epiACO-A Method for Identifying Epistasis Based on Ant Colony Optimization Algorithm

来源 :第七届全国生物信息学与系统生物学学术大会 | 被引量 : 0次 | 上传用户:helloMrFat
下载到本地 , 更方便阅读
声明 : 本文档内容版权归属内容提供方 , 如果您对本文有版权争议 , 可与客服联系进行内容授权或下架
论文部分内容阅读
  With the rapidly development of DNA sequencing and bioinformatics technique,a huge amount of high-dimensional single-nucleotide polymorphism (SNP) data is produced.Although many approaches for detection of the complex associations between SNPs and common human diseases in genome-wide association studies have been proposed,some of them only confine to explore on single genetic markers.Recently,an increasing number of studies have found that one of the most important factors for emergence and development of complex diseases is the interactions between SNPs,that is to say,epistasis or epistatic interactions.As a consequence,more and more studies caught great attention on epistatic interactions.In this study,a method named epiACO based on ant colony optimization algorithm is proposed for identifying epistatic interactions.In epiACO,a fitness function Svalue which combined mutual information with Bayesian networks is introduced for detecting epistatic interactions.Svalue has effectively solved the unicity of one evaluation measure and greatly improved the detection power of epiACO.Furthermore,a self-adaption adjustment parameter is designed to improve the processing capacity of models displaying no marginal effects in epiACO.Unlike the traditional process way of the identified solutions,a memory based strategy is designed to dispose the optimal solutions of epiACO,which records the optimal solutions to compare with the solutions that identified at current iteration and get final suspected solutions.The memory based strategy effectively improves the computational efficiency,enhances the processing ability of all optimal solutions and generates a more accurate way for detecting epistasis.Furthermore,a post-processing tactics is also employed to improve the power of detecting pure epistasis.Experiments of epiACO are compared with some other representative methods which are AntMiner,IACO,AntEpiSeeker and MACOED in both simulated and real age-related macular degeneration datasets.Results show that epiACO outperforms others in detection power for a large scale SNP datasets and might provides some significant clues on heuristics for inferring epistatic interactions.
其他文献
目的 观察二氢杨梅素(dihydromyricetin,DMY)对小鼠局灶性脑缺血再灌注(ischemia/reperfusion,I/R)损伤后炎症反应的影响.方法 雄性昆明种小鼠随机分为3组,即假手术组、I/R模型组及DMY(500mg·kg-1)组.改良线栓法制备小鼠大脑中动脉阻塞/再灌注(middle cerebral artery occlusion/reperfusion,MCAO/R
Background Exposure to a moderate to high dose of ionizing radiation (IR) not only causes acute radiation syndrome but also induces long-term (LT) bone marrow (BM) injury.The latter effect of IR is pr
目的 平滑肌22α(SM22α)是平滑肌细胞(VSMC)骨架相关蛋白,参与VSMC骨架重构,与动脉粥样硬化、高血压等血管重塑性疾病与关.本研究旨在在SM22α基因内部引入LoxP序列,制备基于Cre/LoxP系统的SM22α条件性基因敲除小鼠,研究其在VSMC骨架重构中的作用机制.方法 利用CRISPR/Cas9技术编辑小鼠SM22α基因.在外显子1~2和3~4的非编码区各设计sgRNA位点并将其
目的 分析Mylpf基因在糖尿病长爪沙鼠6种组织中的表达水平,进而探究长爪沙鼠糖尿病发生的分子机制.方法 选取糖尿病长爪沙鼠和正常沙鼠各6只,使用Real-time PCR和Western blotting技术分别检测动物的骨骼肌、肝脏、脂肪、肾脏、心脏和脑组织中Mylpf的mRNA和蛋白表达水平.结果 Real-time PCR的结果表明,在骨骼肌、心脏和脑组织中,Mylpf在糖尿病组mRNA表
目的 高胆固醇血症会使机体心血管系统发生损伤,Ghrelin是一种脑肠肽,其与受体(GHSR-la)结合有保护血管内皮功能、抑制血管炎症、改善心功能等作用.本研究拟通过人工低氧对高胆固醇血症小鼠进行干预,观察心肌形态的变化和Ghrelin相关蛋白变化,探究低氧暴露对高胆固醇血症小鼠心肌损伤调控的影响.方法 30只刚离乳C57BL/6小鼠,随机分为对照组(NC,8只)和高胆固醇血症组(H,22只).
会议
目的 利用生化标记方法和微卫星方法分析封闭群KM小鼠群体遗传结构特征,探索封闭群群体遗传结构的最佳分析方法.方法 应用14个生化标记位点和30个微卫星位点,检测30只KM小鼠的遗传质量.应用软件计算封闭群群体的遗传结构参数.结果 生化标记方法检测得到的群体平均杂合度是0.2163,多态性信息含量是0.1699,等位基因数是1.3903.微卫星方法检测得到的群体平均杂合度是0.4864,多态性信息含
目的 初到高原地区的人会出现不同程度的肌肉丢失现象,肌肉丢失是由于高原低氧环境引起的.本研究探究了模拟4000m海拔高度的低氧环境中大鼠肌肉丢失的情况,比较不同低氧暴露时间肌肉丢失水平,为研究低氧诱导肌肉丢失机制提供合适的研究模型.方法 SD大鼠20只,分为常氧组(n=10)、低氧组(n=10).常氧组大鼠饲养于20.9%氧浓度的环境,低氧组大鼠饲养于12.6%氧浓度的环境(相当于海拔4000 m
目的 比较分离培养与PCR方法鉴定实验动物金黄色葡萄球菌和绿脓杆的异同.方法 采用传统分离培养的方法对35只大小鼠金黄色葡萄球菌和绿脓杆菌进行检测;提取SP和NAC平板24h培养物核酸进行PCR检测.结果 分离培养法检出4只金黄色葡萄球菌阳性,8只绿脓杆菌阳性.PCR鉴定出4只金黄色葡萄球菌阳性,15只绿脓杆菌阳性.结论 PCR方法不仅快速、准确,可防止漏检、误判.
目的 应用RNA干扰技术抑制自噬调控基因Beclin1的表达,检测Beclin1表达对裸鼹鼠皮肤成纤维细胞增殖与凋亡的影响以及P53、BAX、 Bcl2等基因表达的影响.方法 分别检测裸鼹鼠成纤维细胞经饥饿、H2O2刺激等处理后Beclin1的表达,然后采用设计的Beclin l基因的干扰RNA及阴性对照分别瞬时转染裸鼹鼠成纤维细胞.采用Real-timePCR及Westem blot法检测沉默效
目的 比较研究氯化钴(CoCl2)对裸鼹鼠及C57BL/6j小鼠肝星形细胞增殖和凋亡的影响.方法 采用活细胞计数试剂盒(CCK8)法和流式细胞术分别检测不同浓度CoCl2对裸鼹鼠和小鼠肝星形细胞增殖活力以及和凋亡水平的影响.采用蛋白印迹测定CoCl2处理后裸鼹鼠肝星形细胞低氧诱导因子1α(HIF-1 α)和凋亡相关蛋白(BCL2、BAX)的表达水平.结果 低浓度(50μmol/L)CoCl2对C5