Wednesday, May 6, 2009

Annotation evaluation

A few years ago, a friend of mine was an author on an article about global gene coexpression analysis. In the article, they looked across many experiments to find pairs of genes that consistently shared patterns of expression (indicating likely co-regulation). As one of the validations of their globally co-expressed gene-pairs, they measured whether or not the sets were also co-annotated with the same biological process label from the gene ontology. The idea being that if they were co-expressed they should be more likely to belong to the same biological process.

This suggested to me at the time that this kind of analysis might somehow be turned on its head to provide evidence regarding the quality of the annotations themselves. Basically each annotation would be treated as a hypothesis and then continually subjected to testing. So the assertion GeneA is part of Biological Process Y would be strengthened if GeneB was co-expressed with GeneA and was also a part of the same biological process. I imagine there would be many other forms of such evidence.

Just wanted to jot that down..