第三代聚焦人类线粒体的cDNA微阵列及其用于基因表达分析的生物信息学工具。

Third-generation human mitochondria-focused cDNA microarray and its bioinformatic tools for analysis of gene expression.

作者信息

Bai Xueyan, Wu Jun, Zhang Qiuyang, Alesci Salvatore, Manoli Irini, Blackman Marc R, Chrousos George P, Goldstein Allan L, Rennert Owen M, Su Yan A

机构信息

The George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA.

出版信息

Biotechniques. 2007 Mar;42(3):365-75. doi: 10.2144/000112388.

DOI:10.2144/000112388

PMID:17390543

Abstract

To facilitate profiling mitochondrial transcriptomes, we developed a third-generation human mitochondria-focused cDNA microarray (hMitChip3) and its bioinformatic tools. hMitChip3 consists of the 37 mitochondrial DNA-encoded genes, 1098 nuclear DNA-encoded and mitochondria-related genes, and 225 controls, each in triplicate. The bioinformatic tools included data analysis procedures and customized database for interpretation of results. The database associated 645 molecular functions with 946 hMitChip3 genes, 612 biological processes with 930 genes, 172 cellular components with 869 genes, 107 biological chemistry pathways with 476 genes, 23 reactome events with 227 genes, 320 genetic disorders with 237 genes, and 87 drugs targets with 55 genes. To test these tools, hMitChip3 was used to compare expression profiles between human melanoma cell lines UACC903 (rapidly dividing) and UACC903(+6) (slowly dividing). Our results demonstrated internal gene-set consistency (correlation R > or = 0.980 +/- 0.005) and interexperimental reproducibility (R > or = 0.931 +/- 0.013). Expression patterns of 16 genes, involved in DNA, RNA, or protein biosyntheses in mitochondrial and other organelles, were consistent with the proliferation rates of both cell lines, and the patterns of 6 tested genes were verified by quantitative reverse transcription PCR (RT-PCR). Thus, hMitChip3 and its bioinformatics software provide an integrated tool for profiling mitochondria-focused gene expression.

摘要

为便于分析线粒体转录组，我们开发了第三代聚焦于人类线粒体的cDNA微阵列（hMitChip3）及其生物信息学工具。hMitChip3由37个线粒体DNA编码基因、1098个核DNA编码且与线粒体相关的基因以及225个对照组成，每个均有三个重复。生物信息学工具包括数据分析程序和用于结果解释的定制数据库。该数据库将645种分子功能与946个hMitChip3基因相关联，612个生物学过程与930个基因相关联，172个细胞成分与869个基因相关联，107条生物化学途径与476个基因相关联，23个反应组事件与227个基因相关联，320种遗传疾病与237个基因相关联，87个药物靶点与55个基因相关联。为测试这些工具，使用hMitChip3比较了人类黑色素瘤细胞系UACC903（快速分裂）和UACC903(+6)（缓慢分裂）之间的表达谱。我们的结果证明了内部基因集的一致性（相关性R≥0.980±0.005）和实验间的可重复性（R≥0.931±0.013）。16个参与线粒体和其他细胞器中DNA、RNA或蛋白质生物合成的基因的表达模式与两种细胞系的增殖率一致，并且6个测试基因的模式通过定量逆转录PCR（RT-PCR）得到了验证。因此，hMitChip3及其生物信息学软件为分析聚焦于线粒体的基因表达提供了一个综合工具。