The identification of functional gene modules that are derived from integration of information from different types of networks is a powerful strategy for interpreting the etiology of complex diseases such as rheumato...The identification of functional gene modules that are derived from integration of information from different types of networks is a powerful strategy for interpreting the etiology of complex diseases such as rheumatoid arthritis （RA）. Genetic variants are known to increase the risk of developing RA. Here, a novel method, the construction of a genetic network, was used to mine functional gene modules linked with RA. A polymorphism interaction analy- sis （PIA） algorithm was used to obtain cooperating single nucleotide polymorphisms （SNPs） that contribute to RA disease. The acquired SNP pairs were used to construct a SNP-SNP network. Sub-networks defined by hub SNPs were then extracted and turned into gene modules by mapping SNPs to genes using dbSNP database. We per- formed Gene Ontology （GO） analysis on each gene module, and some GO terms enriched in the gene modules can be used to investigate clustered gene function for better understanding RA pathogenesis. This method was applied to the Genetic Analysis Workshop 15 （GAW 15） RA dataset. The results show that genes involved in func- tional gene modules, such as CD160 （rs744877） and RUNX1 （rs2051179）, are especially relevant to RA, which is supported by previous reports. Furthermore, the 43 SNPs involved in the identified gene modules were found to be the best classifiers when used as variables for sample classification.展开更多
Riboflavin/UV-mediated corneal collagen cross-linking can increase the mechanical strength of the cornea and prevent or delay corneal expansion and keratoconus progression.We performed quantitative analysis of protein...Riboflavin/UV-mediated corneal collagen cross-linking can increase the mechanical strength of the cornea and prevent or delay corneal expansion and keratoconus progression.We performed quantitative analysis of protein iTRAQ in rabbit eye white matter after cross-linking to explore the changes of protein expression in cornea at different times after cross-linking and to understand the process of corneal stroma remodeling after cross-linking.The screening conditions are fold Change1.2 and P-value<0.05,we identified 713 and 38 differentially expressed proteins in cornea at 1 week and 1 month after cross-linking.There were 16 differentially expressed proteins at two time points after corneal cross-linking.By annotating the functions of these proteins,we identified some proteins that affect the mechanical properties of the cornea,and these proteins are involved in cell growth,oxidative stress response,and signal transduction in the cornea.It has a guiding role in studying the corneal stroma remodeling process after collagen crosslinking.展开更多
基金supported in part by the National Natural Science Foundation of China (Grant No. 30871394, 30370798 and 30571034)the Science Technology Development Projects of Beijing Municipal Education Commission (KM200910025006 and KM201210025008)
文摘The identification of functional gene modules that are derived from integration of information from different types of networks is a powerful strategy for interpreting the etiology of complex diseases such as rheumatoid arthritis （RA）. Genetic variants are known to increase the risk of developing RA. Here, a novel method, the construction of a genetic network, was used to mine functional gene modules linked with RA. A polymorphism interaction analy- sis （PIA） algorithm was used to obtain cooperating single nucleotide polymorphisms （SNPs） that contribute to RA disease. The acquired SNP pairs were used to construct a SNP-SNP network. Sub-networks defined by hub SNPs were then extracted and turned into gene modules by mapping SNPs to genes using dbSNP database. We per- formed Gene Ontology （GO） analysis on each gene module, and some GO terms enriched in the gene modules can be used to investigate clustered gene function for better understanding RA pathogenesis. This method was applied to the Genetic Analysis Workshop 15 （GAW 15） RA dataset. The results show that genes involved in func- tional gene modules, such as CD160 （rs744877） and RUNX1 （rs2051179）, are especially relevant to RA, which is supported by previous reports. Furthermore, the 43 SNPs involved in the identified gene modules were found to be the best classifiers when used as variables for sample classification.
基金This work was financially supported by the National Natural Science Foundation of China(NSFC)(grant number 31370952,31,470,914).
文摘Riboflavin/UV-mediated corneal collagen cross-linking can increase the mechanical strength of the cornea and prevent or delay corneal expansion and keratoconus progression.We performed quantitative analysis of protein iTRAQ in rabbit eye white matter after cross-linking to explore the changes of protein expression in cornea at different times after cross-linking and to understand the process of corneal stroma remodeling after cross-linking.The screening conditions are fold Change1.2 and P-value<0.05,we identified 713 and 38 differentially expressed proteins in cornea at 1 week and 1 month after cross-linking.There were 16 differentially expressed proteins at two time points after corneal cross-linking.By annotating the functions of these proteins,we identified some proteins that affect the mechanical properties of the cornea,and these proteins are involved in cell growth,oxidative stress response,and signal transduction in the cornea.It has a guiding role in studying the corneal stroma remodeling process after collagen crosslinking.
