A whole host of papers published Wednesday in Nature (as well as several other journals) show just how much we still have to learn about our favorite lab subjects.

In general, the researchers found, the systems that control gene activity are largely the same between mice and men. But the places where genes differ may help scientists explain the limitations of some studies that use mice.

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Wednesday's studies come from a research effort called Mouse ENCODE, an offshoot of the Encyclopedia of DNA Elements (ENCODE) which began in 2003. ENCODE catalogs elements of the human genome that guide cell function.

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Mouse ENCODE looked at over 100 mouse cell types and tissues, comparing them to their corresponding elements in humans.

"They're great model organisms, don't get me wrong, but there are definitely profound differences," said Michael Snyder, chair of genetics at Stanford, who co-authored the main paper. "At the end of the day, a mouse is a mouse and a human is a human, and pinning down where those differences occur is important."

He and his colleagues were surprised to find that certain mouse tissues had more in common with each other than with their human analogies, for example.

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"So a mouse liver is a lot more similar to a mouse kidney, in terms of gene expression, than a human liver, and that was a surprise," Snyder said. "In hindsight, this makes a lot of sense."

The genes that are more consistent across mouse tissue than when compared to the corresponding tissues in humans are those involved in metabolism, he said. Since a mouse heart beats 10 times faster than a human's, it's not hard to believe that the two organisms have very different metabolic systems.

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Mouse ENCODE's database will be an important tool for researchers hoping to learn about humans by using mice, Snyder said, but there's still a lot to learn.

"If this were an opera, we'd have a few bars of a few pieces. We're not seeing the whole show yet," he said.

But while researchers should be careful not to oversimplify the translation of mouse results to human implications, Snyder emphasized that the rodents were still incredibly important scientific tools.