Functional annotation prediction: all for one and one for all

In an era of rapid genome sequencing and high-throughput technology, automatic function prediction for a novel sequence is of utter importance in bioinformatics. While automatic annotation methods based on local alignment searches can be simple and straightforward, they suffer from several drawbacks, including relatively low sensitivity and assignment of incorrect annotations that are not associated with the region of similarity. ProtoNet is a hierarchical organization of the protein sequences in the UniProt database. Although the hierarchy is constructed in an unsupervised automatic manner, it has been shown to be coherent with several biological data sources. We extend the ProtoNet system in order to assign functional annotations automatically. By leveraging on the scaffold of the hierarchical classification, the method is able to overcome some frequent annotation pitfalls.     

The chromosomal passenger complex: one for all and all for one

The chromosomal passenger complex-composed of Aurora B kinase and its regulatory subunits INCENP, Survivin, and Borealin-modulates multiple events during mitosis. In this issue, Jeyaprakash et al. (2007) report the crystal structure of the regulatory subunit complex and reveal how interactions between these proteins promote the targeting and function of the chromosomal passenger complex during mitosis.     

A cluster-gene: evidence for one gene, one polypeptide, five enzymes.

Experiments with mice show that the pre-carcinogen vinyl chloride is metabolically converted to a short-lived alkylating intermediate which introduces the 2-oxoethyl group onto nucleophilic sites in DNA and proteins. The absolute and relative amounts of alkylated products support the hypothesis that the main reactive metabolite is chloroethylene oxide.     

A Group Sequential Method for one Standard Control and more than one Experimental Treatment

Many group-sequential test procedures have been proposed to meet the ethical need for interim analyses. All of these papers, however, focus their discussion on the situation where there are only one standard control and one experimental treatment. In this paper, we consider a trial with one standard control, but with more than one experimental treatment. We have developed a group-sequential test procedure to accommodate any finite number of experimental treatments. To facilitate the practical application of the proposed test procedure, on the basis of Monte Carlo simulation, we have derived the critical values of α-levels equal to 0.01, 0.05 and 0.10 for the number of experimental treatments ranging from 2 to 4 and the number of multiple group sequential analysis ranging from 1 to 10. Comparing with a single non-sequential analysis that has a reasonable power (say, 0.80), we have demonstrated that the application of the proposed test procedure may substantially reduce the required sample size without seriously sacrificing the original power.     

MPN tables for more than one test

Summary MPN tables are presented, restricted to those tube combinations that are acceptable considering the number of tests performed (1, 2, 3, 5, or 10). Confidence limits of 95 and 99% are given for each result.