Analysis of tag-position bias in MPSS technology.
Analysis of tag-position bias in MPSS technology.
复制标题
MPSS技术中标签位置偏差的分析。
DOI：
10.1186/1471-2164-7-77
复制
发表时间：
2006-04-07
期刊：
影响因子：
4.4
通讯作者：
Rattray, Magnus
中科院分区：
文献类型：
--
作者：
Chen, Junfeng;Rattray, Magnus
大规模平行特征测序（MPSS）技术是最近发展起来的一种高通量技术，用于测量样品中mRNA转录物的浓度。以前已经观察到，转录物中签名标签的位置（与3′端的距离）会影响测量，但这种影响尚未得到详细研究。我们利用拟南芥、水稻和人类的公开数据，量化了经典和签名MPSS技术中标签位置偏差的影响。我们使用非线性回归方法研究了测量浓度与标签位置之间的关系。所观察到的关系在不同的数据集之间是大致一致的。我们发现经典MPSS数据和签名MPSS数据都存在不同的显著偏差。在Classic MPSS数据中，标签位置在中间范围的基因平均测量丰度最高，而标签位置在远离3'端的高范围的基因测量丰度显著降低。对于签名MPSS数据，高范围标签位置基因倾向于在标签位置和测量丰度之间有一个平坦的关系。因此，我们的结果证实，签名MPSS方法解决了经典MPSS方法的一个实质性问题。对于经典和签名MPSS数据，低范围标签位置基因的测量丰度和标签位置之间存在正相关。与mRNA长度和外显子数量的影响相比，标签位置偏倚在arabadops中似乎更为显著。标签位置偏差既反映在具有显著标签计数的基因的测量丰度上，也反映在未表达基因的鉴定比例上。在经典和签名MPSS方法中，使用MPSS技术测量mRNA转录物丰度时应考虑标签位置偏差。
Massively Parallel Signature Sequencing (MPSS) technology was recently developed as a high-throughput technology for measuring the concentration of mRNA transcripts in a sample. It has previously been observed that the position of the signature tag in a transcript (distance from 3' end) can affect the measurement, but this effect has not been studied in detail. We quantify the effect of tag-position bias in Classic and Signature MPSS technology using published data from Arabidopsis, rice and human. We investigate the relationship between measured concentration and tag-position using nonlinear regression methods. The observed relationship is shown to be broadly consistent across different data sets. We find that there exist different and significant biases in both Classic and Signature MPSS data. For Classic MPSS data, genes with tag-position in the middle-range have highest measured abundance on average while genes with tag-position in the high-range, far from the 3' end, show a significant decrease. For Signature MPSS data, high-range tag-position genes tend to have a flatter relationship between tag-position and measured abundance. Thus, our results confirm that the Signature MPSS method fixes a substantial problem with the Classic MPSS method. For both Classic and Signature MPSS data there is a positive correlation between measured abundance and tag-position for low-range tag-position genes. Compared with the effects of mRNA length and number of exons, tag-position bias seems to be more significant in Arabadopsis. The tag-position bias is reflected both in the measured abundance of genes with a significant tag count and in the proportion of unexpressed genes identified. Tag-position bias should be taken into consideration when measuring mRNA transcript abundance using MPSS technology, both in Classic and Signature MPSS methods.
登录
查看更多内容
影响因子：
64.5
作者：
Velculescu, VE;Zhang, L;Kinzler, KW
通讯作者：
Kinzler, KW
影响因子：
8.6
作者：
Furusawa, C;Kaneko, K
通讯作者：
Kaneko, K
DOI：
10.1073/pnas.0406555102
发表时间：
2005-02-01
影响因子：
11.1
作者：
Stolovitzky, GA;Kundaje, A;Roach, JC
通讯作者：
Roach, JC
影响因子：
7
作者：
Meyers, BC;Tej, SS;Decola, S
通讯作者：
Decola, S
影响因子：
5.8
作者：
Akmaev, VR;Wang, CJ
通讯作者：
Wang, CJ