{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T08:24:49Z","timestamp":1760171089851,"version":"3.37.3"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2018,7,19]],"date-time":"2018-07-19T00:00:00Z","timestamp":1531958400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Strategic Priority Research Program of the Chinese Academy of Sciences","award":["XDA08020302"],"award-info":[{"award-number":["XDA08020302"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The complex cellular networks underlying phenotypes are formed by the interacting gene modules. Building and analyzing genome-wide and high-quality Gene Co-expression Networks (GCNs) is useful for uncovering these modules and understanding the phenotypes of an organism.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Using large-scale RNA-seq samples, we constructed high coverage and confident GCNs in two monocot species rice and maize, and two eudicot species Arabidopsis and soybean, and subdivided them into co-expressed gene modules. Taking rice as an example, we discovered many interesting and valuable modules, for instance, pollen-specific modules and starch biosynthesis module. We explored the regulatory mechanism of modules and revealed synergistic effects of gene expression regulation. In addition, we discovered that the modules conserved among plants participated in basic biological processes, whereas the species-specific modules were involved in spatiotemporal-specific processes linking genotypes to phenotypes. Our study suggests gene regulatory relationships and modules relating to cellular activities and agronomic traits in several model and crop plants, and thus providing a valuable data source for plant genetics research and breeding.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The analyzed gene expression data, reconstructed GCNs, modules and detailed annotations can be freely downloaded from ftp:\/\/47.94.193.106\/pub.<\/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\/bty642","type":"journal-article","created":{"date-parts":[[2018,7,19]],"date-time":"2018-07-19T10:11:53Z","timestamp":1531995113000},"page":"361-364","source":"Crossref","is-referenced-by-count":7,"title":["Systematic discovery of novel and valuable plant gene modules by large-scale RNA-seq samples"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6691-1139","authenticated-orcid":false,"given":"Hua","family":"Yu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Plant Genomics, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, China"},{"name":"University of Chinese Academy of Sciences, Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lu","family":"Lu","sequence":"additional","affiliation":[{"name":"School of Computer and Information Engineering, NanTong Institute of Technology, Nantong, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bingke","family":"Jiao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Genomics, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, China"},{"name":"University of Chinese Academy of Sciences, Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chengzhi","family":"Liang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Genomics, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, China"},{"name":"University of Chinese Academy of Sciences, Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,7,19]]},"reference":[{"key":"2023013107242249600_bty642-B1","doi-asserted-by":"crossref","first-page":"R106.","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome Biol"},{"key":"2023013107242249600_bty642-B2","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1093\/nar\/27.1.297","article-title":"Plant cis-acting regulatory DNA elements (PLACE) database: 1999","volume":"27","author":"Higo","year":"1999","journal-title":"Nucleic Acids Res"},{"key":"2023013107242249600_bty642-B3","first-page":"42, D1182\u2013D1187","article-title":"PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors","author":"Jin","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023013107242249600_bty642-B4","first-page":"004","article-title":"Correlation between components and molecule structure of rice starch and eating quality","volume":"1","author":"Jin","year":"2011","journal-title":"Jiangsu J. 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