{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T05:06:57Z","timestamp":1768453617957,"version":"3.49.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2023,1,19]],"date-time":"2023-01-19T00:00:00Z","timestamp":1674086400000},"content-version":"vor","delay-in-days":18,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32270208"],"award-info":[{"award-number":["32270208"]}],"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":["32230089"],"award-info":[{"award-number":["32230089"]}],"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":["32070139"],"award-info":[{"award-number":["32070139"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Technical System of Chinese Herbal Medicine Industry","award":["CARS-21"],"award-info":[{"award-number":["CARS-21"]}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["KYCXJC2022003"],"award-info":[{"award-number":["KYCXJC2022003"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Fungi form a large and heterogeneous group of eukaryotic organisms with diverse ecological niches. The high importance of fungi contrasts with our limited understanding of fungal lifestyle and adaptability to environment. Over the last decade, the high-throughput sequencing technology produced tremendous RNA-sequencing (RNA-seq) data. However, there is no comprehensive database for mycologists to conveniently explore fungal gene expression and alternative splicing. Here, we have developed FungiExp, an online database including 35\u00a0821 curated RNA-seq samples derived from 220 fungal species, together with gene expression and alternative splicing profiles. It allows users to query and visualize gene expression and alternative splicing in the collected RNA-seq samples. Furthermore, FungiExp contains several online analysis tools, such as differential\/specific, co-expression network and cross-species gene expression conservation analysis. Through these tools, users can obtain new insights by re-analyzing public RNA-seq data or upload personal data to co-analyze with public RNA-seq data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The FungiExp is freely available at https:\/\/bioinfo.njau.edu.cn\/fungiExp.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad042","type":"journal-article","created":{"date-parts":[[2023,1,19]],"date-time":"2023-01-19T12:01:40Z","timestamp":1674129700000},"source":"Crossref","is-referenced-by-count":6,"title":["FungiExp: a user-friendly database and analysis platform for exploring fungal gene expression and alternative splicing"],"prefix":"10.1093","volume":"39","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":"Yapin","family":"Shi","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":"Zhuoran","family":"Guan","sequence":"additional","affiliation":[{"name":"College of Information Management, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2973-0010","authenticated-orcid":false,"given":"Danyu","family":"Shen","sequence":"additional","affiliation":[{"name":"Department of Plant Pathology, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5226-6642","authenticated-orcid":false,"given":"Daolong","family":"Dou","sequence":"additional","affiliation":[{"name":"Department of Plant Pathology, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China"}]}],"member":"286","published-online":{"date-parts":[[2023,1,19]]},"reference":[{"key":"2023013106110162600_btad042-B1","doi-asserted-by":"crossref","DOI":"10.1128\/microbiolspec.FUNK-0052-2016","article-title":"Fungal diversity revisited: 2.2 to 3.8 million species","volume":"5","author":"Hawksworth","year":"2017","journal-title":"Microbiol. Spectr"},{"key":"2023013106110162600_btad042-B2","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":"2023013106110162600_btad042-B3","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1186\/1471-2105-9-559","article-title":"WGCNA: an R package for weighted correlation network analysis","volume":"9","author":"Langfelder","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023013106110162600_btad042-B4","doi-asserted-by":"crossref","first-page":"882","DOI":"10.1093\/bioinformatics\/bts034","article-title":"The SVA package for removing batch effects and other unwanted variation in high-throughput experiments","volume":"28","author":"Leek","year":"2012","journal-title":"Bioinformatics"},{"key":"2023013106110162600_btad042-B5","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2023013106110162600_btad042-B6","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"2023013106110162600_btad042-B7","doi-asserted-by":"crossref","first-page":"E5593","DOI":"10.1073\/pnas.1419161111","article-title":"rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data","volume":"111","author":"Shen","year":"2014","journal-title":"Proc. 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