Expression of liver cancer associated gene HCCA3

AIM: To study and clone a novel liver cancer related gene, and to explore the molecular basis of liver cancer genesis. METHODS: Using mRNA differential display polymerase chain reaction (DDPCR), we investigated the difference of mRNA in human hepatocellular carcinoma (HCC) and paired surrounding liver tissues, and got a gene probe. By screening a human placenta cDNA library and genomic homologous extend, we obtained a full-length cDNA named HCCA3. We analyzed the expression of this novel gene in 42 pairs of HCC and the surrounding liver tissues, and distribution in human normal tissues by means of Northern blot assay. RESULTS: A full-length cDNA of liver cancer associated gene HCCA3 has been submitted to the GeneBank nucleotide sequence databases (Accession No. AF276707). The positive expression rate of this gene was 78.6% (33/42) in HCC tissues, and the clinical pathological data showed that the HCCA3 was closely associated with the invasion of tumor capsule (P=0.023) and adjacant small metastasis satellite nodules lesions (P=0.041). The HCCA3 was widely distributed in the human normal tissues, which was intensively expressed in lungs, brain and colon tissues, while lowly expressed in the liver tissues. CONCLUSION: A novel full-length cDNA was cloned and differentiated, which was highly expressed in liver cancer tissues. The high expression was closely related to the tumor invasiveness and metastasis,that may be the late heredited change in HCC genesis.

Rice bicoid-related cDNA sequence and its expression during early embryogenesis

Bicoid is one of the important Drosophila maternal genes involved in the control of embryo polarity and larvae segmentation. To clone and characterize the rice bicoid-related genes, one cDNA clone, Rb24 (EMBL accession number: AJ2771380), was isolated by screening of rice unmature seed cDNA library. Sequence analysis indicates that Rb24 contains a putative amino acid sequence, which is homologous to unique 8 amino acids sequence within Drosophila bicoid homeodomain (50% identity, 75% similarity) and involves a lys-9 in putative helix 3. Northern blot analysis of rice RNA has shown that this sequence is expressed in a tissue-specific manner. The transcript was detected strongly in young panicles, but less in young leaves and roots. This results are further confirmed with paraffin section in situ hybridization. The signal is intensive in rice globular embryo and located at the apical tip of the embryo, then, along with the development of embryo, the signal is getting reduced and transfers into both sides of embryo. The existence of bicoid-related sequence in rice embryo and the similarity of polar distribution of bicoid and Rb24 mRNA in early embryo development may implicates a conserved maternal regulation mechanism of body axis presents in Drosophila and in rice.

ELOVL3在预测肝细胞癌预后中的作用

目的探索精准预测肝细胞癌患者预后的分子标志物。方法在TCGA数据库下载肝细胞癌(LIHC)样本的mRNA表达数据及相应的临床预后数据,并且收集从2017年1月1日至2022年1月1日在新疆维吾尔自治区人民医院接受肝切除手术的91例肝细胞癌(HCC)患者的临床病理资料和随访资料。用R软件筛查差异表达基因(DEGs)后,进一步进行Cox单变量回归分析和LASSO回归分析筛出与HCC患者生存相关的风险基因;用R软件的ggplot2分析包和免疫组织化学染色法分析ELOVL3在不同肝组织上的表达情况,Survival分析包实现Kaplan-Meier生存分析。结果初步筛查得到752个DEGs,包括表达上调的247个基因和505个下调基因。进一步通过Cox回归分析得出175个与HCC患者的生存显著相关的基因集,LASSO回归分析,挑出14个与HCC患者生存密切相关的风险基因。最终通过预实验和文献调研将目标基因确定为ELOVL3。TCGA-LIHC的分析结果显示:ELOVL3在癌组织中的表达量明显高于正常肝组织(P<0.001),而且该基因在癌组织中的表达量也高于互相匹配的癌旁组织(P<0.001)。免疫组化染色结果提示:ELOVL3在59例(64.8%)患者的肝癌组织中表达阳性,而32例(35.2%)患者的肝癌组织中没有表达;在互相匹配的癌旁组织中表达均为阴性。生存分析结果显示ELOVL3阳性患者的5年生存率明显比ELOVL3阴性患者低(r=0.028);ELOVL3高表达的患者总体生存率相对于ELOVL3低表达的患者低,而且表达量越高,预后越差(HR=1.7,P=0.008)。结论ELOVL3的表达与HCC患者的不良预后相关,而且具有做预测HCC预后的新型分子标志物的潜力。

