{"id":5783,"date":"2023-09-04T03:37:29","date_gmt":"2023-09-04T03:37:29","guid":{"rendered":"https:\/\/cm.vastapps.dev\/tcia-analysis-result\/tcga-ov-proteogenomics\/"},"modified":"2023-09-13T12:10:09","modified_gmt":"2023-09-13T12:10:09","slug":"tcga-ov-proteogenomics","status":"publish","type":"tcia_analysis_result","link":"https:\/\/cm.vastapps.dev\/tcia-analysis-result\/tcga-ov-proteogenomics\/","title":{"rendered":"TCGA-OV-PROTEOGENOMICS"},"featured_media":0,"template":"","cancer_types":["Ovarian"],"citations":[4785,4786,2925],"full_export":"<h2 id=\"IntegrationofCTbasedQualitativeandRadiomicFeatureswithProteomicVariablesinPatientswithHighGradeSerousOvarianCancer:AnExploratoryAnalysis(TCGAOVProteogenomics)-Summary\">Summary<\/h2><h3 id=\"IntegrationofCTbasedQualitativeandRadiomicFeatureswithProteomicVariablesinPatientswithHighGradeSerousOvarianCancer:AnExploratoryAnalysis(TCGAOVProteogenomics)-Objectives\">Objectives<\/h3><p>To investigate the association between CT imaging traits and texture metrics with proteomic data in patients with high-grade serous ovarian cancer (HGSOC).<\/p><h3 id=\"IntegrationofCTbasedQualitativeandRadiomicFeatureswithProteomicVariablesinPatientswithHighGradeSerousOvarianCancer:AnExploratoryAnalysis(TCGAOVProteogenomics)-Methods\">Methods<\/h3><p>This retrospective, hypothesis-generating study included 20 <a href=\"https:\/\/wiki.cancerimagingarchive.net\/pages\/viewpage.action?pageId=7569497\">The Cancer Genome Atlas Ovarian Cancer Collection (TCGA-OV)<\/a> patients with HGSOC prior to primary cytoreductive surgery. Two readers independently assessed the contrast-enhanced computed tomography (CT) images and extracted 33 imaging traits, with a third reader adjudicating in the event of a disagreement. In addition, all sites of suspected HGSOC were manually segmented texture features were computed from each tumour site. Three texture features that represented intra-and inter-site tumour heterogeneity were used for analysis. An integrated analysis of transcriptomic and proteomic data identified proteins with conserved expression between primary tumour sites and metastasis. Correlations between protein-abundance and various CT imaging traits and texture features were assessed using the Kendall tau rank correlation-coefficient and the Mann-Whitney U test, whereas the area under the receiver-operating characteristic curve (AUC) was reported as a metric of the strength and the direction of the association. p values &lt; 0.05 were considered significant.<\/p><h3 id=\"IntegrationofCTbasedQualitativeandRadiomicFeatureswithProteomicVariablesinPatientswithHighGradeSerousOvarianCancer:AnExploratoryAnalysis(TCGAOVProteogenomics)-Results\">Results<\/h3><p>Four proteins were associated with CT-based imaging traits, with the strongest correlation observed between the CRIP2 protein and disease in the mesentery (p&lt;0.001, AUC=0.05). The abundance of three proteins was associated with texture features that represented intra-and inter-site tumour heterogeneity, with the strongest negative correlation between the CKB protein and cluster dissimilarity (p=0.047, \ud835\udf0f =0.326).<\/p><h3 id=\"IntegrationofCTbasedQualitativeandRadiomicFeatureswithProteomicVariablesinPatientswithHighGradeSerousOvarianCancer:AnExploratoryAnalysis(TCGAOVProteogenomics)-Conclusion\">Conclusion<\/h3><p>This study provides the first insights into the potential associations between standard-of-care CT imaging traits and texture measures of intra-and inter-site heterogeneity, and the abundance of several proteins.