基于基因功能表达谱的疾病分类:抗基因缺失的稳健性

利用基因表达谱数据,按Gene Ontology基因功能分类体系,将基因模块化地组织到具有显著生物学意义的低维差异表达功能模块单元中,构造新的指标用于分类疾病样本,从而提出了基于功能表达谱的分析新途径。新算法可稳健地抗基因检测缺失,抗基因表达变异,抗检测误差,并可以显著地降低分类特征维数(参与疾病分类的基因数目)。采用淋巴瘤数据集,比较了基于功能表达谱和常规的基因表达谱的决策树分类器。结果显示,基于功能表达谱可以得到高准确度的疾病样本分类结果,能够直接从功能水平上给出相应的生物学解释。通过仿真分析,进一步显示了基于功能表达谱的分类方法具有抗基因检测缺失的稳健性。     

痰湿体质的分子生物学特征

文章以探索痰湿质的分子机制为目的,在临床流行病学调查的基础上,分别选择 -例典型痰湿质和 -例典型平和质受试对象,采用 .//0123456 7282’95: ;<::58= %"> .44<0检测技术检测基因组 ?@.,结合前期基因表达谱芯片分析痰湿质的差异表达基因结果,筛选痰湿质相关基因及单核苷酸多态性位点。试对痰湿质与平和质组间表达有显著差异的 ++!个基因进行分析,与平和质比较,初步筛选出痰湿质 %个相关基因共 个 A@B位点。同时进一步对相关基因功能分析显示,痰湿体质相关基因主要基因功能为酶活性、固醇运载体 活性等功能,参与糖异生途径、脂肪酸生物合成途径、胆固醇代谢过程、脂肪酸氧化作用、棕色脂肪细胞分化、 细胞葡萄糖调节平衡作用、体温调节作用等生物学过程,痰湿质者在分子水平上具有代谢紊乱的总体特征, 对其分子生物学特征进行了初步探索。     

基于浅层卷积神经网络的面部表情识别

面部表情识别在人机交互等领域中发挥着重要作用,采用深度学习方法提高了模型精度,但过深的网络加大了计算成本,造成识别滞后和性能低下的问题.本文提出了一种浅层卷积神经网络模型,它受到Xception网络的启发,结合了残差模块和深度可分离卷积,同时引入了功能模块与网络进行融合.微调后的网络结构简单、模型较小,在FER2013数据集上获得了66.12％的准确率,优于多个对比网络.最后,本文搭建了一个可视化系统来验证所提模型在自然场景下的性能,验证结果与实验结论一致.     

基于三种贝叶斯方法的结核病基因数据挖掘及生物信息学分析

确定结核病易感宿主基因对结核病的治疗与防控起着关键作用,而目前只有少数基因被证实与其相关.本文基于结核病患者外周血单核细胞基因芯片数据集GSE54992,先通过两种基于贝叶斯框架的方法:信息先验性贝叶斯检验和线性模型及经验贝叶斯方法对该数据集进行分析并筛选出正常样本与活动性结核病患者样本之间的差异表达基因,发现了319个被两种方法均识别出的差异表达基因.再利用这些基因对独立验证集GSE83456进行建模,通过朴素贝叶斯分类器验证,得出了较高的分类准确率.最后通过GO功能富集分析和KEGG通路分析,从生物学角度分析了结核病发病的分子机制.该研究突出了三种贝叶斯方法的综合应用在基因数据分析中的重要作用,为发掘结核病特异性生物标志物提出了新的综合策略,为结核病的预防、诊断和治疗提供了重要线索。     

小白鼠缺氧信息的获得、传导和储存的分子机理研究

通过不同缺氧程度小白鼠模型,同时利用心肌组织的核DNA片段的基因体外表达和mRNA体外翻译,观察到了心肌缺氧信息获得、传导和储存的分子机理.观察结果表明:心肌等胞质中氧代谢相关的已有基因的开关蛋白质复合体等参与了人工轻度快速缺氧信息的获得;心肌等胞质中已有n mRNA链状复合体中mRNA迅速翻译出蛋白质,心肌等组织可传导较严重快速缺氧信息;心肌等细胞核内已有氧代谢相关的活性核基因迅速表达出自己编码的蛋白质,心肌等以储存较长时间严重缺氧信息.昆明种小白鼠在中国西藏拉萨郊区自然缺氧条件下饲喂30天,长期缺氧信息的储存分子机制与上述小白鼠较长时间严重缺氧模型类似,同时原有的和新形成的细胞的核DNA片段上的氧代谢等相关的核基因分别表达出较多蛋白质,并引起小白鼠的耳朵和尾巴增长等体型的明显变化.     