DENGENE:一种高精度的基于密度的适用于基因表达数据的聚类算法

根据基因表达数据的特点,提出一种高精度的基于密度的聚类算法DENGENE。DENGENE通过定义一致性检测和引进峰点改进搜索方向,使得算法能够更好地处理基因表达数据。为了评价算法的性能,选取了两组广为使用的测试数据,即啤酒酵母基因表达数据集对算法来进行测试。实验结果表明,与基于模型的五种算法、CAST算法、K-均值聚类等相比,DENGENE在滤除噪声和聚类精度方面取得了显著的改善。

Applying a highly specific and reproducible cDNA RDA method to clone garlic up-regulated genes in human gastric cancer cells

AIM: To develop and optimize cDNA representational difference analysis (cDNA RDA) method and to identify and clone garlic up-regulated genes in human gastric cancer (HGC) cells. METHODS: We performed cDNA RDA method by using abundant double-stranded cDNA messages provided by two self-constructed cDNA libraries (Allitridi-treated and paternal HGC cell line BGC823 cells cDNA libraries respectively). Bam H I and Xho I restriction sites harbored in the library vector were used to select representations. Northern and Slot blots analyses were employed to identify the obtained difference products. RESULTS: Fragments released from the cDNA library vector after restriction endonuclease digestion acted as good marker indicating the appropriate digestion degree for library DNA. Two novel expressed sequence tags (ESTs) and a recombinant gene were obtained. Slot blots result showed a 8-fold increase of glia-derived nexin/protease nexin 1 (GDN/PN1) gene expression level and 4-fold increase of hepatitis B virus x-interacting protein (XIP) mRNA level in BGC823 cells after Allitridi treatment for 72h. CONCLUSION: Elevated levels of GDN/PN1 and XIP mRNAs induced by Allitridi provide valuable molecular evidence for elucidating the garlic's efficacies against neurodegenerative and inflammatory diseases. Isolation of a recombinant gene and two novel ESTs further show cDNA RDA based on cDNA libraries to be a powerful method with high specificity and reproducibility in cloning differentially expressed genes.

Outlier Analysis for Gene Expression Data

The rapid developments of technologies that generate arrays of gene dataenable a global view of the transcription levels of hundreds of thousands of genes simultaneously.The outlier detection problem for gene data has its importance but together with the difficulty ofhigh dimensionality. The sparsity of data in high-dimensional space makes each point a relativelygood outlier in the view of traditional distance-based definitions. Thus, finding outliers in highdimensional data is more complex. In this paper, some basic outlier analysis algorithms arediscussed and a new genetic algorithm is presented. This algorithm is to find best dimensionprojections based on a revised cell-based algorithm and to give explanations to solutions. It cansolve the outlier detection problem for gene expression data and for other high dimensional data aswell.

The expression and antigenicity identification of recombinant rat TGF-β1 in bacteria

In order to study structure-function details of TGF-beta1, the recombinant mature form of rat TGF-beta1 was expressed in bacteria. Synthesis of the 112 amino-acid carboxyl-terminal part of TGF-beta1 (amino acid 279-390) was controlled by an inducible gene expression system based on bacteriophage T7 RNA polymerase. This system allowed an active and selective synthesis of recombinant TGF-beta1. The molecular weight of expressed TGF-alpha1 monomer determined on SDS-polyacrylamide gel under reducing conditions was about 13 kD. Serial detergent washes combined with a single gel-filtration purification step were sufficient to purify the expression product to homogeneity. Amino-terminal sequencing revealed that the N-terminal of the recombinant protein was identical to the published data. In Western blot analysis the recombinant polypeptide showed excellent antigenicity against polyclonal TGF-beta1 antibody. The mature recombinant rat TGF-beta1 expressed in this study provides a useful tool for future detailed structural and functional studies.

