ReCGiP, a database of reproduction candidate genes in pigs based on bibliomics.
BACKGROUND
Reproduction in pigs is one of the most economically important traits. To improve the reproductive performances, numerous studies have focused on the identification of candidate genes. However, it is hard for one to read all literatures thoroughly to get information. So we have developed a database providing candidate genes for reproductive researches in pig by mining and processing existing biological literatures in human and pigs, named as ReCGiP.


METHODS
Based on text-mining and comparative genomics, ReCGiP presents diverse information of reproduction-relevant genes in human and pig. The genes were sorted by the degree of relevance with the reproduction topics and were visualized in a gene's co-occurrence network where two genes were connected if they were co-cited in a PubMed abstract. The 'hub' genes which had more 'neighbors' were thought to be have more important functions and could be identified by the user in their web browser. In addition, ReCGiP provided integrated GO annotation, OMIM and biological pathway information collected from the Internet. Both pig and human gene information can be found in the database, which is now available.


CONCLUSIONS
ReCGiP is a unique database providing information on reproduction related genes for pig. It can be used in the area of the molecular genetics, the genetic linkage map, and the breeding of the pig and other livestock. Moreover, it can be used as a reference for human reproduction research.
Yang
Lun
L
School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
Zhang
Xiangzhe
X
Chen
Jian
J
Wang
Qishan
Q
Wang
Lishan
L
Jiang
Yue
Y
Pan
Yuchun
Y
D000818:Animals; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D053263:Gene Regulatory Networks; D005796:Genes; D056726:Genetic Association Studies / Q000379:methods; D023281:Genomics / Q000379:methods; D012098:Reproduction / Q000235:genetics*; D015398:Signal Transduction / Q000235:genetics; D013552:Swine / Q000235:genetics*