Analyzing Tag-Position Bias in MPSS Technology
Author Information
Author(s): Chen Junfeng, Rattray Magnus
Primary Institution: University of Manchester
Hypothesis
The position of the signature tag in a transcript affects the measurement of mRNA transcript abundance.
Conclusion
Tag-position bias should be considered when measuring mRNA transcript abundance using MPSS technology.
Supporting Evidence
- Classic MPSS data shows a greater percentage of low-count genes in the high tag-position range.
- Signature MPSS data shows a flatter relationship between tag-position and measured abundance.
- Tag-position bias is more significant in Arabidopsis compared to mRNA length and number of exons.
Takeaway
The position of tags in mRNA can change how much of it we think is there, so we need to be careful when measuring it.
Methodology
Nonlinear regression methods were used to analyze the relationship between tag-position and measured RNA abundance.
Potential Biases
Some MPSS tags could be mapped to more than one part of the genome, leading to potential inaccuracies.
Limitations
Not all genes can be identified using MPSS technology, and some may not appear in the library due to long distances between the 3' end and the first Sau3A site.
Participant Demographics
Data from Arabidopsis, rice, and human samples were analyzed.
Digital Object Identifier (DOI)
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