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With a flood of cancer genome sequences expected soon, distinguishing 'driver' from 'passenger' mutations will be an important task. Wang et al. describe a bioinformatic method for identifying cancer-associated fusions and apply it to discover a recurrent rearrangement in lung cancer.
Modulatory proteins ensure that transcription factors are active when and where they should be. Wang et al. describe an algorithm for identifying modulators from a compendium of gene expression profiles and experimentally validate four diverse modulators of the MYC oncogene in human B cells.
Although multiple reaction monitoring (MRM) mass spectrometry holds considerable promise for quantifying candidate protein biomarkers in blood, transferability of MRM assays between laboratories has never been shown. Addona et al. assess the reproducibility, dynamic range and limits of detection and quantification of MRM across multiple sites.
Transfection of siRNAs and miRNAs into cells has been observed to generate unexpected effects in the form of gene upregulation. By statistically analyzing published transfection experiments, Khan et al. explain these effects with a model that the transfected RNAs compete with miRNAs naturally expressed by the cell.