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<!DOCTYPE html> <html > <head> <meta charset="utf-8"> <meta rel="search" type="application/opensearchdescription+xml" href="/open_search.xml" title="Academia.edu"> <meta content="width=device-width, initial-scale=1" name="viewport"> <meta name="google-site-verification" content="bKJMBZA7E43xhDOopFZkssMMkBRjvYERV-NaN4R6mrs"> <meta name="csrf-param" content="authenticity_token" /> <meta name="csrf-token" content="gPJi4dRhfGFPsg96KI50JydVjPuv+2aV9OVwGq2I8BtoSoGbT4g5HNiLsPPgrmR7JznF/f+rVFami/NkHKT78Q==" /> <meta name="citation_title" content="Analysis of blood-based gene expression in idiopathic Parkinson disease" /> <meta name="citation_journal_title" content="Neurology" /> <meta name="citation_author" content="ROn Shamir" /> <meta name="twitter:card" content="summary" /> <meta name="twitter:url" content="https://www.academia.edu/73257120/Analysis_of_blood_based_gene_expression_in_idiopathic_Parkinson_disease" /> <meta name="twitter:title" content="Analysis of blood-based gene expression in idiopathic Parkinson disease" /> <meta name="twitter:description" content="Objective:To examine whether gene expression analysis of a large-scale Parkinson disease (PD) patient cohort produces a robust blood-based PD gene signature compared to previous studies that have used relatively small cohorts (≤220" /> <meta name="twitter:image" content="http://a.academia-assets.com/images/twitter-card.jpeg" /> <meta property="fb:app_id" content="2369844204" /> <meta property="og:type" content="article" /> <meta property="og:url" content="https://www.academia.edu/73257120/Analysis_of_blood_based_gene_expression_in_idiopathic_Parkinson_disease" /> <meta property="og:title" content="Analysis of blood-based gene expression in idiopathic Parkinson disease" /> <meta property="og:image" content="http://a.academia-assets.com/images/open-graph-icons/fb-paper.gif" /> <meta property="og:description" content="Objective:To examine whether gene expression analysis of a large-scale Parkinson disease (PD) patient cohort produces a robust blood-based PD gene signature compared to previous studies that have used relatively small cohorts (≤220" /> <meta property="article:author" content="https://independent.academia.edu/ROnShamir" /> <meta name="description" content="Objective:To examine whether gene expression analysis of a large-scale Parkinson disease (PD) patient cohort produces a robust blood-based PD gene signature compared to previous studies that have used relatively small cohorts (≤220" /> <title>(PDF) Analysis of blood-based gene expression in idiopathic Parkinson disease | ROn Shamir - Academia.edu</title> <link rel="canonical" href="https://www.academia.edu/73257120/Analysis_of_blood_based_gene_expression_in_idiopathic_Parkinson_disease" /> <script async src="https://www.googletagmanager.com/gtag/js?id=G-5VKX33P2DS"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'G-5VKX33P2DS', { cookie_domain: 'academia.edu', send_page_view: false, }); gtag('event', 'page_view', { 'controller': "single_work", 'action': "show", 'controller_action': 'single_work#show', 'logged_in': 'false', 'edge': 'unknown', // Send nil if there is no A/B test bucket, in case some records get logged // with missing data - that way we can distinguish between the two cases. // ab_test_bucket should be of the form <ab_test_name>:<bucket> 'ab_test_bucket': null, }) </script> <script> var $controller_name = 'single_work'; var $action_name = "show"; var $rails_env = 'production'; var $app_rev = 'b67ef4c3c1ecbe370843942feb5e75d02a3437b4'; var $domain = 'academia.edu'; var $app_host = "academia.edu"; var $asset_host = "academia-assets.com"; var $start_time = new Date().getTime(); var $recaptcha_key = "6LdxlRMTAAAAADnu_zyLhLg0YF9uACwz78shpjJB"; var $recaptcha_invisible_key = "6Lf3KHUUAAAAACggoMpmGJdQDtiyrjVlvGJ6BbAj"; var $disableClientRecordHit = false; </script> <script> window.require = { config: function() { return function() {} } } </script> <script> window.Aedu = window.Aedu || {}; window.Aedu.hit_data = null; window.Aedu.serverRenderTime = new Date(1732765993000); window.Aedu.timeDifference = new Date().getTime() - 1732765993000; </script> <script type="application/ld+json">{"@context":"https://schema.org","@type":"ScholarlyArticle","abstract":"Objective:To examine whether gene expression analysis of a large-scale Parkinson disease (PD) patient cohort produces a robust blood-based PD gene signature compared to previous studies that have used relatively small cohorts (≤220 samples).Methods:Whole-blood gene expression profiles were collected from a total of 523 individuals. After preprocessing, the data contained 486 gene profiles (n = 205 PD, n = 233 controls, n = 48 other neurodegenerative diseases) that were partitioned into training, validation, and independent test cohorts to identify and