title: SpermatogenesisOnline 1.0: a resource for spermatogenesis based on manual literature curation and genome-wide data mining.
abstract: Human infertility affects 10-15% of couples, half of which is attributed to the male partner. Abnormal spermatogenesis is a major cause of male infertility. Characterizing the genes involved in spermatogenesis is fundamental to understand the mechanisms underlying this biological process and in developing treatments for male infertility. Although many genes have been implicated in spermatogenesis, no dedicated bioinformatic resource for spermatogenesis is available. We have developed such a database, SpermatogenesisOnline 1.0 (http://mcg.ustc.edu.cn/sdap1/spermgenes/), using manual curation from 30 233 articles published before 1 May 2012. It provides detailed information for 1666 genes reported to participate in spermatogenesis in 37 organisms. Based on the analysis of these genes, we developed an algorithm, Greed AUC Stepwise (GAS) model, which predicted 762 genes to participate in spermatogenesis (GAS probability >0.5) based on genome-wide transcriptional data in Mus musculus testis from the ArrayExpress database. These predicted and experimentally verified genes were annotated, with several identical spermatogenesis-related GO terms being enriched for both classes. Furthermore, protein-protein interaction analysis indicates direct interactions of predicted genes with the experimentally verified ones, which supports the reliability of GAS. The strategy (manual curation and data mining) used to develop SpermatogenesisOnline 1.0 can be easily extended to other biological processes.
authors.affiliation: Hefei National Laboratory for Physical Sciences at Microscale and Department of Life Sciences, University of Science and Technology of China, Hefei 230027, China.
authors.forename: Yuanwei
authors.initials: Y
authors.lastname: Zhang
authors.forename: Liangwen
authors.initials: L
authors.lastname: Zhong
authors.forename: Bo
authors.initials: B
authors.lastname: Xu
authors.forename: Yifan
authors.initials: Y
authors.lastname: Yang
authors.forename: Rongjun
authors.initials: R
authors.lastname: Ban
authors.forename: Jun
authors.initials: J
authors.lastname: Zhu
authors.forename: Howard J
authors.initials: HJ
authors.lastname: Cooke
authors.forename: Qiaomei
authors.initials: Q
authors.lastname: Hao
authors.forename: Qinghua
authors.initials: Q
authors.lastname: Shi
mesh_terms: D000818:Animals; D002417:Cattle; D057225:Data Mining; D030541:Databases, Genetic; D023281:Genomics; D006801:Humans; D020407:Internet; D008297:Male; D051379:Mice; D058977:Molecular Sequence Annotation; D051381:Rats; D013091:Spermatogenesis / Q000235:genetics*; D059467:Transcriptome; D014584:User-Computer Interface