<\/p><p><br\/><\/p><div class=\"tab-style-builtin\"><div class=\"localtabs-macro\"><div class=\"aui-tabs horizontal-tabs\" role=\"application\" data-aui-responsive=\"true\"><ul class=\"tabs-menu\"><li class=\"menu-item bv-localtab  active-tab \"><a href=\"#48464392225c3eafe0bf4cca84c3c2c8dc83351f\"><strong>Data Access<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#4846439225a66644c5bc42e3a5fca212ea7eb5d6\"><strong>Citations &amp; Data Usage Policy<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#48464392e94693cfe6204477a1e146058a8bb564\"><strong>Versions<\/strong><\/a> <\/li><\/ul><div class=\"tabs-pane  active-pane \" id=\"48464392225c3eafe0bf4cca84c3c2c8dc83351f\" active=\"true\" name=\"Data Access\" ><h3 id=\"IntegrationofCTbasedQualitativeandRadiomicFeatureswithProteomicVariablesinPatientswithHighGradeSerousOvarianCancer:AnExploratoryAnalysis(TCGAOVProteogenomics)-DataAccess\"><span style=\"color: rgb(23,43,77);\">Data Access<\/span><\/h3><p><span style=\"color: rgb(23,43,77);\"><br\/><\/span><\/p><div class=\"table-wrap\"><table class=\"fixed-table wrapped confluenceTable\"><colgroup><col style=\"width: 302.0px;\"\/><col style=\"width: 311.0px;\"\/><col style=\"width: 311.0px;\"\/><\/colgroup><tbody><tr><th class=\"confluenceTh\">Data Type<\/th><th class=\"confluenceTh\">Download all or Query\/Filter<\/th><th class=\"confluenceTh\">License<\/th><\/tr><tr><td class=\"confluenceTd\">Images (DICOM, 3 GB)<\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p><br\/>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/48464392\/2020-02-26_Images_from_HGSOC_proteomics.tcia?api=v2\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span><br\/><\/p><span style=\"color: rgb(33,37,41);text-decoration: none;\">(Download requires\u00a0<\/span><span style=\"color: rgb(33,37,41);text-decoration: none;\">the<span>\u00a0<\/span><\/span><a rel=\"nofollow\" href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\" style=\"text-decoration: none;text-align: left;\">NBIA Data Retriever<\/a><span style=\"color: rgb(33,37,41);\">)<\/span><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/3.0\/\" class=\"external-link\" rel=\"nofollow\">CC BY 3.0<\/a><\/p><\/div><\/td><\/tr><tr><td class=\"confluenceTd\">Image Analyses, Proteogenomic features, and Clinical data (CSV)<\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p><br\/>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/48464392\/2020_02_26_HGSOC_proteomics.csv?api=v2\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span><\/p><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/3.0\/\" class=\"external-link\" rel=\"nofollow\">CC BY 3.0<\/a><\/p><\/div><\/td><\/tr><\/tbody><\/table><\/div><p style=\"text-align: left;\">Click the Versions tab for more info about data releases.<\/p><p class=\"xmsonormal\" style=\"text-align: left;\"><span style=\"color: rgb(33,37,41);\">Please<span>\u00a0<\/span><\/span><a class=\"external-link\" style=\"text-decoration: none;text-align: left;\" href=\"http:\/\/www.cancerimagingarchive.net\/support\/\" rel=\"nofollow\">contact TCIA's Helpdesk<\/a><span style=\"color: rgb(33,37,41);\"> <\/span><span style=\"color: rgb(23,43,77);\">with any questions regarding usage.<\/span><\/p><p><strong><span style=\"color: rgb(29,28,29);text-decoration: none;\">Collections Used in this Third Party Analysis<\/span><\/strong><br style=\"text-decoration: none;text-align: left;\"\/><span style=\"color: rgb(29,28,29);text-decoration: none;\">Below is a list of the Collections used in these analyses:<\/span><\/p><ul><li><span style=\"color: rgb(29,28,29);text-decoration: none;\"><a href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2016.NDO1MDFQ\" class=\"external-link\" rel=\"nofollow\">TCGA-OV<\/a><\/span><\/li><\/ul><\/div><div class=\"tabs-pane \" id=\"4846439225a66644c5bc42e3a5fca212ea7eb5d6\" name=\"Citations BITVOODOO_ANDamp; Data Usage Policy\" ><h3 