Third-generation human mitochondria-focused cDNA microarray and its bioinformatic tools for analysis of gene expression
Third-generation human mitochondria-focused cDNA microarray and its bioinformatic tools for analysis of gene expression
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DOI：
10.2144/000112388
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发表时间：
2007-03-01
期刊：
影响因子：
2.7
通讯作者：
Su, Yan A.
中科院分区：
文献类型：
--
作者：
Bai, Xueyan;Wu, Jun;Su, Yan A.
为了便于分析线粒体转录本，我们开发了第三代人线粒体聚焦的基因芯片(HMitChip3)及其生物信息学工具。HMitChip3包括37个线粒体DNA编码基因，1098个核DNA编码基因和线粒体相关基因，以及225个对照基因，每个基因都是三个副本。生物信息学工具包括数据分析程序和用于解释结果的定制数据库。该数据库涉及645个分子，功能涉及946个hMitChip3基因，涉及612个生物过程，涉及930个基因，涉及172个细胞成分，涉及869个基因，涉及107个生物化学途径，涉及476个基因，涉及23个反应组事件，涉及227个基因，涉及320个遗传疾病，涉及237个基因，涉及87个药物靶标，涉及55个基因。为了测试这些工具，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)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+/-10.005)和实验间的重复性(R>；=0.931+/-0.013)。线粒体和其他细胞器中涉及DNA、RNA或蛋白质生物合成的16个基因的表达模式与两种细胞系的增殖率和模式一致。用定量逆转录聚合酶链式反应(RT-PCR)对6个基因进行了验证。因此，hMitChip3及其生物信息学软件为大量关注线粒体的基因表达提供了一个集成的工具。
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 in mitochondria -related genes, and 225 controls, each in triplicate. The bioinformatic tools included data anal sis 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 (rapidlly dividing) and UACC903(+6) (slowly dividing). Our results demonstrated internal gene-set consistency (correlation R > 0.980 +/- 10.005) and interexperimental reproducibility (R >= 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 pattern. of 6 tested genes were verified by quantitative reverse transcription PCR (RT-PCR). Thus, hMitChip3 and its bioinformatics software provide an integrated tool for profliling mitochondria-focused gene expression.