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Carnegie Mellon U. transforms DNA microarrays with standard Internet communications tool

ul, they present a sampling problem," Bar-Joseph said. "DNA microarrays only take static snapshots of gene activity over time. In between these snapshots, genes could be activated and we just don't see them turning on. Our protocol will offer greater overall sensitivity in detecting the expression of any gene, even if a gene turns on when no microarray sampling takes place."

Bar-Joseph's procedure is based on a "check-sum" protocol initially developed to ensure that email messages sent via the Internet don't become garbled in transmission. In the standard Internet check-sum protocol, bits of information that begin as one value (0 or 1) may inadvertently flip to the opposite value as they move from one computer to the next in the form of an email. This data loss, ascribed to noise in the communication channel, is checked by counting the number of 1's in the message. If this number is odd, then the last bit is set to 1; otherwise it is set to 0. By comparing the number of 1's on the sending end with the value of the last bit on the receiving end, the recipient's computer can determine whether the message was accurately received. If not, the recipient's computer asks the sender's computer to forward the message again.

Bar-Joseph's method carries out a similar analysis of the microarray snapshots by "checking" the sum of a set of DNA microarray data points over time (a time series experiment) against the "summary" of the temporal response. If the two sets of results are equal, then what is captured by the DNA microarray time series is real. If the time series results produce a lower value than the microarray summary, the protocol indicates that the researchers have missed a gene's activation somewhere in their time series.

Just as important, according to Bar-Joseph, is whether a DNA microarray summary value exceeds its time sequence value. If that's the case, then researchers have likely identified gene activity that should be attributed to chang
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Source:Carnegie Mellon University


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