id=\"IntegrationofCTbasedQualitativeandRadiomicFeatureswithProteomicVariablesinPatientswithHighGradeSerousOvarianCancer:AnExploratoryAnalysis(TCGAOVProteogenomics)-Citations&amp;DataUsagePolicy\">Citations &amp; Data Usage Policy\u00a0<\/h3><p class=\"auto-cursor-target\">\n<p>\nUsers must abide by the <a href=\"https:\/\/wiki.cancerimagingarchive.net\/x\/c4hF\" class=\"external-link\" rel=\"nofollow\">TCIA Data Usage Policy and Restrictions<\/a>. Attribution should include references to the following citations:\n<\/p><\/p><div class=\"confluence-information-macro confluence-information-macro-information\"><p class=\"title\">Data Citation<\/p><span class=\"aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon\"><\/span><div class=\"confluence-information-macro-body\"><p>Beer, L., Sahin, H., Blazic, I., Vargas, H. A., Veeraraghavan, H., Kirby, J., Fevrier-Sullivan, B., Freymann, J., Jaffe, C., Conrads, T., Maxwell, G., Darcy, K., Huang, E., &amp; Sala, E. (2019). <strong>Data from Integration of CT-based Qualitative and Radiomic Features with Proteomic Variables in Patients with High-Grade Serous Ovarian Cancer: An Exploratory Analysis\u00a0(TCGA-OV-Proteogenomics) [Data set]<\/strong>. The Cancer Imaging Archive. <a href=\"https:\/\/doi.org\/10.7937\/TCIA.2019.9stoinf1\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.7937\/TCIA.2019.9stoinf1<\/a><\/p><\/div><\/div><div class=\"confluence-information-macro confluence-information-macro-information\"><p class=\"title\">Publication Citation<\/p><span class=\"aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon\"><\/span><div class=\"confluence-information-macro-body\"><p><span style=\"color: rgb(51,51,51);\">Beer, L., Sahin, H., Bateman, N. W., Blazic, I., Vargas, H. A., Veeraraghavan, H., Kirby, J., Fevrier-Sullivan, B., Freymann, J. B., Jaffe, C. C., Brenton, J., Micc\u00f3, M., Nougaret, S., Darcy, K. M., Maxwell, G. L., Conrads, T. P., Huang, E., &amp; Sala, E. (2020). <strong>Integration of proteomics with CT-based qualitative and radiomic features in high-grade serous ovarian cancer patients: an exploratory analysis<\/strong>. European Radiology, 30(8), 4306\u20134316. <a href=\"https:\/\/doi.org\/10.1007\/s00330-020-06755-3\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.1007\/s00330-020-06755-3<\/a> <\/span><\/p><\/div><\/div><div class=\"confluence-information-macro confluence-information-macro-information\"><p class=\"title\">TCIA Citation<\/p><span class=\"aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon\"><\/span><div class=\"confluence-information-macro-body\"><p>Clark, K., Vendt, B., Smith, K., Freymann, J., Kirby, J., Koppel, P., Moore, S., Phillips, S., Maffitt, D., Pringle, M., Tarbox, L., &amp; Prior, F. (2013). <strong>The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository<\/strong>. Journal of Digital Imaging, 26(6), 1045\u20131057. <a href=\"https:\/\/doi.org\/10.1007\/s10278-013-9622-7\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.1007\/s10278-013-9622-7<\/a><\/p><\/div><\/div><h3 id=\"IntegrationofCTbasedQualitativeandRadiomicFeatureswithProteomicVariablesinPatientswithHighGradeSerousOvarianCancer:AnExploratoryAnalysis(TCGAOVProteogenomics)-OtherPublicationsUsingThisData\">Other Publications Using This Data<\/h3><p><span>TCIA maintains<\/span>\u00a0<a rel=\"nofollow\" href=\"https:\/\/www.cancerimagingarchive.net\/publications\/\" class=\"external-link\">a list of publications<\/a> <span> that leverage TCIA data. <\/span> If you have a manuscript you'd like to add please <a class=\"external-link\" href=\"http:\/\/www.cancerimagingarchive.net\/support\/\" rel=\"nofollow\">contact TCIA's Helpdesk<\/a>.