摘要
为进一步分析腺瘤相对正常SSH文库(A-N)的差异表达候选基因的表达谱,结合通用的生物信息学软件,自行开发、搭建包括核酸自动分析平台及GetUni软件包的生物信息学平台,实现了将A-N文库109个差异克隆序列与本地下载的非冗余核酸数据库、人UniGene数据库比对、聚类,至获取差异表达候选基因的自动化分析。对这些基因进行GOTM(GOTree Machine)初步生物信息学分析及RT-PCR验证。结果共发现62个候选基因,包括6个核糖体蛋白成员,6个免疫相关基因。Reg4和FAM46A两个基因出现频次最高,分别为13次和4次,半定量RT-PCR显示这两个基因分别在10/10和9/10例腺瘤相对正常黏膜表达上调。对于这些差异表达候选基因的进一步分析和研究将有助于揭示结肠腺瘤发生的分子机制。
We established a colonic adenoma-normal mucosa suppressive subtraction hybridization （SSH） library in 1999. In this study, we wanted to explore the expression profile of all candidate genes in this library. We developed an EST pipeline which contained two in-house software packages, nucleic acid analytical software and GetUni. The nucleic acid analytical software, an integrator of the universal bioinformatics tools including phred, phd2 fasta, cross_match, repeatmasker and blast2.0, can blast sequences of differential clones with the downloaded non-redudant nucleotide （NR） database. GetUni can cluster these NR sequences into Unigene via matching with the downloaded Homo sapiens UniGene database. Sixty-two candidate genes in A-N library were obtained via the high throughput automatic gene expression bioinformatics pipeline. Gene Ontology online analysis revealed that ribosome genes and immunity-regulating genes were the two most common categories in the KEGG or Biocarta Pathway. We also detected the expression of 2 genes with highest hits, Reg4 and FAM46A, by semi-quantitative RT-PCR. Both genes were up-regulated in 10 or 9 out of 10 adenomas in comparison with the paired normal mucosa, respectively. The candidate genes in A-N library would be of great significance in disclosing the molecular mechanism underlying in colonic adenoma initiation and progression.
出处
《遗传》
CAS
CSCD
北大核心
2006年第4期385-392,共8页
Hereditas（Beijing)
基金
国家自然科学基金资助项目(编号:30371605
30370636)~~
