Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips.
Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips.
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DOI：
10.1186/1471-2105-8-13
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发表时间：
2007-01-15
影响因子：
3
通讯作者：
Harrison, Andrew P
中科院分区：
文献类型：
--
作者：
Stalteri, Maria A;Harrison, Andrew P
Affyscore基因芯片技术可以并行观察数万个基因。重要的是，探针集注释是可靠的，以便可以对经历差异表达的基因进行生物学推断。代表相同基因的探针组可能预期显示相似的倍数变化/z分数，然而事实并非如此。我们对小鼠Surf 4进行了案例研究，之所以选择它是因为据报道，2004年初，Affytelum和Bioconductor在MOE 430 A阵列上用相同的8个探针组代表了该基因。只有五个探针组实际上检测到Surf 4转录本。两个探针组检测Surf 2的剪接变体。我们还研究了在一个公共领域的微阵列实验中的八个探针集的表达变化。Surf 4的转录本在时间上是相关的，类似地，Surf 2的转录本也在时间上是相关的。然而，Surf 4和Surf 2的转录本不相关。这一原理证明表明，对表达的观察可以用来确认或以其他方式确认注释差异。我们还研究了RAE 230 A阵列上的探针组，这些探针组被分配到相同的LocusID，但在大鼠的三个不同实验中的任何一个中显示出差异表达的较大差异。发现具有高方差的探针集组代表选择性剪接、使用选择性poly（A）信号或不正确注释的情况。我们的研究结果表明，一些探针集不应被视为独特的措施，转录，因为个别探针映射到一个以上的转录依赖于生物条件。我们的研究结果强调了在评估探针组是否都测量相同的转录本时需要小心。
Affymetrix GeneChip technology enables the parallel observations of tens of thousands of genes. It is important that the probe set annotations are reliable so that biological inferences can be made about genes which undergo differential expression. Probe sets representing the same gene might be expected to show similar fold changes/z-scores, however this is in fact not the case. We have made a case study of the mouse Surf4, chosen because it is a gene that was reported to be represented by the same eight probe sets on the MOE430A array by both Affymetrix and Bioconductor in early 2004. Only five of the probe sets actually detect Surf4 transcripts. Two of the probe sets detect splice variants of Surf2. We have also studied the expression changes of the eight probe sets in a public-domain microarray experiment. The transcripts for Surf4 are correlated in time, and similarly the transcripts for Surf2 are also correlated in time. However, the transcripts for Surf4 and Surf2 are not correlated. This proof of principle shows that observations of expression can be used to confirm, or otherwise, annotation discrepancies. We have also investigated groups of probe sets on the RAE230A array that are assigned to the same LocusID, but which show large variances in differential expression in any one of three different experiments on rat. The probe set groups with high variances are found to represent cases of alternative splicing, use of alternative poly(A) signals, or incorrect annotations. Our results indicate that some probe sets should not be considered as unique measures of transcription, because the individual probes map to more than one transcript dependent upon the biological condition. Our results highlight the need for care when assessing whether groups of probe sets all measure the same transcript.