UCSC Browser Research Articles

Hedgehogs, humans and high‐school science

The ‘Lisbon strategy’, adopted by the member states of the European Union (EU) in 2000, aims to make Europe the most dynamic and competitive knowledge‐based economy in the world by 2010. The overall aim is to increase the levels of investment that member states put into scientific research up to and beyond 3% of their Gross Domestic Product. Although this aim will certainly not be met in the expected timeframe, it is noble and important nonetheless. > …even if the members of the EU increase investment into research, it will be in vain if they do not also work to increase the number of researchers However, even if the members of the EU increase investment into research, it will be in vain if they do not also work to increase the number of researchers. Indeed, the current number of researchers per 100,000 citizens in the EU is considerably lower than the figure for the USA or Japan. As scientists, we have virtually no possibility to influence how much money our governments spend on research and development, but we can have a much more active role in making science a more attractive career option for young people—notably high‐school students. Various projects and initiatives in EU countries and the USA have sought to achieve this aim by forging closer links between schools and universities or research institutes. Here, we describe the Cus‐Mi‐Bio (Centre University School of Milan for Bioscience Education; www.cusmibio.unimi.it) project that was developed at the University of Milano, Italy. The project's aim is to raise the levels of interest and enthusiasm of high‐school students for the life sciences, and hopefully to attract some of them to a career in science. There are various negative perceptions of science that need to be overcome when persuading students that it is a worthy career …

GENCODE: producing a reference annotation for ENCODE

BackgroundThe GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results.ResultsThe GENCODE gene features are divided into eight different categories of which only the first two (known and novel coding sequence) are confidently predicted to be protein-coding genes. 5' rapid amplification of cDNA ends (RACE) and RT-PCR were used to experimentally verify the initial annotation. Of the 420 coding loci tested, 229 RACE products have been sequenced. They supported 5' extensions of 30 loci and new splice variants in 50 loci. In addition, 46 loci without evidence for a coding sequence were validated, consisting of 31 novel and 15 putative transcripts. We assessed the comprehensiveness of the GENCODE annotation by attempting to validate all the predicted exon boundaries outside the GENCODE annotation. Out of 1,215 tested in a subset of the ENCODE regions, 14 novel exon pairs were validated, only two of them in intergenic regions.ConclusionIn total, 487 loci, of which 434 are coding, have been annotated as part of the GENCODE reference set available from the UCSC browser. Comparison of GENCODE annotation with RefSeq and ENSEMBL show only 40% of GENCODE exons are contained within the two sets, which is a reflection of the high number of alternative splice forms with unique exons annotated. Over 50% of coding loci have been experimentally verified by 5' RACE for EGASP and the GENCODE collaboration is continuing to refine its annotation of 1% human genome with the aid of experimental validation.