{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,26]],"date-time":"2025-09-26T00:19:43Z","timestamp":1758845983607,"version":"3.44.0"},"reference-count":21,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2025,5,2]],"date-time":"2025-05-02T00:00:00Z","timestamp":1746144000000},"content-version":"vor","delay-in-days":121,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004835","name":"Zhejiang University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004835","id-type":"DOI","asserted-by":"publisher"}]},{"name":"SRTP Program of Zhejiang University","award":["Y202304085"],"award-info":[{"award-number":["Y202304085"]}]},{"DOI":"10.13039\/501100004835","name":"Zhejiang University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004835","id-type":"DOI","asserted-by":"publisher"}]},{"name":"SRTP Program of Zhejiang University","award":["Y202304085"],"award-info":[{"award-number":["Y202304085"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,5,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Neurological disorders pose significant global health challenges due to their complex etiology and insufficient understanding of underlying mechanisms. Signal transduction pathways are critical in the pathophysiology of these diseases and have been extensively studied to develop therapeutic interventions. However, existing databases for biological signal pathways often overlook the dynamic interactions between entities within these pathways and lack standardized representations of the signaling processes. To address these limitations, we present STCDB4ND, a specialized database focused on signal transduction pathways associated with neurological diseases. Utilizing the ST classification system, STCDB4ND provides a unified framework for pathway representation, emphasizing interactions and pathway characteristics. The database features advanced visualization tools, network analysis capabilities, and a key factor identification module, enabling researchers to comprehensively study these complex networks. Our analysis of neurological disease-related pathways using STCDB4ND revealed key signaling factors and supported existing findings on pathogenic mechanisms STCDB4ND serves as a valuable resource for advancing the understanding of neurological disease pathways and promoting novel therapeutic approaches. And we believe that STCDB will provide greater convenience for researchers in various fields as we expand the STCDB system\u2019s database in the future.<\/jats:p>\n               <jats:p>Database URL: https:\/\/bis.zju.edu.cn\/STCDB<\/jats:p>","DOI":"10.1093\/database\/baaf032","type":"journal-article","created":{"date-parts":[[2025,5,2]],"date-time":"2025-05-02T12:37:11Z","timestamp":1746189431000},"source":"Crossref","is-referenced-by-count":0,"title":["STCDB4ND: a signal transduction classification database for neurological diseases"],"prefix":"10.1093","volume":"2025","author":[{"given":"Boyan","family":"Gong","sequence":"first","affiliation":[{"name":"Department of Bioinformatics, Institute of Biophysics, College of Life Sciences; Institute of Hematology, Zhejiang University School of Medicine, The First Affiliated Hospital, Zhejiang University , Hangzhou 310058,","place":["China"]}]},{"given":"Sida","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Institute of Biophysics, College of Life Sciences; Institute of Hematology, Zhejiang University School of Medicine, The First Affiliated Hospital, Zhejiang University , Hangzhou 310058,","place":["China"]}]},{"given":"Yifan","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Institute of Biophysics, College of Life Sciences; Institute of Hematology, Zhejiang University School of Medicine, The First Affiliated Hospital, Zhejiang University , Hangzhou 310058,","place":["China"]}]},{"given":"Liya","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Institute of Biophysics, College of Life Sciences; Institute of Hematology, Zhejiang University School of Medicine, The First Affiliated Hospital, Zhejiang University , Hangzhou 310058,","place":["China"]}]},{"given":"Ralf","family":"Hofest\u00e4dt","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics\/Medical Informatics, Faculty of Technology, Bielefeld University , Bielefeld 33501,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9677-1699","authenticated-orcid":false,"given":"Ming","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Institute of Biophysics, College of Life Sciences; Institute of Hematology, Zhejiang University School of Medicine, The First Affiliated Hospital, Zhejiang University , Hangzhou 310058,","place":["China"]},{"name":"Zhejiang Key Laboratory of Multi-omics Precision Diagnosis and Treatment of Liver Diseases, Zhejiang University , Hangzhou 310058,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2025,5,2]]},"reference":[{"key":"2025092510531218100_R1","doi-asserted-by":"publisher","first-page":"2411","DOI":"10.1021\/acs.jafc.3c07536","article-title":"Therapeutic potential of natural compounds from herbs and nutraceuticals in alleviating neurological disorders: targeting the wnt signaling pathway","volume":"72","author":"Li","year":"2024","journal-title":"J Agr Food Chem"},{"key":"2025092510531218100_R2","doi-asserted-by":"crossref","DOI":"10.1093\/database\/bau126","article-title":"Comparison of human cell signaling pathway databases\u2014evolution, drawbacks and challenges","volume":"2015","author":"Chowdhury","year":"2015","journal-title":"Database"},{"year":"2023","author":"Elsevier. EmBiology Biological data structured for insights Elsevier [DB\/OL]","key":"2025092510531218100_R3"},{"year":"2023","author":"QIAGEN. Ingenuity Pathway Analysis QIAGEN Digital Insights [DB\/OL]","key":"2025092510531218100_R4"},{"key":"2025092510531218100_R5","doi-asserted-by":"crossref","first-page":"D545","DOI":"10.1093\/nar\/gkaa970","article-title":"KEGG: integrating viruses and cellular organisms","volume":"49","author":"Kanehisa","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2025092510531218100_R6","doi-asserted-by":"publisher","first-page":"D613","DOI":"10.1093\/nar\/gkaa1024","article-title":"WikiPathways: connecting communities","volume":"49","author":"Martens","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2025092510531218100_R7","doi-asserted-by":"publisher","first-page":"D638","DOI":"10.1093\/nar\/gkac1000","article-title":"The STRING database in 2023: protein\u2013protein association networks and functional enrichment analyses for any sequenced genome of interest","volume":"51","author":"Szklarczyk","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025092510531218100_R8","article-title":"A new version of the ANDSystem tool for automatic extraction of knowledge from scientific publications with expanded functionality for reconstruction of associative gene networks by considering tissue-specific gene expression","volume":"20","author":"A","year":"2019","journal-title":"BMC Bioinf"},{"key":"2025092510531218100_R9","doi-asserted-by":"publisher","first-page":"D456","DOI":"10.1093\/nar\/gkh079","article-title":"STCDB: signal transduction classification database","volume":"32","author":"Chen","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2025092510531218100_R10","doi-asserted-by":"publisher","first-page":"2214","DOI":"10.1111\/febs.16274","article-title":"Enzyme nomenclature and classification: the state of the art","volume":"290","author":"McDonald","year":"2023","journal-title":"Febs J"},{"key":"2025092510531218100_R11","doi-asserted-by":"publisher","first-page":"D687","DOI":"10.1093\/nar\/gkab1028","article-title":"The reactome pathway knowledgebase 2022","volume":"50","author":"Gillespie","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025092510531218100_R12","doi-asserted-by":"publisher","first-page":"D523","DOI":"10.1093\/nar\/gkac1052","article-title":"UniProt: the universal protein knowledgebase in 2023","volume":"51","author":"Bateman","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025092510531218100_R13","doi-asserted-by":"publisher","first-page":"D930","DOI":"10.1093\/nar\/gky1075","article-title":"ChEMBL: towards direct deposition of bioassay data","volume":"47","author":"Mendez","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2025092510531218100_R14","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","article-title":"Identification of common molecular subsequences","volume":"147","author":"Smith","year":"1981","journal-title":"J Mol Biol"},{"volume-title":"Research on Key Node Identification Technology of Directed Weighted Complex Network Based on Link Relationship [Master]","year":"2012","author":"Hu","key":"2025092510531218100_R15"},{"key":"2025092510531218100_R16","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1016\/S0169-7552(98)00110-X","article-title":"The anatomy of a large-scale hypertextual web search engine","volume":"30","author":"Brin","year":"1998","journal-title":"Computer Networks and ISDN Systems"},{"key":"2025092510531218100_R17","doi-asserted-by":"crossref","DOI":"10.4137\/GRSB.S13204","article-title":"Pathway analysis of ChIP-Seq-based NRF1 target genes suggests a logical hypothesis of their involvement in the pathogenesis of neurodegenerative diseases","volume":"7","author":"Satoh","year":"2013","journal-title":"Gene Regulation and Systems Biology"},{"key":"2025092510531218100_R18","doi-asserted-by":"publisher","first-page":"D1236","DOI":"10.1093\/nar\/gkad961","article-title":"DiSignAtlas: an atlas of human and mouse disease signatures based on bulk and single-cell transcriptomics[J]","volume":"52","author":"Zhai","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2025092510531218100_R19","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbad237","article-title":"Network integration and protein structural binding analysis of neurodegeneration-related interactome","volume":"24","author":"Chen","year":"2023","journal-title":"Brief Bioinform"},{"key":"2025092510531218100_R20","doi-asserted-by":"publisher","DOI":"10.3389\/fcell.2022.1090765","article-title":"Targeting N-type calcium channels in young-onset of some neurological diseases","volume":"10","author":"Antunes","year":"2022","journal-title":"Front Cell Dev Biol"},{"key":"2025092510531218100_R21","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.abo6889","article-title":"A microtubule stabilizer ameliorates protein pathogenesis and neurodegeneration in mouse models of repetitive traumatic brain injury","volume":"15","author":"Zhao","year":"2023","journal-title":"Sci Transl Med"}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baaf032\/63045365\/baaf032.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baaf032\/63045365\/baaf032.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,25]],"date-time":"2025-09-25T14:53:18Z","timestamp":1758811998000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baaf032\/8124069"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025]]},"references-count":21,"URL":"https:\/\/doi.org\/10.1093\/database\/baaf032","relation":{},"ISSN":["1758-0463"],"issn-type":[{"type":"electronic","value":"1758-0463"}],"subject":[],"published-other":{"date-parts":[[2025]]},"published":{"date-parts":[[2025]]},"article-number":"baaf032"}}