validate a gene signature. Batch-effect reduction and cross-validation were performed to ensure signature reliability. Finally, functional and pathway enrichment analyses were applied to the signature to identify PD-associated gene networks.Results:A gene signature of 100 probes that mapped to 87 genes, corresponding to 64 upregulated and 23 downregulated genes differentiating between patients with idiopathic PD and controls, was ident...","author":[{"@context":"https://schema.org","@type":"Person","name":"ROn Shamir"}],"contributor":[],"dateCreated":"2022-03-07","dateModified":null,"datePublished":null,"headline":"Analysis of blood-based gene expression in idiopathic Parkinson disease","inLanguage":"en","keywords":["Cognitive Science","Neurology","Biomarkers","Biology","Medicine","Neurodegenerative Diseases","Transcriptome","Humans","Female","Male","ROC Curve","Gene Regulatory Networks","Clinical Sciences","Microarray Analysis","Reproducibility of Results","Neurosciences","Parkinson Disease","Gene expression profiling","Cohort Studies"],"locationCreated":null,"publication":"Neurology","publisher":{"@context":"https://schema.org","@type":"Organization","name":"Ovid Technologies (Wolters Kluwer Health)"},"image":null,"thumbnailUrl":null,"url":"https://www.academia.edu/73257120/Analysis_of_blood_based_gene_expression_in_idiopathic_Parkinson_disease","sourceOrganization":[{"@context":"https://schema.org","@type":"EducationalOrganization","name":null}]}</script><link rel="stylesheet" media="all" href="//a.academia-assets.com/assets/single_work_page/loswp-102fa537001ba4d8dcd921ad9bd56c474abc201906ea4843e7e7efe9dfbf561d.css" /><link rel="stylesheet" media="all" href="//a.academia-assets.com/assets/design_system/body-8d679e925718b5e8e4b18e9a4fab37f7eaa99e43386459376559080ac8f2856a.css" /><link rel="stylesheet" media="all" href="//a.academia-assets.com/assets/design_system/button-3cea6e0ad4715ed965c49bfb15dedfc632787b32ff6d8c3a474182b231146ab7.css" /><link rel="stylesheet" media="all" 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After preprocessing, the data contained 486 gene profiles (n = 205 PD, n = 233 controls, n = 48 other neurodegenerative diseases) that were partitioned into training, validation, and independent test cohorts to identify and validate a gene signature. Batch-effect reduction and cross-validation were performed to ensure signature reliability. Finally, functional and pathway enrichment analyses were applied to the signature to identify PD-associated gene networks.Results:A gene signature of 100 probes that mapped to 87 genes, corresponding to 64 upregulated and 23 downregulated genes differentiating between patients with idiopathic PD and controls, was ident...","publisher":"Ovid Technologies (Wolters Kluwer Health)","publication_name":"Neurology"},"document_type":"paper","pre_hit_view_count_baseline":null,"quality":"low","language":"en","title":"Analysis of blood-based gene expression in idiopathic Parkinson disease","broadcastable":true,"draft":null,"has_indexable_attachment":true,"indexable":true}}["work"]; window.loswp.workCoauthors = [159390476]; window.loswp.locale = "en"; window.loswp.countryCode = "SG"; window.loswp.cwvAbTestBucket = ""; window.loswp.designVariant = "ds_vanilla"; window.loswp.fullPageMobileSutdModalVariant = "control"; window.loswp.useOptimizedScribd4genScript = false; window.loswp.appleClientId = 'edu.academia.applesignon';</script><script defer="" src="https://accounts.google.com/gsi/client"></script><div class="ds-loswp-container"><div class="ds-work-card--grid-container"><div class="ds-work-card--container js-loswp-work-card"><div class="ds-work-card--cover"><div class="ds-work-cover--wrapper"><div class="ds-work-cover--container"><button class="ds-work-cover--clickable js-swp-download-button" data-signup-modal="{"location":"swp-splash-paper-cover","attachmentId":81847780,"attachmentType":"pdf"}"><img alt="First page of “Analysis of blood-based gene expression in idiopathic Parkinson disease”" class="ds-work-cover--cover-thumbnail" src="https://0.academia-photos.com/attachment_thumbnails/81847780/mini_magick20220307-11672-1w2vees.png?1646672754" /><img alt="PDF Icon" class="ds-work-cover--file-icon" src="//a.academia-assets.com/assets/single_work_splash/adobe.icon-574afd46eb6b03a77a153a647fb47e30546f9215c0ee6a25df597a779717f9ef.svg" /><div class="ds-work-cover--hover-container"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span><p>Download Free PDF</p></div><div class="ds-work-cover--ribbon-container">Download Free PDF</div><div class="ds-work-cover--ribbon-triangle"></div></button></div></div></div><div class="ds-work-card--work-information"><h1 class="ds-work-card--work-title">Analysis of blood-based gene expression in idiopathic Parkinson disease</h1><div class="ds-work-card--work-authors ds-work-card--detail"><a class="ds-work-card--author