{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T12:17:30Z","timestamp":1791202650412,"version":"4.2.0"},"reference-count":58,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2013,2,4]],"date-time":"2013-02-04T00:00:00Z","timestamp":1359936000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,2,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>New technologies for systems-level determinants of human exposure to drugs, industrial chemicals, pesticides, and other environmental agents provide an invaluable opportunity to extend the understanding of human health and potential environmental hazards. We report here the development of a new computational-systems toxicology framework, called predictive toxicogenomics-derived models (PTDMs). PTDMs integrate three networks of chemical\u2013gene interactions (CGIs), chemical\u2013disease associations (CDAs) and gene\u2013disease associations (GDAs) to infer chemical hazard profiles, identify exposure data gaps and to incorporate genes and disease networks into chemical safety evaluations. Three comprehensive networks addressing CGI, CDA and GDA extracted from the comparative toxicogenomics database (CTD) were constructed. The areas under the receiver operating characteristics curve ranged from 0.85 to 0.97 and were yielded using our methodology using a 10-fold cross validation by a simulation carried out 100 times. As the illustrated examples show, we predicted new potential target genes and diseases for bisphenol A and aspirin. The molecular hypothesis and experimental evidence from published literature for these predictions were provided. The results demonstrated that our method has potential applications for chemical profiling in human health exposure and environmental hazard assessment.<\/jats:p>\n                  <jats:p\/>","DOI":"10.1039\/c3mb25309k","type":"journal-article","created":{"date-parts":[[2013,2,4]],"date-time":"2013-02-04T11:28:16Z","timestamp":1359977296000},"page":"1316-1325","source":"Crossref","is-referenced-by-count":27,"title":["Prediction of human genes and diseases targeted by xenobiotics using predictive toxicogenomic-derived models (PTDMs)"],"prefix":"10.1093","volume":"9","author":[{"given":"Feixiong","family":"Cheng","sequence":"first","affiliation":[{"name":"Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology a , 130 Meilong Road, Shanghai 200237 China \u00a0 ytang234@ecust.edu.cn \u00a0 +86-21-6425-3651 \u00a0 +86-21-6425-1052"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weihua","family":"Li","sequence":"additional","affiliation":[{"name":"Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology a , 130 Meilong Road, Shanghai 200237 China \u00a0 ytang234@ecust.edu.cn \u00a0 +86-21-6425-3651 \u00a0 +86-21-6425-1052"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yadi","family":"Zhou","sequence":"additional","affiliation":[{"name":"Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology a , 130 Meilong Road, Shanghai 200237 China \u00a0 ytang234@ecust.edu.cn \u00a0 +86-21-6425-3651 \u00a0 +86-21-6425-1052"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Li","sequence":"additional","affiliation":[{"name":"Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology a , 130 Meilong Road, Shanghai 200237 China \u00a0 ytang234@ecust.edu.cn \u00a0 +86-21-6425-3651 \u00a0 +86-21-6425-1052"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Shen","sequence":"additional","affiliation":[{"name":"Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology a , 130 Meilong Road, Shanghai 200237 China \u00a0 ytang234@ecust.edu.cn \u00a0 +86-21-6425-3651 \u00a0 +86-21-6425-1052"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip W","family":"Lee","sequence":"additional","affiliation":[{"name":"Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology a , 130 Meilong Road, Shanghai 200237 China \u00a0 ytang234@ecust.edu.cn \u00a0 +86-21-6425-3651 \u00a0 +86-21-6425-1052"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yun","family":"Tang","sequence":"additional","affiliation":[{"name":"Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology a , 130 Meilong Road, Shanghai 200237 China \u00a0 ytang234@ecust.edu.cn \u00a0 +86-21-6425-3651 \u00a0 +86-21-6425-1052"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,2,4]]},"reference":[{"key":"2026012913100972600_cit1","doi-asserted-by":"crossref","first-page":"3046","DOI":"10.1021\/es2033857","volume":"46","author":"Mattingly","year":"2012","journal-title":"Environ. 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Cardiol."},{"key":"2026012913100972600_cit52","doi-asserted-by":"crossref","first-page":"1859","DOI":"10.1056\/NEJMoa1202299","volume":"366","author":"Homma","year":"2012","journal-title":"N. Engl. J. Med."},{"key":"2026012913100972600_cit53","doi-asserted-by":"crossref","first-page":"691","DOI":"10.1136\/jnnp.74.5.691","volume":"74","author":"Strupp","year":"2003","journal-title":"J. Neurol., Neurosurg. Psychiatry"},{"key":"2026012913100972600_cit54","doi-asserted-by":"crossref","first-page":"029","DOI":"10.1111\/j.1476-5381.1983.tb09359.x","volume":"78","author":"Johnston","year":"1983","journal-title":"Br. J. 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