Microarray and EST database estimates of mRNA expression levels differ: the protein length versus expression curve...

Area of Science:

• Genomics
• Bioinformatics
• Evolutionary Biology

Background:

• Estimating gene expression levels is crucial but existing methods show fair correlation and potential systematic biases.
• Gene length is a suspected factor influencing the accuracy of gene expression rate estimations.
• Conflicting reports exist on the relationship between C. elegans protein length and expression level, depending on the estimation method used.

Purpose of the Study:

• To investigate systematic biases in gene expression rate estimation using microarray and Expressed Sequence Tag (EST) data.
• To determine the relationship between C. elegans protein length and gene expression level.
• To resolve discrepancies in previous findings regarding protein length and expression level.

Main Methods:

• Analyzing gene expression rates using microarray data.
• Analyzing gene expression rates using abundance within the Expressed Sequence Tag (EST) database.
• Constructing protein length versus expression level curves for C. elegans using both methods.

Main Results:

• Microarray data indicated a monotonic decrease in length with expression level.
• EST data showed a non-monotonic relationship between length and expression level.
• A systematic bias related to gene length was observed in the ratio of expression levels estimated by EST to microarray data.

Conclusions:

• The length bias appears to stem primarily from the EST abundance method, unlike microarray data.
• Removing length bias reconciles findings from both methods, showing a monotonic decrease in spliced length with expression level.
• Standard RNA controls are recommended for normalizing length bias in gene expression measurements.