js-wsj-grid-card-author ds2-5-body-md ds2-5-body-link" data-author-id="159390476" href="https://independent.academia.edu/ROnShamir"><img alt="Profile image of ROn Shamir" class="ds-work-card--author-avatar" src="//a.academia-assets.com/images/s65_no_pic.png" />ROn Shamir</a></div><div class="ds-work-card--detail"><p class="ds-work-card--detail ds2-5-body-sm">Neurology</p><div class="ds-work-card--work-metadata"><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">visibility</span><p class="ds2-5-body-sm" id="work-metadata-view-count">…</p></div><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">description</span><p class="ds2-5-body-sm">8 pages</p></div><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">link</span><p class="ds2-5-body-sm">1 file</p></div></div><script>(async () => { const workId = 73257120; const worksViewsPath = "/v0/works/views?subdomain_param=api&work_ids%5B%5D=73257120"; const getWorkViews = async (workId) => { const response = await fetch(worksViewsPath); if (!response.ok) { throw new Error('Failed to load work views'); } const data = await response.json(); return data.views[workId]; }; // Get the view count for the work - we send this immediately rather than waiting for // the DOM to load, so it can be available as soon as possible (but without holding up // the backend or other resource requests, because it's a bit expensive and not critical). const viewCount = await getWorkViews(workId); const updateViewCount = (viewCount) => { const viewCountNumber = Number(viewCount); if (!viewCountNumber) { throw new Error('Failed to parse view count'); } const commaizedViewCount = viewCountNumber.toLocaleString(); const viewCountBody = document.getElementById('work-metadata-view-count'); if (viewCountBody) { viewCountBody.textContent = `${commaizedViewCount} views`; } else { throw new Error('Failed to find work views element'); } }; // If the DOM is still loading, wait for it to be ready before updating the view count. if (document.readyState === "loading") { document.addEventListener('DOMContentLoaded', () => { updateViewCount(viewCount); }); // Otherwise, just update it immediately. } else { updateViewCount(viewCount); } })();</script></div><p class="ds-work-card--work-abstract ds-work-card--detail ds2-5-body-md">Objective:To examine whether gene expression analysis of a large-scale Parkinson disease (PD) patient cohort produces a robust blood-based PD gene signature compared to previous studies that have used relatively small cohorts (≤220 samples).Methods:Whole-blood gene expression profiles were collected from a total of 523 individuals. After preprocessing, the data contained 486 gene profiles (n = 205 PD, n = 233 controls, n = 48 other neurodegenerative diseases) that were partitioned into training, validation, and independent test cohorts to identify and validate a gene signature. Batch-effect reduction and cross-validation were performed to ensure signature reliability. Finally, functional and pathway enrichment analyses were applied to the signature to identify PD-associated gene networks.Results:A gene signature of 100 probes that mapped to 87 genes, corresponding to 64 upregulated and 23 downregulated genes differentiating between patients with idiopathic PD and controls, was ident...</p><div class="ds-work-card--button-container"><button class="ds2-5-button js-swp-download-button" data-signup-modal="{"location":"continue-reading-button--work-card","attachmentId":81847780,"attachmentType":"pdf","workUrl":"https://www.academia.edu/73257120/Analysis_of_blood_based_gene_expression_in_idiopathic_Parkinson_disease"}">See full PDF</button><button class="ds2-5-button ds2-5-button--secondary js-swp-download-button" data-signup-modal="{"location":"download-pdf-button--work-card","attachmentId":81847780,"attachmentType":"pdf","workUrl":"https://www.academia.edu/73257120/Analysis_of_blood_based_gene_expression_in_idiopathic_Parkinson_disease"}"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span>Download PDF</button></div></div></div></div><div data-auto_select="false" data-client_id="331998490334-rsn3chp12mbkiqhl6e7lu2q0mlbu0f1b" data-doc_id="81847780" data-landing_url="https://www.academia.edu/73257120/Analysis_of_blood_based_gene_expression_in_idiopathic_Parkinson_disease" data-login_uri="https://www.academia.edu/registrations/google_one_tap" data-moment_callback="onGoogleOneTapEvent" id="g_id_onload"></div><div class="ds-top-related-works--grid-container"><div class="ds-related-content--container ds-top-related-works--container"><h2 class="ds-related-content--heading">Related papers</h2><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="0" data-entity-id="99197132" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/99197132/Characterizing_the_Expression_Patterns_of_Parkinson_s_Disease_Associated_Genes">Characterizing the Expression