{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T09:29:05Z","timestamp":1740130145686,"version":"3.37.3"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,10,22]],"date-time":"2022-10-22T00:00:00Z","timestamp":1666396800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32230089","32270208","32070139"],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Technical System of Chinese Herbal Medicine Industry","award":["CARS-21"]},{"DOI":"10.13039\/100007540","name":"Jiangsu Agricultural Science and Technology Innovation Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007540","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Innovative Experimental Program for College Students","award":["202110307064"]},{"DOI":"10.13039\/100007709","name":"Michigan State University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007709","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100011138","name":"MSU AgBioResearch","doi-asserted-by":"publisher","award":["MICL02560"],"id":[{"id":"10.13039\/100011138","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"Abstract<\/jats:title>\n Over the last decade, RNA-seq has produced a massive amount of plant transcriptomic sequencing data deposited in public databases. Reanalysis of these public datasets can generate additional novel hypotheses not included in original studies. However, the large data volume and the requirement for specialized computational resources and expertise present a barrier for experimental biologists to explore public repositories. Here, we introduce PlantExp (https:\/\/biotec.njau.edu.cn\/plantExp), a database platform for exploration of plant gene expression and alternative splicing profiles based on 131\u00a0423 uniformly processed publicly available RNA-seq samples from 85 species in 24 plant orders. In addition to two common retrieval accesses to gene expression and alternative splicing profiles by functional terms and sequence similarity, PlantExp is equipped with four online analysis tools, including differential expression analysis, specific expression analysis, co-expression network analysis and cross-species expression conservation analysis. With these online analysis tools, users can flexibly customize sample groups to reanalyze public RNA-seq datasets and obtain new insights. Furthermore, it offers a wide range of visualization tools to help users intuitively understand analysis results. In conclusion, PlantExp provides a valuable data resource and analysis platform for plant biologists to utilize public RNA-seq. datasets.<\/jats:p>","DOI":"10.1093\/nar\/gkac917","type":"journal-article","created":{"date-parts":[[2022,10,22]],"date-time":"2022-10-22T09:57:53Z","timestamp":1666432673000},"page":"D1483-D1491","source":"Crossref","is-referenced-by-count":16,"title":["PlantExp: a platform for exploration of gene expression and alternative splicing based on public plant RNA-seq samples"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5638-8612","authenticated-orcid":false,"given":"Jinding","family":"Liu","sequence":"first","affiliation":[{"name":"Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China"},{"name":"Department of Animal Science, Michigan State University , East Lansing, MI 48824, USA"}]},{"given":"Yaru","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Information Management, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China"}]},{"given":"Yiqing","family":"Zheng","sequence":"additional","affiliation":[{"name":"College of Information Management, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China"}]},{"given":"Yali","family":"Zhu","sequence":"additional","affiliation":[{"name":"College of Information Management, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China"}]},{"given":"Yapin","family":"Shi","sequence":"additional","affiliation":[{"name":"College of Information Management, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China"}]},{"given":"Zhuoran","family":"Guan","sequence":"additional","affiliation":[{"name":"College of Information Management, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China"}]},{"given":"Kun","family":"Lang","sequence":"additional","affiliation":[{"name":"College of Information Management, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China"}]},{"given":"Danyu","family":"Shen","sequence":"additional","affiliation":[{"name":"Department of Plant Pathology, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6788-8364","authenticated-orcid":false,"given":"Wen","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Animal Science, Michigan State University , East Lansing, MI 48824, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5226-6642","authenticated-orcid":false,"given":"Daolong","family":"Dou","sequence":"additional","affiliation":[{"name":"Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China"},{"name":"Department of Plant Pathology, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China"}]}],"member":"286","published-online":{"date-parts":[[2022,10,22]]},"reference":[{"key":"2023010804324213000_B1","doi-asserted-by":"crossref","first-page":"D387","DOI":"10.1093\/nar\/gkab1053","article-title":"The sequence read archive: a decade more of explosive growth","volume":"50","author":"Katz","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2023010804324213000_B2","doi-asserted-by":"crossref","first-page":"D106","DOI":"10.1093\/nar\/gkab1051","article-title":"The european nucleotide archive in 2021","volume":"50","author":"Cummins","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2023010804324213000_B3","doi-asserted-by":"crossref","first-page":"D102","DOI":"10.1093\/nar\/gkab995","article-title":"DNA data bank of japan (DDBJ) update report 2021","volume":"50","author":"Okido","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2023010804324213000_B4","doi-asserted-by":"crossref","first-page":"D18","DOI":"10.1093\/nar\/gkaa1022","article-title":"Database resources of the national genomics data center, china national center for bioinformation in 2021","volume":"49","author":"Members","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2023010804324213000_B5","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1038\/nbt.3838","article-title":"Reproducible RNA-seq analysis using recount2","volume":"35","author":"Collado-Torres","year":"2017","journal-title":"Nat. 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