基于GEO数据库分析非小细胞肺癌癌组织中配对盒基因8的表达及其与病人预后的关系

目的探讨基于高通量基因表达数据库(Gene expression Omnibus,GEO数据库)分析配对盒基因8(PAX8)在非小细胞肺癌(NSCLC)病人癌组织中的表达情况及与预后的关系。方法利用在线工具Oncomine分析PAX8在NSCLC与正常肺组织的表达情况,基于GEO数据库下载相关芯片数据(GSE77803),收集156例NSCLC组织的基因表达谱及相关临床数据,采用中位数法将其分为PAX8低表达组(n=78)和PAX8高表达组(n=78)。分析PAX8的表达与病人性别、年龄、病理类型、T分期、N分期和术后复发情况之间的关系;采用生存分析PAX8的表达与病人预后生存之间的关系;采用基因本体(GO)注释分析PAX8基因的功能,采用KEGG PATHWAY分析PAX8可能参与的信号通路。结果TCGA Lung 2数据集共检测了1537个样本,其中正常肺组织样本390例,肺癌组织样本共721例,血液样本420例,无意义样本6例。与正常肺组织相比,PAX8在肺腺癌和肺鳞癌中表达水平明显升高(P<0.05);基于GEO数据库中GSE77803(GPL570)数据集分析,NSCLC癌组织中PAX8的表达水平与病人的T分期、N分期和是否复发有关(P<0.05),生存分析显示,癌组织中PAX8低表达病人的总生存率为52.94%,中位生存期为54.6个月,显著高于PAX8高表达病人(34.35%,48.6个月)(log-rankχ~2=4.609,P=0.032)。PAX8低表达病人无病生存率为42.50%,中位生存期为51.7个月,显著高于PAX8高表达病人(28.71%,40.8个月)(log-rankχ~2=5.712,P=0.017);GO注释和KEGG分析显示,PAX8可能参与调节NSCLC发生发展相关的信号通路的表达。结论PAX8蛋白在肺腺癌和肺鳞癌中均存在异常高表达,PAX8低表达NSCLC病人具有更高的生存率。

基于混合进化算法的特征选择方法研究

特征选择(Feature Selection,FS)是一种有效的数据预处理方法,它可以通过选择高维数据中一组具有高相关性和低冗余性的特征,从而解决数据冗余引起的维数灾难.目前许多计算方法已经被应用于求解FS问题,其中基于教与学优化(Teaching and Learning-based Optimization Algorithm,TLBO)的特征选择模型由于其高效的全局搜索能力受到越来越多学者的关注.然而,随着数据规模的不断扩大,这些算法所具有的模型不稳定、模型精确度低和局部搜索能力差等局限性,使算法的研究逐步陷入困境.为解决上述问题,本文提出了融合教与学优化算法与局部搜索方法(Local Search,LS)的混合进化Wrapper算法模型(Teaching and Learning-based Optimization-Local Search Algorithm,TLBOLS).首先,由于传统的教与学优化算法不能直接用于求解特征选择问题,算法在初始化阶段将实数型编码转为二进制编码,然后为保证种群的多样性,在教阶段引入最差个体重启机制,并针对进化班级过程中学习者与教学者两种身份采用不同值的TF值,提出二进制的教与学特征选择算法(Binary Teaching and Learning-based Optimization-Local Search Algorithm,BTLBOLS).随后,提出结合多操作的局部搜索方法和变邻域搜索逐渐增强扰动力度,提高整个种群的个体质量.为优化特征选择结果,BTLBOLS利用综合评价指标作为目标函数指导整体进化过程.实验选取45个高维癌症基因表达数据集进行测试并与十种特征选择算法相比,实验结果表明,相比其他算法,BTLBOLS在分类准确率和特征个数上都具有一定优势,算法分类性能有效提高.

