ABSTRACT
In this study, a software tool (IFGFA) for identification of featured genes from gene expression data based on latent factor analysis was developed. Despite the availability of computational methods and statistical models appropriate for analyzing special genomic data, IFGFA provides a platform for predicting colon cancer-related genes and can be applied to other cancer types. The computational framework behind IFGFA is based on the well-established Bayesian factor and regression model and prior knowledge about the gene from OMIM. We validated the predicted genes by analyzing somatic mutations in patients. An interface was developed to enable users to run the computational framework efficiently through visual programming. IFGFA is executable in a Windows system and does not require other dependent software packages. This program can be freely downloaded at http://www.fupage.org/downloads/ifgfa.zip.
Subject(s)
Factor Analysis, Statistical , Gene Expression Profiling/methods , Software , Algorithms , Bayes Theorem , Colonic Neoplasms/diagnosis , Colonic Neoplasms/genetics , Computational Biology/methods , Humans , Oligonucleotide Array Sequence Analysis/methods , Sequence Analysis, DNA/methods , TranscriptomeABSTRACT
The main aim of this study was to understand the relationship between the drug-resistant characteristics of Klebsiella pneumoniae and CTX-M-type extended spectrum ß-lactamases (ESBLs), and to detect the distributions of CTX-M-type ESBLs in clinically isolated strains. CTX-M ESBL genes isolated from the clinical samples were amplified by polymerase chain reaction and identified by sequence analysis; the antibiotic susceptibility of the samples was determined using the Kirby-Bauer disc-diffusion method. One hundred and five strains among the 246 isolated strains of K. pneumoniae tested positive for ESBL production (42.68%); 92 of these produced CTX-M ESBLs. Of the 92 CTX-M ESBL strains, 81 produced CTX-M-1 ESBLs and 11 produced CTX-M-25 ESBLs. Fifty-seven of the CTX-M-1 ESBL- and six of the CTX-M-25 ESBL-producing bacteria had CTX-M ESBL genes that coexisted in the plasmid and chromosome. The Kirby-Bauer antibiotic susceptibility method revealed that CTX-M ESBL-positive strains showed a higher rate of resistance to cefazolin, cefoxitin, cefuroxime, ceftazidime, cefotaxime, aztreonam, levofloxacin, and cotrimoxazole, compared to the CTX-M ESBL-negative strains (P < 0.05). The CTX-M ESBL genes were commonly observed in the K. pneumoniae isolated from respiratory tract samples; these were significantly associated with the drug-resistant characteristics of K. pneumoniae to ß-lactam antibiotics.
Subject(s)
Drug Resistance, Bacterial , Klebsiella pneumoniae/enzymology , Respiratory Mucosa/microbiology , beta-Lactamases/genetics , Humans , Klebsiella pneumoniae/drug effects , Klebsiella pneumoniae/genetics , Klebsiella pneumoniae/isolation & purificationABSTRACT
Male infertility is a complex multifactorial and polygenic disease, and genetic factors play an important role in its formation and development. Recently, the association between follicle stimulating hormone receptor (FSHR) gene polymorphisms and male infertility risk has attracted widespread attention due to the unique biological functions of FSH. The aim of this study was to further explore the associations between the Thr307Ala and Asn680Ser polymorphisms of the FSHR gene and male infertility. A case-control study of 212 infertile and 164 fertile men from North China was performed. FSHR polymorphism genotypes were obtained through direct DNA sequencing. A meta-analysis was also performed. In the single-site association analysis, no significant associations were identified between FSHR Thr307Ala and Asn680Ser polymorphisms and male infertility (P > 0.05). However, we found that the combined genotypic frequency of Thr/Ala + Asn/Asn was higher in infertile patients than in controls (6.6 vs 1.8%; odds ratio (OR) = 3.795; 95% confidence interval (CI): 1.072-13.434, P = 0.027). In the meta-analysis, there was also no evidence of FSHR polymorphism (rs 6165 and rs 6168) association with male infertility (P > 0.05). However, we found that the combined genotypes Thr/Thr + Asn/Asn had an increased risk of male infertility (OR = 1.238; 95%CI: 1.001-1.537, P = 0.049). Our studies further confirmed reports that there were no significant associations between the FSHR Thr307Ala and Asn680Ser polymorphisms and male infertility risk. However, a combined FSHR genotype showed significant association with male infertility.