Patterns of Parkinson’s Disease Associated Genes</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="65502062" href="https://independent.academia.edu/kuokuoli">kuokuo li</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Frontiers in Neuroscience, 2021</p><p class="ds-related-work--abstract ds2-5-body-sm">BackgroundThe expression pattern represents a quantitative phenotype that provides an in-depth view of the molecular mechanism in Parkinson’s disease (PD); however, the expression patterns of PD-associated genes (PAGs) and their relation to age at onset (AAO) remain unclear.MethodsThe known PD-causing genes and PD-risk genes, which were collected from latest published authoritative meta-analysis, were integrated as PAGs. The expression data from Genotype-Tissue Expression database, Allen Brian Map database, and BrainSpan database, were extracted to characterize the tissue specificity, inhibitory-excitatory neuron expression profile, and spatio-temporal expression pattern of PAGs, respectively. The AAO information of PD-causing gene was download from Gene4PD and MDSgene database.ResultsWe prioritized 107 PAGs and found that the PAGs were more likely to be expressed in brain-related tissues than non-brain tissues and that more PAGs had higher expression levels in excitatory neurons th...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Characterizing the Expression Patterns of Parkinson’s Disease Associated Genes","attachmentId":100349031,"attachmentType":"pdf","work_url":"https://www.academia.edu/99197132/Characterizing_the_Expression_Patterns_of_Parkinson_s_Disease_Associated_Genes","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/99197132/Characterizing_the_Expression_Patterns_of_Parkinson_s_Disease_Associated_Genes"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="1" data-entity-id="114939486" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/114939486/Gene_Expression_Differences_in_Peripheral_Blood_of_Parkinson_s_Disease_Patients_with_Distinct_Progression_Profiles">Gene Expression Differences in Peripheral Blood of Parkinson’s Disease Patients with Distinct Progression Profiles</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="15302355" href="https://ucl.academia.edu/LilachSoreq">Lilach Soreq</a></div><p class="ds-related-work--metadata ds2-5-body-xs">PLOS ONE, 2016</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Gene Expression Differences in Peripheral Blood of Parkinson’s Disease Patients with Distinct Progression Profiles","attachmentId":111494065,"attachmentType":"pdf","work_url":"https://www.academia.edu/114939486/Gene_Expression_Differences_in_Peripheral_Blood_of_Parkinson_s_Disease_Patients_with_Distinct_Progression_Profiles","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/114939486/Gene_Expression_Differences_in_Peripheral_Blood_of_Parkinson_s_Disease_Patients_with_Distinct_Progression_Profiles"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="2" data-entity-id="78250440" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/78250440/Found_in_transcription_accurate_Parkinsons_disease_classification_in_peripheral_blood">Found in transcription: accurate Parkinson's disease classification in peripheral blood</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="192816283" href="https://svgipsar.academia.edu/PRAVEENSHARMA">PRAVEEN SHARMA</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Journal of Parkinson's disease, 2013</p><p class="ds-related-work--abstract ds2-5-body-sm">A blood-based test for the early detection of Parkinson&#39;s disease (PD) would be an important diagnostic tool and useful for patient selection when developing novel drugs or treatments for the disease. Here, we aimed to identify potential biomarkers associated with PD. We applied gene expression profiling to the study of peripheral blood from 75 healthy control subjects and 79 PD patients at different stages of the disease. Healthy control subjects were matched for age and gender with PD subjects, and the diagnosis of patients was based on clinical evaluation by specialists in movement disorders. RNA was extracted from the blood samples and the gene expressions were measured using the Illumina HumanHT-12 v4.0 Expression BeadChip. Our results support previous studies that gene expression in blood may be instrumental in the search for molecular biomarkers for PD. Single cross-validation results show that PD can be correctly classified from healthy controls with an agreement of 88% ...