A new algorithm weighs in | Nature Reviews Genetics
A new algorithm weighs in | Nature Reviews Genetics"
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So, how does the GRAM algorithm work? First, it examines DNA-binding data and identifies sets of genes that are bound by common sets of transcriptional regulators. Next, it uses expression
data to identify a subset of the genes, the expression of which is highly correlated. Finally, the algorithm searches the DNA-binding data again, using less stringent criteria, to find more
genes of similar expression that are also bound by the same transcription factors.
The authors put the GRAM algorithm to the test in Saccharomyces cerevisiae by applying it to genome-wide location data for 106 transcription factors and >500 expression experiments — in this
way, they identified 106 sets of co-expressed genes that are bound by the same transcription factors. These so-called gene modules contain 655 genes and are regulated by 68 transcription
factors. Because gene modules link the common expression pattern of a set of genes to a set of regulators, the authors were also able to predict that 11 of the regulators were activators — a
finding that was confirmed by previous experimental work.
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