| Fertility refers to the ability of animals to maintain normal reproductive function and fertility under normal fertility conditions.The genetic basis of individual differences in fertility is important for the reproductive development of mammals,especially humans and livestock.The transition from estrus to lactation has important effects on animal health,lactation capacity and reproductive performance,which directly affects the economic benefits of animal husbandry.Therefore,exploring genes related to fertility and elucidating their molecular mechanisms provide guidance for the diagnosis and treatment of infertility and sub-fertility in domestic animals,and also provide an important reference for the research on how to improve the fertility of related domestic animals.However,there is currently a lack of a platform that integrates genetic information and environmental factors for the relevant personnel to use.Therefore,Fif Base(http://www.nwsuaflmz.com/Fifbase)was constructed in this study to provide more systematic information on fertility to relevant researchers.In this study,RNA-seq data and text data related to fertility of 10 species including pig,cow and chicken were integrated and analyzed,and genes related to fertility were carefully and comprehensively mined.On this basis,Fif Base,a comprehensive database platform for gene annotation and analysis of domestic animal fertility was established.This platform contains fertility information of 10 species,including the chromosome location,alias,gene description,genome version,text information,and environmental factors,Gene structure,GO term,Pathway information,expression information,PPI(protein-protein interaction)network,genome visualization and other information,providing users with a comprehensive resource library for easy retrieval.1.Analysis of fecundity related genes of poultry and livestock based on text miningIn this process,Pub Med database was used as the data source,and 75 fertility indicators and 47 environmental factors or their lexicological variant keywords were combined with 15 species names to form the subject words.Text mining technology was used to obtain known literatures related to fertility and extract genes related to fertility.Finally,more than 100,000 literature related to fertility were obtained,among which 28,127 genes were involved.After filtering by manual retrieval,455 articles were screened,covering 10 species and involving 470 fertility genes.GO enrichment analysis of these genes showed that they were all significantly correlated with the pathways of pregnancy,gestation and reproduction.2.Integrated analysis of RNA-seq sequencing data of poultry and livestock fertilityBased on GEO,SRA,this research collected RNA-seq data related to fertility of poultry and livestock systematically,and 14 sets of RNA-seq data sets related to fertility of pig,cow,chicken and duck were obtained.Differential expression analysis was performed on this data set,and finally 1089 differentially expressed genes related to fertility were identified.3.Build a database platformBase on the above work,text mining data and RNA-seq data were further processed and annotated.Based on this,this study constructed a database related to the genetic information of livestock and poultry propagation based on LAMP architecture.The database covers the filtered omics data of 10 species of poultry and livestock and specific genetic data related to fertility.In order to further improve the user's needs for the use of the poultry and livestock genetic database,The database provides a user-friendly interface for users to browse,retrieve and download fertility-related genetic information in order to further improve user needs for using the fertility-related genetic database for poultry and livestock.In addition,in order to help users search whether the genes they are interested in are related to fertility,BLAST sequence alignment analysis tool was also embedded in this study to provide users with online sequence alignment service.BLAST sequence alignment analysis tool is also embedded in this study to provide users with online sequence alignment service.The genome browser provided in the database can help users view the details of the gene and provide users with a graphical display service.This study combined text mining and RNA-seq data mining to obtain fertility-related information,and constructed a biological information database focusing on fertility-related genes of poultry and livestock.On the one hand,it provide data support for breeding research.On the other hand,it provides a reference for researchers to explore the function of these genes and their potential applications in animal husbandry. |
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