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Found in transcription: accurate Parkinson's disease classification in peripheral blood","attachmentId":85362699,"attachmentType":"pdf","work_url":"https://www.academia.edu/78250440/Found_in_transcription_accurate_Parkinsons_disease_classification_in_peripheral_blood","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/78250440/Found_in_transcription_accurate_Parkinsons_disease_classification_in_peripheral_blood"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="3" data-entity-id="54909416" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/54909416/A_systems_biology_approach_towards_the_identification_of_candidate_therapeutic_genes_and_potential_biomarkers_for_Parkinson_s_disease">A systems biology approach towards the identification of candidate therapeutic genes and potential biomarkers for Parkinson’s disease</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="11153236" href="https://independent.academia.edu/KarthicRajamanickam">Karthic Rajamanickam</a></div><p class="ds-related-work--metadata ds2-5-body-xs">PLOS ONE</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"A systems biology approach towards the identification of candidate therapeutic genes and potential biomarkers for Parkinson’s disease","attachmentId":71040382,"attachmentType":"pdf","work_url":"https://www.academia.edu/54909416/A_systems_biology_approach_towards_the_identification_of_candidate_therapeutic_genes_and_potential_biomarkers_for_Parkinson_s_disease","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/54909416/A_systems_biology_approach_towards_the_identification_of_candidate_therapeutic_genes_and_potential_biomarkers_for_Parkinson_s_disease"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="4" data-entity-id="13770043" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/13770043/ParkDB_a_Parkinsons_disease_gene_expression_database">ParkDB: a Parkinson's disease gene expression database</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="32880689" href="https://independent.academia.edu/WEmmett">W. Emmett</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Database, 2011</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"ParkDB: a Parkinson's disease gene expression database","attachmentId":44973311,"attachmentType":"pdf","work_url":"https://www.academia.edu/13770043/ParkDB_a_Parkinsons_disease_gene_expression_database","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/13770043/ParkDB_a_Parkinsons_disease_gene_expression_database"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="5" data-entity-id="10364952" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/10364952/Database_tool_ParkDB_a_Parkinson_s_disease_gene_expression_database">Database tool ParkDB: a Parkinson’s disease gene expression database</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="25470407" href="https://ki.academia.edu/JesperTegner">Jesper Tegner</a></div><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Database tool ParkDB: a Parkinson’s disease gene expression database","attachmentId":36431887,"attachmentType":"pdf","work_url":"https://www.academia.edu/10364952/Database_tool_ParkDB_a_Parkinson_s_disease_gene_expression_database","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/10364952/Database_tool_ParkDB_a_Parkinson_s_disease_gene_expression_database"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="6" data-entity-id="43451800" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/43451800/A_Computational_Approach_to_Identify_Blood_Cell_Expressed_Parkinsons_Disease_Biomarkers_that_are_Coordinately_Expressed_in_Brain_Tissue">A Computational Approach to Identify Blood Cell-Expressed Parkinson's Disease Biomarkers that are Coordinately Expressed in Brain Tissue</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="96422644" href="https://independent.academia.edu/RanaHumayanKabir">Humayan Kabir Rana</a><span>, </span><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="721850" href="https://rajshahi.academia.edu/MdBabulIslam">Md. Babul Islam</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Computers in Biology and Medicine, 2019</p><p class="ds-related-work--abstract ds2-5-body-sm">Identification of genes whose regulation of expression is functionally similar in both brain tissue and blood cells could in principle enable monitoring of significant neurological traits and disorders by analysis of blood samples. We thus employed transcriptional analysis of pathologically affected tissues, using agnostic approaches to identify overlapping gene functions and integrating this transcriptomic information with expression quantitative trait loci (eQTL) data. Here, we estimate the correlation of gene expression in the top-associated cis-eQTLs of brain tissue and blood cells in Parkinson's Disease (PD). We introduced quantitative frameworks to reveal the complex relationship of various biasing genetic factors in PD, a neurodegenerative disease. We examined gene expression microarray and RNA-Seq datasets from human brain and blood tissues from PD-affected and control individuals. Differentially expressed genes (DEG) were identified for both brain and blood cells to determine common DEG