ARTADE2DB: Improved Statistical Inferences for Arabidopsis Gene Functions and Structure Predictions by Dynamic Structure-Based Dynamic Expression (DSDE) Analyses
ARTADE2DB: Improved Statistical Inferences for Arabidopsis Gene Functions and Structure Predictions by Dynamic Structure-Based Dynamic Expression (DSDE) Analyses
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DOI：
10.1093/pcp/pcq202
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发表时间：
2011-02-01
影响因子：
4.9
通讯作者：
Toyoda, Tetsuro
中科院分区：
文献类型：
--
作者：
Iida, Kei;Kawaguchi, Shuji;Toyoda, Tetsuro
全基因组拼接阵列和高通量测序仪等用于观察高分辨率基因组活动的技术的最新进展为理解基因组功能提供了详细的信息。然而，50%已知的拟南芥基因的功能仍不清楚，或仅根据蛋白质基序或相似性等静态分析进行注释。在本文中，我们描述了基于动态结构的动态表达(DSDE)分析，它顺序地预测转录本的结构和功能特征。我们发现，DSDE分析比基于静态结构的动态表达(SSDE)分析或基于先前确定的拟南芥基因结构的常规共表达分析更准确地推断基因功能12%。这一结果表明，在转录调控和动力学的系统生物学中，比固定的常规注释结构更精确的结构信息对于共表达分析至关重要。我们的DSDE方法，拟南芥平铺阵列外显子版本2检测和过度表示分析(ARTADE2-ORA)，通过结合两种统计分析来精确预测每个基因结构：多个转录组测量的探针共表达分析和基因组序列的马尔可夫模型分析。ARTADE2-ORA成功识别了约90%的功能注释基因的真实功能，推测了98%的功能未知基因的功能，并预测了1489个新的基因结构和功能。我们开发了一个数据库ARTADE2DB，该数据库不仅集成了ARTADE2-ORA预测的信息，还集成了注释和其他功能信息，如表型和文献引用，有望为拟南芥功能基因组学的研究做出贡献。网址：http://artade.org..
Recent advances in technologies for observing high-resolution genomic activities, such as whole-genome tiling arrays and high-throughput sequencers, provide detailed information for understanding genome functions. However, the functions of 50% of known Arabidopsis thaliana genes remain unknown or are annotated only on the basis of static analyses such as protein motifs or similarities. In this paper, we describe dynamic structure-based dynamic expression (DSDE) analysis, which sequentially predicts both structural and functional features of transcripts. We show that DSDE analysis inferred gene functions 12% more precisely than static structure-based dynamic expression (SSDE) analysis or conventional co-expression analysis based on previously determined gene structures of A. thaliana. This result suggests that more precise structural information than the fixed conventional annotated structures is crucial for co-expression analysis in systems biology of transcriptional regulation and dynamics. Our DSDE method, ARabidopsis Tiling-Array-based Detection of Exons version 2 and over-representation analysis (ARTADE2-ORA), precisely predicts each gene structure by combining two statistical analyses: a probe-wise co-expression analysis of multiple transcriptome measurements and a Markov model analysis of genome sequences. ARTADE2-ORA successfully identified the true functions of about 90% of functionally annotated genes, inferred the functions of 98% of functionally unknown genes and predicted 1,489 new gene structures and functions. We developed a database ARTADE2DB that integrates not only the information predicted by ARTADE2-ORA but also annotations and other functional information, such as phenotypes and literature citations, and is expected to contribute to the study of the functional genomics of A. thaliana. URL: http://artade.org..