<\/p><\/div><div class=\"tabs-pane \" id=\"48464392e94693cfe6204477a1e146058a8bb564\" name=\"Versions\" ><h3 id=\"IntegrationofCTbasedQualitativeandRadiomicFeatureswithProteomicVariablesinPatientswithHighGradeSerousOvarianCancer:AnExploratoryAnalysis(TCGAOVProteogenomics)-Version1(Current):2020\/04\/06\">Version 1 (Current): 2020\/04\/06<\/h3><div class=\"table-wrap\"><table class=\"fixed-table wrapped confluenceTable\"><colgroup> <col style=\"width: 302.0px;\"\/> <col style=\"width: 311.0px;\"\/> <\/colgroup><tbody><tr><th class=\"confluenceTh\">Data Type<\/th><th class=\"confluenceTh\">Download all or Query\/Filter<\/th><\/tr><tr><td class=\"confluenceTd\">Images (DICOM, 3 GB)<\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p><a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/48464392\/2020-02-26_Images_from_HGSOC_proteomics.tcia?version=1&amp;modificationDate=1586798558792&amp;api=v2\" data-linked-resource-id=\"70223864\" data-linked-resource-version=\"1\" data-linked-resource-type=\"attachment\" data-linked-resource-default-alias=\"2020-02-26_Images_from_HGSOC_proteomics.tcia\" data-linked-resource-content-type=\"application\/octet-stream\" data-linked-resource-container-id=\"48464392\" data-linked-resource-container-version=\"33\"><span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\"><img class=\"confluence-embedded-image confluence-thumbnail\" draggable=\"false\" height=\"30\" src=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/embedded-page\/DOI\/Integration%20of%20CT-based%20Qualitative%20and%20Radiomic%20Features%20with%20Proteomic%20Variables%20in%20Patients%20with%20High-Grade%20Serous%20Ovarian%20Cancer:%20An%20Exploratory%20Analysis%20(TCGA-OV-Proteogenomics)\/tcia_wiki_download_button.png?api=v2\"><\/span><\/a><\/p><p><span style=\"color: rgb(33,37,41);text-decoration: none;\">(Download requires\u00a0<\/span><span style=\"color: rgb(33,37,41);text-decoration: none;\">the<span>\u00a0<\/span><\/span><a style=\"text-decoration: none;text-align: left;\" href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\" rel=\"nofollow\">NBIA Data Retriever<\/a><span style=\"color: rgb(33,37,41);\">)<\/span><\/p><\/div><\/td><\/tr><tr><td colspan=\"1\" class=\"confluenceTd\">Image Analyses, Proteogenomic features, and Clinical data (CSV)<\/td><td colspan=\"1\" class=\"confluenceTd\"><div class=\"content-wrapper\"><p><a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/48464392\/2020_02_26_HGSOC_proteomics.csv?version=1&amp;modificationDate=1583430919148&amp;api=v2\" data-linked-resource-id=\"68551336\" data-linked-resource-version=\"1\" data-linked-resource-type=\"attachment\" data-linked-resource-default-alias=\"2020_02_26_HGSOC_proteomics.csv\" data-linked-resource-content-type=\"text\/csv\" data-linked-resource-container-id=\"48464392\" data-linked-resource-container-version=\"33\"><span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\"><img class=\"confluence-embedded-image confluence-thumbnail\" draggable=\"false\" height=\"30\" src=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/embedded-page\/DOI\/Integration%20of%20CT-based%20Qualitative%20and%20Radiomic%20Features%20with%20Proteomic%20Variables%20in%20Patients%20with%20High-Grade%20Serous%20Ovarian%20Cancer:%20An%20Exploratory%20Analysis%20(TCGA-OV-Proteogenomics)\/tcia_wiki_download_button.png?api=v2\"><\/span><\/a><\/p><\/div><\/td><\/tr><\/tbody><\/table><\/div><\/div><\/div><\/div><\/div><div><p><br\/><\/p><\/div>","make_new_version_button":"","related_collections":["TCGA-OV"],"result_doi":"10.7937\/TCIA.2019.9stoinf1","versions":false,"cancer_locations":["Ovary"],"publications_related":"","result_download_info":"<br\/>\n\nClick the Versions tab for more info about data releases.\nPlease\u00a0<a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\">contact TCIA's Helpdesk<\/a> with any questions regarding usage.