In an education piece in PLoS Computational Biology, Ewan Birney's group gives some data mining solutions, particularly for using BioMart. First, the team describes how to use BioMart to join two different datasets to come up with a list of human carbohydrate metabolism enzymes. Then they walk the reader through scripts to use with BioConductor to query relevant databases. Finally, they give a glimpse into Galaxy and how it can be used to search for a certain motif. Researchers led by Olga Troyanskaya report combining information from a variety of genome-scale and individual mouse studies to create a global functional network for mice that includes linkages among 20,581 protein-coding genes. They also show by studying the Nanog homeobox gene that the network can predict novel functional assignments. A Web-based version of their tool is available here. In PLoS ONE, European researchers say that oncogenes are hypermethylated in human embryonic stem cells. They compared the DNA promoter methylation patterns of 807 cancer-related genes in hESCs, differentiated adult tissues, and cancer cell lines. Their results suggest that DNA methylation is involved in gene expression in human stem cells. Michel Morange reviews a new book, called Rebels, Mavericks, and Heretics in Biology, in PLoS Biology, that aims to examine biology from the perch of the 'rebels.' That list includes: Alfred Russel Wallace, Barbara McClintock, Oswald Avery, Carl Woese, Stephen Jay Gould, and more.
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