{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T00:53:22Z","timestamp":1775264002750,"version":"3.50.1"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,12,21]],"date-time":"2021-12-21T00:00:00Z","timestamp":1640044800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81703945"],"award-info":[{"award-number":["81703945"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31800678"],"award-info":[{"award-number":["31800678"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Science and Technology Innovation Project of Colleges and Universities in Shanxi Province","award":["2019\u00a0L0360"],"award-info":[{"award-number":["2019\u00a0L0360"]}]},{"name":"Science and Technology Innovation Project of Colleges and Universities in Shanxi Province","award":["2019\u00a0L0365"],"award-info":[{"award-number":["2019\u00a0L0365"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>One of the most difficult problems that hinder the development and application of herbal medicine is how to illuminate the global effects of herbs on the human body. Currently, the chemo-centric network pharmacology methodology regards herbs as a mixture of chemical ingredients and constructs the \u2018herb-compound-target-disease\u2019 connections based on bioinformatics methods, to explore the pharmacological effects of herbal medicine. However, this approach is severely affected by the complexity of the herbal composition. Alternatively, gene-expression profiles induced by herbal treatment reflect the overall biological effects of herbs and are suitable for studying the global effects of herbal medicine. Here, we develop an online transcriptome-based multi-scale network pharmacology platform (TMNP) for exploring the global effects of herbal medicine. Firstly, we build specific functional gene signatures for different biological scales from molecular to higher tissue levels. Then, specific algorithms are designed to measure the correlations of transcriptional profiles and types of gene signatures. Finally, TMNP uses pharmacotranscriptomics of herbal medicine as input and builds associations between herbs and different biological scales to explore the multi-scale effects of herb medicine. We applied TMNP to a single herb Astragalus membranaceus and Xuesaitong injection to demonstrate the power to reveal the multi-scale effects of herbal medicine. TMNP integrating herbal medicine and multiple biological scales into the same framework, will greatly extend the conventional network pharmacology model centering on the chemical components, and provide a window for systematically observing the complex interactions between herbal medicine and the human body. TMNP is available at http:\/\/www.bcxnfz.top\/TMNP.<\/jats:p>","DOI":"10.1093\/bib\/bbab542","type":"journal-article","created":{"date-parts":[[2021,11,25]],"date-time":"2021-11-25T12:12:04Z","timestamp":1637842324000},"source":"Crossref","is-referenced-by-count":21,"title":["TMNP: a transcriptome-based multi-scale network pharmacology platform for herbal medicine"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8858-8106","authenticated-orcid":false,"given":"Peng","family":"Li","sequence":"first","affiliation":[{"name":"College of Basic Sciences, Shanxi Agricultural University, Taigu 030801, China"}]},{"given":"Haoran","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Basic Sciences, Shanxi Agricultural University, Taigu 030801, China"}]},{"given":"Wuxia","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Basic Sciences, Shanxi Agricultural University, Taigu 030801, China"}]},{"given":"Yuanyuan","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Basic Sciences, Shanxi Agricultural University, Taigu 030801, China"}]},{"given":"Lingmin","family":"Zhan","sequence":"additional","affiliation":[{"name":"College of Basic Sciences, Shanxi Agricultural University, Taigu 030801, China"}]},{"given":"Ning","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Computer and Information Technology and Beijing Key Lab of Traffic Data Analysis and Mining, Beijing Jiaotong University, Beijing 100044, China"}]},{"given":"Caiping","family":"Chen","sequence":"additional","affiliation":[{"name":"College of Basic Sciences, Shanxi Agricultural University, Taigu 030801, China"}]},{"given":"Bangze","family":"Fu","sequence":"additional","affiliation":[{"name":"School of Biomedicine, Beijing City University, Beijing 100094, China"}]},{"given":"Jinzhong","family":"Zhao","sequence":"additional","affiliation":[{"name":"College of Basic Sciences, Shanxi Agricultural University, Taigu 030801, China"}]},{"given":"Xuezhong","family":"Zhou","sequence":"additional","affiliation":[{"name":"School of Computer and Information Technology and Beijing Key Lab of Traffic Data Analysis and Mining, Beijing Jiaotong University, Beijing 100044, China"}]},{"given":"Shuzhen","family":"Guo","sequence":"additional","affiliation":[{"name":"School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China"}]},{"given":"Jianxin","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China"}]}],"member":"286","published-online":{"date-parts":[[2021,12,21]]},"reference":[{"key":"2022012000331273400_ref1","doi-asserted-by":"crossref","first-page":"984","DOI":"10.1093\/bib\/bbt063","article-title":"Modern bioinformatics meets traditional Chinese 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