嵌入代价敏感的极限学习机相异性集成的基因表达数据分类

极限学习机的相异性集成算法(Dissimilarity Based Ensemble of Extreme Learning Machine,D-ELM)在基因表达数据分类中能够得到较稳定的分类效果,然而这种分类算法是基于分类精度的,当所给样本的误分类代价不相等时,不能直接实现代价敏感分类过程中的最小平均误分类代价的要求。通过在分类过程中引入概率估计以及误分类代价和拒识代价重新构造分类结果,提出了基于相异性集成极限学习机的代价敏感算法(CS-D-ELM)。该算法被运用到基因表达数据集上,得到了较好的分类效果。

基于MapReduce的基因数据密度层次聚类算法

随着生物信息技术的快速发展,基因表达数据的规模急剧增长,这给传统的基因表达数据聚类算法带来了严峻的挑战.基于密度的层次聚类(DHC)能够较好地解决基因表达数据嵌套类问题且鲁棒性较好,但处理海量数据的效率不高.为此,提出了基于MapReduce的密度层次聚类算法——DisDHC.该算法首先进行数据分割,在每个子集上利用DHC进行聚类获得稀疏化的数据;在此基础上再次进行DHC聚类;最终产生整体数据的密度中心点.在酵母数据集、酵母细胞周期数据集、人血清数据集上进行实验,结果表明,DisDHC算法在保持DHC聚类效果的同时,极大地缩短了聚类时间.

面向药物发现和精准医疗的基因表达谱分析

作为功能基因组学中重要的组成部分,基因表达谱在生物学、医学和药物研发等多个领域发挥着重要作用.特别是随着精准医疗概念的提出,整合多组学数据用于个性化医疗是未来的发展趋势.本文从基因表达谱的基本概念出发,重点介绍面向药物发现的基因表达谱分析方法,即基于关联图谱的方法、基于基因调控网络的方法和基于多组学数据整合的方法.系统整理了各种方法的研究进展,特别是在抗癌药物研发领域的最新进展,为利用基因表达谱数据进行药物研发提供方法借鉴.

基因表达数据中局部模式的查询

基因表达数据分析一般是通过挖掘局部模式来实现的。保序子矩阵是局部模式挖掘中一种经典的模型,可以获取到在若干条件下表现出一致趋势的一组基因。高通量基因微阵列技术的进步,促进了海量基因表达数据的产生,使得对高性能基因表达数据分析算法的需求极为迫切。现有方法大多数是通过批量挖掘的方法来分析数据,即使有通过查询方式来获取精确结果的方法,其全面性与性能也有待提高。为了提高数据分析的效率与准确性,首先提出一种基于前缀树的基因表达数据索引gIndex,然后给出了一种基于列关键词查询的保序子矩阵分析方法 GEQc。其不经过批量挖掘,只需要建立索引并通过关键词来完成正相关/负相关/时滞等模式的查询。实验结果表明,与现有方法相比,所提算法具有良好的数据分析效率与可扩展性。

基因的无树评估(英文)

传统基于表达式树ET的基因评估从性能角度讲主要缺点是:重复遍历表达式树和进行大量重复计算。提出基于Scale的基因评估。变量矩阵用来避免基因评估中的重复计算。实验表明,在绝大多数数据分布下和参数选择情况下:基于Scale的基因评估较基于ET的基因评估快3～5倍。

小波包分解和模糊聚类下的基因表达数据分析

针对基因表达数据中存在的噪声对聚类分析结果准确度的影响问题,提出了一种基于小波包分解的基因表达数据模糊聚类分析方案,介绍了理论根据和算法,给出了Matlab仿真结果,并与其他方法聚类的结果进行了比较。结果表明提出的方法能够减少传统聚类方法受到噪声影响的程度,能够挖掘出基因表达数据在时间上的行为特征,对与细胞周期调控有关的基因表达数据的聚类结果划分更为准确和细致。

GABA transporter 1 transcriptional starting site exhibiting tissue specific difference

