Biomedical subjects

Paul Lyons

Publications and source records attributed to Paul Lyons.

2 recordsLinked to original sources

PubMed2003

Advances in spotted microarray resources for expression profiling.

The new millennium has ushered in a new era in human biology. The elucidation of the human genome sequence, together with those of model organisms, provides us with an unprecedented insight into the makeup of our genetic blueprint. The challenge now is to figure out how all the constituent pieces fit together to form the whole picture, and the consequences of what happens when the process goes awry. One experimental tool that has the potential to provide enormous insights into this complex process is expression profiling using microarrays. The past few years have seen a considerable growth in the availability and use of microarrays. Fuelled in part by the many genome projects currently underway, there has been a large increase in the number of organisms for which microarray reagents are available from both commercial and academic sources. In addition to the increasing number of genome-wide probe sets that are available, a significant amount of attention has been focussed on generating more targeted probe sets that focus in on specific pathways or biological processes. Finally, the microarray field is starting to see a shift away from the use of cDNAs or polymerase chain reaction (PCR) products as probes towards the use of 50-70mer oligonucleotide probes with all of the potential advantages that they offer. The aim of this review is to provide an overview of what is currently available in terms of spotted microarray reagents both with respect to pre-made arrays and to probe sets available for arraying.

Computational Biology↗

PubMed2003

Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia.

We report the construction of the mouse full-length cDNA encyclopedia,the most extensive view of a complex transcriptome,on the basis of preparing and sequencing 246 libraries. Before cloning,cDNAs were enriched in full-length by Cap-Trapper,and in most cases,aggressively subtracted/normalized. We have produced 1,442,236 successful 3'-end sequences clustered into 171,144 groups, from which 60,770 clones were fully sequenced cDNAs annotated in the FANTOM-2 annotation. We have also produced 547,149 5' end reads,which clustered into 124,258 groups. Altogether, these cDNAs were further grouped in 70,000 transcriptional units (TU),which represent the best coverage of a transcriptome so far. By monitoring the extent of normalization/subtraction, we define the tentative equivalent coverage (TEC),which was estimated to be equivalent to >12,000,000 ESTs derived from standard libraries. High coverage explains discrepancies between the very large numbers of clusters (and TUs) of this project,which also include non-protein-coding RNAs,and the lower gene number estimation of genome annotations. Altogether,5'-end clusters identify regions that are potential promoters for 8637 known genes and 5'-end clusters suggest the presence of almost 63,000 transcriptional starting points. An estimate of the frequency of polyadenylation signals suggests that at least half of the singletons in the EST set represent real mRNAs. Clones accounting for about half of the predicted TUs await further sequencing. The continued high-discovery rate suggests that the task of transcriptome discovery is not yet complete.

Animals↗