生物信息学基因表达差异分析

基因的差异化表达由多种因素共同导致,并且与许多疾病的发生和发展有密切联系,对差异化表达的基因进行生物信息学以及生物统计学的分析对于研究细胞调节机制和疾病机理有着重要意义。目前,对差异化表达的基因有以下几种主流的研究方法：DNA微阵列（DNA microarray）,抑制性消减杂交（SSH）,基因表达连续性分析（SAGE）,代表性差异分析（RDA）,以及mRNA差异显示PCR（mRNA DDRT-PCR）。目前许多基因差异化表达数据是建立在时段（time series）基础上,因此对基于时间变化的基因差异化表达分析变得尤为重要。本文将对差异化表达基因的几种主流方法进行详细阐述,并介绍一种基于傅里叶函数的时段基因差异化表达分析。     

Outlier sums for differential gene expression analysis

We propose a method for detecting genes that, in a disease group, exhibit unusually high gene expression in some but not all samples. This can be particularly useful in cancer studies, where mutations that can amplify or turn off gene expression often occur in only a minority of samples. In real and simulated examples, the new method often exhibits lower false discovery rates than simple t-statistic thresholding. We also compare our approach to the recent cancer profile outlier analysis proposal of Tomlins and others (2005).     

DNA microarray analysis reveals differential gene expression in the soleus muscle between male and female rats exposed to a high fat diet

It is well recognized that diet-induced dysfunctions in skeletal muscle are closely related with many metabolic diseases, such as obesity and diabetes. In the present study, we identified global changes in gender-dependent gene expressions in the soleus muscle of lean and obese rats fed a high fat diet (HFD), using DNA microarray analysis. Prior to microarray analysis, the body weight gains were found to be higher in male HFD rats than the female HFD rats. To better understand the detailed phenotypic differences in response to HFD feeding, we identified differential gene expression in soleus muscle between the genders. To this end, we extracted and summarized the genes that were up- or down-regulated more than 1.5-fold between the genders in the microarray data. As expected, a greater number of genes encoding myofibrillar proteins and glycolytic proteins were expressed higher in males than females when exposed to HFD, reflecting greater muscular activity and higher capacity for utilizing glucose as an energy fuel. However, a series of genes involved in oxidative metabolism and cellular defenses were more up-regulated in females than males. These results allowed us to conclude that compared to males, females have greater fat clearing capacity in skeletal muscle through the activation of genes encoding enzymes for fat oxidation. In conclusion, our microarray data provide a better understanding of the molecular events underlying gender dimorphism in soleus muscle, and will provide valuable information in improving gender awareness in the health care system.     

Comparative analysis of gene expression between CMS-D8 restored plants and normal non-restoring fertile plants in cotton by differential display

CMS-D8 and its restorer were developed by introducing the cytoplasm and nuclear gene Rf ₂ from the wild diploid Gossypium trilobum (D8) into the cultivated tetraploid Upland cotton (Gossypium hirsutum). No information is available on how the Rf ₂ gene interacts with CMS-associated genes and how CMS-D8 cytoplasm affects nuclear gene expression. The objective of this study was to identify differentially expressed genes in anther tissues between the non-restoring fertile maintainer ARK8518 (rf ₂ rf ₂) and its isogenic heterozygous D8 restorer line, ARK8518R (Rf ₂ rf ₂) with D8 cytoplasm, by mRNA differential display (DD). Out of more than 3,000 DDRT-PCR bands amplified by 31 primer combinations from 12 anchor primers and 8 arbitrary decamer primers, approximately 100 bands were identified as being qualitatively differentially displayed. A total of 38 cDNA fragments including 12 preferentially expressed cDNA bands in anther were isolated, cloned and sequenced. Reverse northern blot analysis showed that only 4 genes, including genes encoding a Cys-3-His zinc finger protein and aminopeptidase, were up-regulated, while 22 genes, including genes for phosphoribosylanthranilate transferase (PAT), starch synthase (SS), 4-coumarate-CoA ligase, electron transporter, calnexin, arginine decarboxylase, and polyubiquitin, were down-regulated in the heterozygous restorer ARK8518R. The down-regulation of SS explains the lack of starch accumulation in sterile rf ₂ pollen grains in the heterozygous restored plants. The molecular mechanism of CMS and its restoration, specifically the possible roles of SS and PAT genes in relation to restoration of Rf ₂ to CMS-D8, are discussed. This investigation represents the first account of such an analysis in cotton.