pennell", "Hon Nian Chua", "Jonathan Edward Perkins", "Stephen James Lye"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0096901.g001", "stats"=>{"downloads"=>4, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_dot_plots_mean_and_standard_deviations_of_gestational_age_at_presentation_of_women_who_did_or_did_not_have_a_spontaneous_preterm_birth_sPTB_within_48_hours_of_hospital_admission_in_the_microarray_A_and_qRT_PCR_B_study_respectively_/1026487", "title"=>"The dot plots (mean and standard deviations) of gestational age at presentation of women who did or did not have a spontaneous preterm birth (sPTB) within 48 hours of hospital admission in the microarray (A) and qRT-PCR (B) study, respectively.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-05-14 02:50:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1497385"], "description"=>"<div><p>Threatened preterm labor (TPTL) is defined as persistent premature uterine contractions between 20 and 37 weeks of gestation and is the most common condition that requires hospitalization during pregnancy. Most of these TPTL women continue their pregnancies to term while only an estimated 5% will deliver a premature baby within ten days. The aim of this work was to study differential whole blood gene expression associated with spontaneous preterm birth (sPTB) within 48 hours of hospital admission. Peripheral blood was collected at point of hospital admission from 154 women with TPTL before any medical treatment. Microarrays were utilized to investigate differential whole blood gene expression between TPTL women who did (n = 48) or did not have a sPTB (n = 106) within 48 hours of admission. Total leukocyte and neutrophil counts were significantly higher (35% and 41% respectively) in women who had sPTB than women who did not deliver within 48 hours (<i>p</i><0.001). Fetal fibronectin (fFN) test was performed on 62 women. There was no difference in the urine, vaginal and placental microbiology and histopathology reports between the two groups of women. There were 469 significant differentially expressed genes (FDR<0.05); 28 differentially expressed genes were chosen for microarray validation using qRT-PCR and 20 out of 28 genes were successfully validated (<i>p</i><0.05). An optimal random forest classifier model to predict sPTB was achieved using the top nine differentially expressed genes coupled with peripheral clinical blood data (sensitivity 70.8%, specificity 75.5%). These differentially expressed genes may further elucidate the underlying mechanisms of sPTB and pave the way for future systems biology studies to predict sPTB.</p></div>", "links"=>[], "tags"=>["Biochemistry", "biomarkers", "Computational biology", "Comparative genomics", "genetics", "genomics", "Diagnostic medicine", "Pathology and laboratory medicine", "Public and occupational health", "Global health", "women's health", "Maternal health", "birth", "Labor and delivery", "Preterm labor", "pregnancy", "Management of high-risk pregnancies", "Obstetrics and gynecology", "spontaneous", "preterm", "women", "threatened"], "article_id"=>1026515, "categories"=>["Biological Sciences"], "users"=>["Yujing Jan Heng", "Craig Edward Pennell", "Hon Nian Chua", "Jonathan Edward Perkins", "Stephen James Lye"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0096901", "stats"=>{"downloads"=>5, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Whole_Blood_Gene_Expression_Profile_Associated_with_Spontaneous_Preterm_Birth_in_Women_with_Threatened_Preterm_Labor_/1026515", "title"=>"Whole Blood Gene Expression Profile Associated with Spontaneous Preterm Birth in Women with Threatened Preterm Labor", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-05-14 02:50:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1497384"], "description"=>"<p>Urine culture, vaginal microbiology and placental histopathology and microbiologic assessments of participants.</p>", "links"=>[], "tags"=>["Biochemistry", "biomarkers", "Computational biology", "Comparative genomics", "genetics", "genomics", "Diagnostic medicine", "Pathology and laboratory medicine", "Public and occupational health", "Global health", "women's health", "Maternal health", "birth", "Labor and delivery", "Preterm labor", "pregnancy", "Management of high-risk pregnancies", "Obstetrics and gynecology", "vaginal", "microbiology", "placental", "histopathology", "microbiologic", "assessments"], "article_id"=>1026514, "categories"=>["Biological Sciences"], "users"=>["Yujing Jan Heng", "Craig Edward Pennell", "Hon Nian Chua", "Jonathan Edward Perkins", "Stephen James Lye"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0096901.t002", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Urine_culture_vaginal_microbiology_and_placental_histopathology_and_microbiologic_assessments_of_participants_/1026514", "title"=>"Urine culture, vaginal microbiology and placental histopathology and microbiologic assessments of participants.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-05-14 02:50:32"}

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Relative Metric

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