overlaps. Based on neighborhood-based bench-marking and multilayer network topology approaches we then developed genetic associations of factors with PD. Overlapping DEG sets underwent gene enrichment using pathway analysis and gene ontology methods, which identified candidate common genes and pathways. We identified 12 significantly dysregulated genes shared by brain and blood cells, which were validated using dbGaP (gene SNP-disease linkage) database for gold-standard benchmarking of their significance in disease processes. Ontological and pathway analyses identified significant gene ontology and molecular pathways that indicate PD progression. In sum, we found possible novel links between pathological processes in brain tissue and blood cells by examining cell pathway commonalities, corroborating these associations using well validated datasets. This demonstrates that for brain-related pathologies combining gene 1 expression analysis and blood cell cis-eQTL is a potentially powerful analytical approach. Thus, our methodologies facilitate data-driven approaches that can advance knowledge of disease mechanisms and may, with clinical validation, enable prediction of neurological dys-function using blood cell transcript profiling.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"A Computational Approach to Identify Blood Cell-Expressed Parkinson's Disease Biomarkers that are Coordinately Expressed in Brain Tissue","attachmentId":63758429,"attachmentType":"pdf","work_url":"https://www.academia.edu/43451800/A_Computational_Approach_to_Identify_Blood_Cell_Expressed_Parkinsons_Disease_Biomarkers_that_are_Coordinately_Expressed_in_Brain_Tissue","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/43451800/A_Computational_Approach_to_Identify_Blood_Cell_Expressed_Parkinsons_Disease_Biomarkers_that_are_Coordinately_Expressed_in_Brain_Tissue"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="7" data-entity-id="55217581" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/55217581/Molecular_markers_of_early_Parkinsons_disease_based_on_gene_expression_in_blood">Molecular markers of early Parkinson's disease based on gene expression in blood</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="52480261" href="https://independent.academia.edu/RoderickJensen">Roderick Jensen</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Proceedings of the National Academy of Sciences, 2007</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Molecular markers of early Parkinson's disease based on gene expression in blood","attachmentId":71193209,"attachmentType":"pdf","work_url":"https://www.academia.edu/55217581/Molecular_markers_of_early_Parkinsons_disease_based_on_gene_expression_in_blood","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/55217581/Molecular_markers_of_early_Parkinsons_disease_based_on_gene_expression_in_blood"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="8" data-entity-id="26616636" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/26616636/A_Cross_Study_Transcriptional_Analysis_of_Parkinsons_Disease">A Cross-Study Transcriptional Analysis of Parkinson's Disease</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="50601060" href="https://independent.academia.edu/PeterSilburn">Peter Silburn</a></div><p class="ds-related-work--metadata ds2-5-body-xs">PLoS ONE, 2009</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"A Cross-Study Transcriptional Analysis of Parkinson's Disease","attachmentId":46902730,"attachmentType":"pdf","work_url":"https://www.academia.edu/26616636/A_Cross_Study_Transcriptional_Analysis_of_Parkinsons_Disease","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/26616636/A_Cross_Study_Transcriptional_Analysis_of_Parkinsons_Disease"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="9" data-entity-id="105156398" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/105156398/Parkinsons_disease_associated_genetic_variation_is_linked_to_quantitative_expression_of_inflammatory_genes">Parkinson's disease-associated genetic variation is linked to quantitative expression of inflammatory genes</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="44323501" href="https://independent.academia.edu/PierceSteven">Steven Pierce</a></div><p class="ds-related-work--metadata ds2-5-body-xs">PloS one, 2017</p><p class="ds-related-work--abstract ds2-5-body-sm">Genome-wide association studies (GWAS) have linked dozens of single nucleotide polymorphisms (SNPs) with Parkinson&#39;s disease (PD) risk. Ascertaining the functional and eventual causal mechanisms underlying these relationships has proven difficult. The majority of risk SNPs, and nearby SNPs in linkage disequilibrium (LD), are found in intergenic or intronic regions and confer risk through allele-dependent expression of multiple unknown target genes. Combining GWAS results with publicly available GTEx data, generated through eQTL (expression quantitative trait loci) identification studies, enables a direct association of SNPs to gene expression levels and aids in narrowing the large population of potential genetic targets for hypothesis-driven experimental cell biology. Separately, overlapping of SNPs with putative enhancer segmentations can strengthen target filtering. We report here the results of analyzing 7,607 PD risk SNPs along with an additional 23,759 high linkage disequil...