基于cDNA微阵列技术对激活蛋白处理水稻后信号传导及防卫反应相关基因的研究

为探讨激活蛋白对植物抗病防虫作用的机理,应用水稻10368条非冗余序列标签(ESTs)所制备的cDNA微阵列及荧光信号Cy3、Cy5杂交体系,对激活蛋白处理水稻后信号传导及防卫反应相关基因进行了研究,并利用半定量RT-PCR方法验证了相关基因的表达.结果表明:激活蛋白处理水稻后1～5d内,诱导了NPR1和bZIP等信号传导相关基因的上调表达,同时对APX、GST、CHS及PR1a等防卫基因的表达也有促进作用.激活蛋白诱导水稻启动了水杨酸介导的系统获得抗性(systemic acquired resistance, SAR)反应.     

基于基因芯片的人参作用脑组织抗衰老基因表达谱的研究

针对D-半乳糖造成的小鼠亚急性衰老模型,采用Cy3和Cy5两种不同的荧光染料通过逆转录反应将人参作用前后的小鼠脑组织细胞mRNA分别标记成两种探针,混合后与小鼠基因芯片杂交。借助计算机分析扫描芯片荧光信号图像,寻找出经人参作用后表达有差异的基因。据此研究人参水煎剂对衰老模型小鼠脑组织细胞基因表达的影响,以深入探讨其作用的分子机制。研究表明,微矩阵基因芯片在研究人参作用前后衰老模型小鼠脑细胞基因表达的改变时,具有快速、高通量、高敏度等特点,为运用生物芯片技术研究中药抗衰老机理提供了有价值的方法。     

cDNA芯片重复探针检测值的一致性分析

通过SOURCE数据库对4套cDNA数据的探针进行了注释,分析了对应同一条Unigene的多个探针的检测值(即重复检测值)之间的相关性.采用两种常规方法处理了重复检测值,比较了这两种处理方法对筛选差异表达基因的影响.结果显示:Unigene的重复检测值之间存在一定比例的负相关;更新探针注释数据后的重复检测值之间的低相关比例减少,高相关比例显著提高;重复点样探针之间的相关性高于其它重复检测值,但是仍有很多低相关;两种处理重复检测值方法对于用基因表达差异显著性分析方法(SAM)与T检验方法筛选差异表达基因影响不大.     

抗稻瘟病新基因pi-hit-1的克隆与功能研究

采用差异显示法(DD-PCR)寻找易感稻瘟病的突变品系与野生型对照品系中的差异表达基因。结果发现与野生型对照相比,Rubisco小亚基、pi-hit．1(AF450251)和pi-hit-2(AF448491)基因在易感稻瘟病的突变品系中高表达,pi-hit-1和pi-hit-2是功能未知的新基因。进一步采用电子克隆和RT-PCR方法克隆了pi-hit-1基因的全长eDNA(AF514859),该基因编码的蛋白质属于ATP依赖的Clp蛋白酶家族。分析pi-hit-1基因的组织特异性表达发现,此基因在叶片组织特异表达。进一步设计接种诱导实验研究pi-hit-1基因表达与水稻稻瘟病易感性的关系。在易感稻瘟病的突变品系中pi-hit-1受稻瘟病菌诱导,接种后其表达量明显升高,而野生型对照品系pi-hit-1基因表达在接种前后无明显变化。比较易感稻瘟病的突变品系与对照品系pi-hit-1基因序列差异发现,稻瘟病敏感品系中pi-hit-1基因第一外显子发生缺失突变使pi-hit-1蛋白功能缺失,导致突变品系易感稻瘟病。这些实验结果提示野生型pi-hit-1是稻瘟病抗性基因。     

人膜补体调节蛋白MCP、CD59在稳定转染的细胞中的共表达及功能研究

采取内核糖体进入位点(IRES)策略构建含人的膜补体调节蛋白基因MCP和CD59的cDNA的双顺反子真核表达载体pcDNA3-MCPIRESCD59,以磷酸钙沉淀法转染NIH3T3细胞,用 G418筛选阳性克隆,并研究MCP和CD59双基因在稳定细胞系中的共表达及保护功能.PCR实验结果显示双基因稳定整合在异源细胞NIH3T3的染色体上,RT-PCR及Western印迹实验分别从 RNA水平和蛋白质水平证实了人补体调节蛋白分子MCP和CD59在细胞系中皆获得同步表达.检测连续传代30次的NIH3T3 pcDNA3-MCPIRESCD59,结果表明人MCP和CD59基因仍稳定整合在细胞基因组中,并未随着传代而丢失,为稳定的转双基因细胞系.补体依赖的细胞毒反应表明,pcDNA3-MCPIRESCD59转染细胞由于MCP和CD59的共表达获得了高于MCP或CD59单一表达时所提供的保护功效,能更好地抑制人补体依赖的细胞毒作用的发生,保护宿主细胞免受人补体的攻击.以上结果表明,所构建的双基因重组表达载体实现了不同人补体调节蛋白基因高效转移和高水平共表达,在克服超急性排斥反应的基因治疗中有潜在的应用价值.     

