Avoiding inconsistencies over time and tracking difficulties in Applied Biosystems AB1700™/Panther™ probe-to-gene annotations -: art. no. 307
Avoiding inconsistencies over time and tracking difficulties in Applied Biosystems AB1700™/Panther™ probe-to-gene annotations -: art. no. 307
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DOI：
10.1186/1471-2105-6-307
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发表时间：
2005-12-22
影响因子：
3
通讯作者：
Benecke, A
中科院分区：
文献类型：
--
作者：
Noth, S;Benecke, A
背景：据报道，商业微阵列平台解决方案的不同版本的探针集标识符之间的探针到基因的注释之间存在显著的不一致。这些不一致导致了对已发表的基因表达结果的误导性或模棱两可的解释。结果：我们在这里报告了应用生物系统AB1700数据的探针到基因注释中的类似不一致，表明这不是一个孤立的问题。此外，在线信息源Panther不提供跟踪这种不一致所需的信息，因此，即使在Panther更新到新的探针到基因注释版本后重新提交正确注释的数据集，也会产生不同的结果，而没有任何关于更改来源的反馈。结论：明确注释对微阵列实验的重要性不可低估。不一致大大降低了这项技术的有用性。分析转录组图谱的新方法通常依赖于来自多个来源的大数据集。如果只能使用最不常见的子集进行分析，则这些方法的预测和分析能力会迅速减弱。我们在这里介绍了需要与原始AB1700数据一起提供的信息，以及为避免不一致和追踪困难而需要与此类数据的生物解释一起提供的信息。
Background: Significant inconsistencies between probe-to-gene annotations between different releases of probe set identifiers by commercial microarray platform solutions have been reported. Such inconsistencies lead to misleading or ambiguous interpretation of published gene expression results.Results: We report here similar inconsistencies in the probe-to-gene annotation of Applied Biosystems AB1700 data, demonstrating that this is not an isolated concern. Moreover, the online information source PANTHER does not provide information required to track such inconsistencies, hence, even correctly annotated datasets, when resubmitted after PANTHER was updated to a new probe-to-gene annotation release, will generate differing results without any feedback on the origin of the change.Conclusion: The importance of unequivocal annotation of microarray experiments can not be underestimated. Inconsistencies greatly diminish the usefulness of the technology. Novel methods in the analysis of transcriptome profiles often rely on large disparate datasets stemming from multiple sources. The predictive and analytic power of such approaches rapidly diminishes if only least-common subsets can be used for analysis. We present here the information that needs to be provided together with the raw AB1700 data, and the information required together with the biologic interpretation of such data to avoid inconsistencies and tracking difficulties.