GABA transporter 1(GAT1) takes important roles in multiple physiological processes through the uptake and release of GABA, but the regulation of GAT1 gene expression in different tissues is rarely known. To address the question, first, 5’ Rapid amplification of cDNA end (RACE) was used to determine GAT1 transcriptional starting sites in neonatal mouse cerebral cortex and intestine, adult mouse brain and adult rat testis. The products of 5’RACE were confirmed by DNA sequencing. We found that the transcript of GAT1 in neonatal mouse cerebral cortex and adult mouse brain starts at the same site (inside of exon 1), while in mouse intestine, GAT1 starts transcription in intron 1, and in rat testis, the transcript of GAT1 has an additional untranslation exon to the 5’ direction.

Generation and analysis of 113 adult stage Schistosoma japonicum (Chinese strain) expressed sequence tags

OBJECTIVE: To rapidly and economically obtain knowledge about adult stage Schistosoma japonicum (Chinese strain) expressed genes using expressed sequence tag (EST). METHODS: A directional cDNA library constructed from Schistosoma japonicum (Chinese strain) adult stage RNA was used to generate expressed sequence tags (ESTs). These were compared against an EMBL-parasites database and GENBANK database by BLASTn and BLASTx. RESULTS: A total of 314 phage clones were randomly selected for generating expressed sequence tags (ESTs). From these clones, 132 EST-quality sequence were obtained. Among these EST-quality sequences, 113 ESTs were successfully submitted to the dbEST at GenBanK. A total of 7.6% of these EST-quality sequences were previously identified sequence of Schistosoma japonicum, while 4.5% were putatively identified sequences of Schistosoma japonicum. A total of 23.5% of these EST-quality sequences were putatively identified sequence of Schistosoma mansoni or other organisms. 57.6% had no matches in the database and were classified as unknown sequences. Most ESTs with the putative protein identified belonged to housekeeping proteins. Information about several interesting genes was found. CONCLUSION: Partial cDNA sequencing to generate expressed sequence tags (ESTs) has the potential to rapidly and economically increase our knowledge about adult stage Schistosoma japonicum (Chinese strain) expressed genes.

人类管家基因和非管家基因microRNA绑定密度的比较及与3′UTR进化保守性关系的分析

目的该研究从整体水平比较microRNA(miRNA)对管家基因和非管家基因的调控差异并研究3'UTR的进化保守性与miRNA对两类基因调控差异之间的相关性。方法通过对3个基于序列的miRNA靶基因预测软件整合分析,并结合基于miRNA-靶基因的表达谱数据相关性分析,以获得miRNA对两类基因的调控情况,同时利用phastCons保守性分值对两类基因的3'UTR区域进行多物种进化分析。结果研究发现miRNA在管家基因的3'UTR上有显著地高密度绑定,管家基因的3'UTR区域具有相对较高的序列保守性。结论该研究结果突出了miRNA对管家基因表达调控的重要作用,对于重新理解miRNA对真核生物基因表达调控作用具有一定的参考价值。

结核病患者外周血液中分子标志物生物信息学分析

结核病(tuberculosis,TB)对人类具有非常大的威胁,感染过结核病的人占世界总人口数的三分之一,而且每年有造成超过一百万人的死亡。为了寻找可用于结核病诊断和治疗的分子标志物,我们从微阵列数据存储中心基因表达综合数据库(gene expression omnibus,GEO)中下载了原始数据,将来源于结核病患者的外周血单核细胞与健康人的基因进行了比较,共分析筛选出310个差异共表达的基因。随后,我们应用DAVID(the database for annotation,visualization and integrated discovery)数据库对这些差异共表达基因进行了GO(gene ontology)功能富集分析和KEGG(kyoto encyclopedia of genes and genomes)通路分析。通过蛋白互作网络,我们找到了CCL20、JAK2、STAT1和IL-1β4个结核病的关键基因。我们的研究表明,数据挖掘和整合能够成为研究结核病诊断标志物及其发生发展机制的有用工具,并可为结核病的诊断和治疗带来新思路。