基于Java的基因本体工具包

针对基因本体的需求,利用Java技术,以模块化设计的方式实现了基因本体工具包GO4J.该系统包括4个模块.解析器模块把GO载入到内存中;图数据结构模块记录了所有的GO条目之间的关系;语义相似性模块评估两个GO条目之间的相似程度;可视化模块直观展示GO条目和根节点之间的路径.GO4J把这4个模块整合到本体浏览器中,可以结合GO注释的生物数据来对具体的生物数据进行分析.     

A novel method to quantify gene set functional association based on gene ontology

Numerous gene sets have been used as molecular signatures for exploring the genetic basis of complex disorders. These gene sets are distinct but related to each other in many cases; therefore, efforts have been made to compare gene sets for studies such as those evaluating the reproducibility of different experiments. Comparison in terms of biological function has been demonstrated to be helpful to biologists. We improved the measurement of semantic similarity to quantify the functional association between gene sets in the context of gene ontology and developed a web toolkit named Gene Set Functional Similarity (GSFS; http://bioinfo.hrbmu.edu.cn/GSFS). Validation based on protein complexes for which the functional associations are known demonstrated that the GSFS scores tend to be correlated with sequence similarity scores and that complexes with high GSFS scores tend to be involved in the same functional catalogue. Compared with the pairwise method and the annotation method, the GSFS shows better discrimination and more accurately reflects the known functional catalogues shared between complexes. Case studies comparing differentially expressed genes of prostate tumour samples from different microarray platforms and identifying coronary heart disease susceptibility pathways revealed that the method could contribute to future studies exploring the molecular basis of complex disorders.     

Systematic functional genomics resource and annotation for poplar

Poplar, as a model species for forestry research, has many excellent characteristics. Studies on functional genes have provided the foundation, at the molecular level, for improving genetic traits and cultivating elite lines. Although studies on functional genes have been performed for many years, large amounts of experimental data remain scattered across various reports and have not been unified via comprehensive statistical analysis. This problem can be addressed by employing bioinformatic methodology and technology to gather and organise data to construct a Poplar Functional Gene Database, containing data on 207 poplar functional genes. As an example, the authors investigated genes of Populus euphratica involved in the response to salt stress. Four small cDNA libraries were constructed and treated with 300 mM NaCl or pure water for 6 and 24 h. Using high‐throughput sequencing, they identified conserved and novel miRNAs that were differentially expressed. Target genes were next predicted and detailed functional information derived using the Gene Ontology database and Kyoto Encyclopedia of Genes and Genomes pathway analysis. This information provides a primary visual schema allowing us to understand the dynamics of the regulatory gene network responding to salt stress in Populus.Inspec keywords: genomics, genetics, RNA, DNA, molecular biophysics, molecular configurations, bioinformatics, statistical analysisOther keywords: systematic functional genomics resource, forestry research, functional genes, molecular level, genetic traits, comprehensive statistical analysis, bioinformatic methodology, Poplar Functional Gene Database, Populus euphratica, salt stress, cDNA libraries, high‐throughput sequencing, miRNA expression, Gene Ontology database, Kyoto Encyclopedia of Genes and Genomes pathway analysis, regulatory gene network     

Global gene expression analysis for evaluation and design of biomaterials

Abstract

Comprehensive gene expression analysis using DNA microarrays has become a widespread technique in molecular biological research. In the biomaterials field, it is used to evaluate the biocompatibility or cellular toxicity of metals, polymers and ceramics. Studies in this field have extracted differentially expressed genes in the context of differences in cellular responses among multiple materials. Based on these genes, the effects of materials on cells at the molecular level have been examined. Expression data ranging from several to tens of thousands of genes can be obtained from DNA microarrays. For this reason, several tens or hundreds of differentially expressed genes are often present in different materials. In this review, we outline the principles of DNA microarrays, and provide an introduction to methods of extracting information which is useful for evaluating and designing biomaterials from comprehensive gene expression data.