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Database Commons - SpermatogenesisOnline

SpermatogenesisOnline

Citations: 7

z-index 0.00

Short name SpermatogenesisOnline
Full name Annotation of Genes/Proteins Involved in Spermatogenesis
Description Spermatogenesis is a sophisticated biological process responsible for development of spermatozoa from spermatogonial stem cells, provides detailed information for 1666 genes reported to participate in spermatogenesis in 37 organisms
URL http://mcg.ustc.edu.cn/sdap1/spermgenes/
Year founded 2012
Last update & version NA    v1.0
Availability Free to all users
University/Institution hosted University of Science and Technology of China
Address Hefei National Laboratory for Physical Sciences at Microscale and Department of Life Sciences,University of Science and Technology of China,Hefei 230027,China
City Hefei
Province/State Anhui
Country/Region China
Contact name Qinghua Shi
Contact email qshi@ustc.edu.cn
Data type(s)
Major organism(s)
Keyword(s)
  • stem cell
Publication(s)
  • SpermatogenesisOnline 1.0: a resource for spermatogenesis based on manual literature curation and genome-wide data mining. [PMID: 23193286]

    Yuanwei Zhang, Liangwen Zhong, Bo Xu, Yifan Yang, Rongjun Ban, Jun Zhu, Howard J Cooke, Qiaomei Hao, Qinghua Shi
    Nucleic acids research 2013:41(Database issue)
    7 Citations (Google Scholar as of 2016-02-29)

    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.

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Tags

Standard, Ontology and Nomenclature
Bos taurus Caenorhabditis elegans Drosophila melanogaster Homo sapiens Mesocricetus auratus Mus musculus Rattus norvegicus Xenopus laevis
stem cell

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Lin Xia [2015-11-20]
    • Lin Xia [2015-06-26]
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