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Parkinson's disease-associated genetic variation is linked to quantitative expression of inflammatory genes","attachmentId":104687228,"attachmentType":"pdf","work_url":"https://www.academia.edu/105156398/Parkinsons_disease_associated_genetic_variation_is_linked_to_quantitative_expression_of_inflammatory_genes","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/105156398/Parkinsons_disease_associated_genetic_variation_is_linked_to_quantitative_expression_of_inflammatory_genes"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div></div></div><div class="ds-sticky-ctas--wrapper js-loswp-sticky-ctas hidden"><div class="ds-sticky-ctas--grid-container"><div class="ds-sticky-ctas--container"><button class="ds2-5-button js-swp-download-button" data-signup-modal="{"location":"continue-reading-button--sticky-ctas","attachmentId":81847780,"attachmentType":"pdf","workUrl":null}">See full PDF</button><button class="ds2-5-button ds2-5-button--secondary js-swp-download-button" data-signup-modal="{"location":"download-pdf-button--sticky-ctas","attachmentId":81847780,"attachmentType":"pdf","workUrl":null}"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span>Download PDF</button></div></div></div><div class="ds-below-fold--grid-container"><div class="ds-work--container js-loswp-embedded-document"><div class="attachment_preview" data-attachment="Attachment_81847780" style="display: none"><div class="js-scribd-document-container"><div class="scribd--document-loading js-scribd-document-loader" style="display: block;"><img alt="Loading..." src="//a.academia-assets.com/images/loaders/paper-load.gif" /><p>Loading Preview</p></div></div><div style="text-align: center;"><div class="scribd--no-preview-alert js-preview-unavailable"><p>Sorry, preview is currently unavailable. You can download the paper by clicking the button above.</p></div></div></div></div><div class="ds-sidebar--container js-work-sidebar"><div class="ds-related-content--container"><h2 class="ds-related-content--heading">Related papers</h2><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="0" data-entity-id="5318566" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/5318566/Genomic_convergence_identifying_candidate_genes_for_Parkinsons_disease_by_combining_serial_analysis_of_gene_expression_and_genetic_linkage">Genomic convergence: identifying candidate genes for Parkinson's disease by combining serial analysis of gene expression and genetic linkage</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="7343021" href="https://independent.academia.edu/YiJuLi">Yi-Ju 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ds2-5-body-xs">ArXiv, 2016</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"A Multivariate Biomarker for Parkinson's Disease","attachmentId":79941293,"attachmentType":"pdf","work_url":"https://www.academia.edu/70068957/A_Multivariate_Biomarker_for_Parkinsons_Disease","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" href="https://www.academia.edu/70068957/A_Multivariate_Biomarker_for_Parkinsons_Disease"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="2" data-entity-id="52226297" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/52226297/Characterization_of_Parkinson_s_disease_using_blood_based_biomarkers_A_multicohort_proteomic_analysis">Characterization of Parkinson’s disease using blood-based biomarkers: A multicohort proteomic analysis</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="1011668" href="https://independent.academia.edu/MarijanPosavi">Marijan Posavi</a></div><p class="ds-related-work--metadata ds2-5-body-xs">PLOS Medicine</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Characterization of Parkinson’s disease using blood-based biomarkers: A multicohort proteomic analysis","attachmentId":69589651,"attachmentType":"pdf","work_url":"https://www.academia.edu/52226297/Characterization_of_Parkinson_s_disease_using_blood_based_biomarkers_A_multicohort_proteomic_analysis","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" href="https://www.academia.edu/52226297/Characterization_of_Parkinson_s_disease_using_blood_based_biomarkers_A_multicohort_proteomic_analysis"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="3" data-entity-id="63140911" data-sort-order="default"><a 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