\n<strong>Collections Used in this Third Party Analysis<\/strong><br\/>Below is a list of the Collections used in these analyses:\n<ul><li><a href=\"https:\/\/doi.org\/10.7937\/K9\/TCIA.2016.NDO1MDFQ\">TCGA-OV<\/a><\/li><\/ul>","result_downloads":[5410,5411],"result_page_accessibility":"Public","version_change_log_archived":"","additional_resources":"","date_updated":"2020-04-15","publications_using":"TCIA maintains\u00a0<a href=\"https:\/\/www.cancerimagingarchive.net\/publications\/\">a list of publications<\/a>  that leverage TCIA data.  If you have a manuscript you'd like to add please <a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\">contact TCIA's Helpdesk<\/a>.","result_title":"Integration of CT-based Qualitative and Radiomic Features with Proteomic Variables in Patients with High-Grade Serous Ovarian Cancer: An Exploratory Analysis","subjects":"20","detailed_description":"","result_short_title":"TCGA-OV-Proteogenomics","supporting_data":["Radiologist assessments of image features","proteogenomic features"],"version_change_log":"","collections":"","result_browse_title":"","version_number":[],"collection_downloads":false,"result_summary":"<h3>Objectives<\/h3>\nTo investigate the association between CT imaging traits and texture metrics with proteomic data in patients with high-grade serous ovarian cancer (HGSOC).\n<h3>Methods<\/h3>\nThis retrospective, hypothesis-generating study included 20 <a href=\"\/pages\/viewpage.action?pageId=7569497\">The Cancer Genome Atlas Ovarian Cancer Collection (TCGA-OV)<\/a> patients with HGSOC prior to primary cytoreductive surgery. Two readers independently assessed the contrast-enhanced computed tomography (CT) images and extracted 33 imaging traits, with a third reader adjudicating in the event of a disagreement. In addition, all sites of suspected HGSOC were manually segmented texture features were computed from each tumour site. Three texture features that represented intra-and inter-site tumour heterogeneity were used for analysis. An integrated analysis of transcriptomic and proteomic data identified proteins with conserved expression between primary tumour sites and metastasis. Correlations between protein-abundance and various CT imaging traits and texture features were assessed using the Kendall tau rank correlation-coefficient and the Mann-Whitney U test, whereas the area under the receiver-operating characteristic curve (AUC) was reported as a metric of the strength and the direction of the association. p values &lt; 0.05 were considered significant.\n<h3>Results<\/h3>\nFour proteins were associated with CT-based imaging traits, with the strongest correlation observed between the CRIP2 protein and disease in the mesentery (p&lt;0.001, AUC=0.05). The abundance of three proteins was associated with texture features that represented intra-and inter-site tumour heterogeneity, with the strongest negative correlation between the CKB protein and cluster dissimilarity (p=0.047, \ud835\udf0f =0.326).\n<h3>Conclusion<\/h3>\nThis study provides the first insights into the potential associations between standard-of-care CT imaging traits and texture measures of intra-and inter-site heterogeneity, and the abundance of several proteins.\n<br\/>","result_featured_image":false,"result_acknowledgements":"","hide_from_browse_table":[],"_links":{"self":[{"href":"https:\/\/cm.vastapps.dev\/api\/v1\/analysis-results\/5783"}],"collection":[{"href":"https:\/\/cm.vastapps.dev\/api\/v1\/analysis-results"}],"about":[{"href":"https:\/\/cm.vastapps.dev\/api\/wp\/v2\/types\/tcia_analysis_result"}],"wp:attachment":[{"href":"https:\/\/cm.vastapps.dev\/api\/wp\/v2\/media?parent=5783"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}