{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T14:33:59Z","timestamp":1761489239179},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The rapid accumulation of microRNAs (miRNAs) and experimental evidence for miRNA interactions has ushered in a new area of miRNA research that focuses on network more than individual miRNA interaction, which provides a systematic view of the whole microRNome. So it is a challenge to infer miRNA functional interactions on a system-wide level and further draw a miRNA functional network (miRFN). A few studies have focused on the well-studied human species; however, these methods can neither be extended to other non-model organisms nor take fully into account the information embedded in miRNA\u2013target and target\u2013target interactions. Thus, it is important to develop appropriate methods for inferring the miRNA network of non-model species, such as soybean (Glycine max), without such extensive miRNA-phenotype associated data as miRNA-disease associations in human.<\/jats:p>\n               <jats:p>Results: Here we propose a new method to measure the functional similarity of miRNAs considering both the site accessibility and the interactive context of target genes in functional gene networks. We further construct the miRFNs of soybean, which is the first study on soybean miRNAs on the network level and the core methods can be easily extended to other species. We found that miRFNs of soybean exhibit a scale-free, small world and modular architecture, with their degrees fit best to power-law and exponential distribution. We also showed that miRNA with high degree tends to interact with those of low degree, which reveals the disassortativity and modularity of miRFNs. Our efforts in this study will be useful to further reveal the soybean miRNA\u2013miRNA and miRNA\u2013gene interactive mechanism on a systematic level.<\/jats:p>\n               <jats:p>Availability and implementation: A web tool for information retrieval and analysis of soybean miRFNs and the relevant target functional gene networks can be accessed at SoymiRNet: http:\/\/nclab.hit.edu.cn\/SoymiRNet.<\/jats:p>\n               <jats:p>Contact: \u00a0maozuguo@hit.edu.cn<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt605","type":"journal-article","created":{"date-parts":[[2013,10,23]],"date-time":"2013-10-23T01:14:23Z","timestamp":1382490863000},"page":"94-103","source":"Crossref","is-referenced-by-count":36,"title":["Inferring the soybean (<i>Glycine max<\/i>) microRNA functional network based on target gene network"],"prefix":"10.1093","volume":"30","author":[{"given":"Yungang","family":"Xu","sequence":"first","affiliation":[{"name":"1 School of Computer Science and Technology, and 2School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, P.R. China"},{"name":"1 School of Computer Science and Technology, and 2School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maozu","family":"Guo","sequence":"additional","affiliation":[{"name":"1 School of Computer Science and Technology, and 2School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoyan","family":"Liu","sequence":"additional","affiliation":[{"name":"1 School of Computer Science and Technology, and 2School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chunyu","family":"Wang","sequence":"additional","affiliation":[{"name":"1 School of Computer Science and Technology, and 2School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yang","family":"Liu","sequence":"additional","affiliation":[{"name":"1 School of Computer Science and Technology, and 2School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,10,22]]},"reference":[{"key":"2023012710380904300_btt605-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/jb\/mvi094","article-title":"Scale-freeness and biological networks","volume":"138","author":"Arita","year":"2005","journal-title":"J. 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