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Maps like Ideker’s can be used not only to provide new therapeutic targets but also to help researchers understand how drugs already being prescribed actually work. James Collins, professor of biomedical engineering at Boston University, says “drug companies are good at seeing if their drug hits its molecular target,” but, beyond that, they don’t investigate what the drug compound affects. Collins says Ideker is “laying a nice foundation for finding out how drugs interact with cells.”

A better understanding of all the molecular-level effects of drugs would give insights into their side effects and also help researchers understand how drugs might be combined for a double whammy. If two drugs have an effect on two different parts of the DNA repair pathway, for example, they could be given to a cancer patient concurrently.

Ideker says he’s expanding on this work to find out what influences the transcription factors in his map have before they start interacting with DNA. Richard Pelroy, program director in the DNA and Chromosome Aberrations Branch of the NCI’s Division of Cancer Biology, says that what happens after genes are expressed is also an important avenue to explore. Ideker’s approach is based on the regulation of gene expression, he says, “but so much happens after genes are expressed.” Many proteins aren’t active the instant they’re made, but must be modified by other proteins.

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