Bioinformatics core facility

Analysis of datasets generated by high‑throughput sequencing and microarrays has continued to be a major focus for the Bioinformatics Core. In the past year, our team has supported a large number of research projects by consulting with scientists, providing input into experimental design, analysing the raw data generated and helping with interpretation of the results. Illumina BeadChip expression arrays and ChIP-seq projects run on the Illumina Genome Analyzer and HiSeq sequencers remain the most popular applications requiring support from the Core, but we have also contributed to projects involving copy number profiling using SNP arrays, exon arrays, amplicon resequencing for SNP analysis, chromosome conformation capture, and resequencing to explore structural variation in cancer genomes.

Throughout the year, we have been running weekly experimental design sessions, jointly with the Genomics Core for genomics projects, and recently have extended the scope of these to cover other technologies. We also run a weekly statistics clinic providing help with the statistical aspects of a wide range of experiments and research questions.

We have continued to develop our analysis pipeline for Illumina BeadChip expression arrays and have tailored our training course in microarray analysis to better reflect the typical interaction of CRI scientists with the Core, placing emphasis on experimental design issues and interpretation of the output from the pipeline. We are also developing an analysis pipeline for ChIP-seq experiments incorporating multiple peak callers to give a high confidence consensus set of locations for DNA-bound proteins or epigenetic marks.

Figure 1
ChIP-seq analysis of histone methylation marks, H3K9me3 and H3K27me3, in human diploid fibroblast cells.

In the coming year, we anticipate increasing demand for downstream bioinformatics support for proteomics data. Working closely with the Proteomics Core, we have assisted with the analysis and visualization of SILAC pulse‑chased mass spectrometry data to investigate protein turnover rates; these are time-course experiments in which incorporation rates for labelled peptides are quantified and anomalous turnover patterns identified.

A further aspect of the Core's work involves maintenance of local installations of key bioinformatics databases and applications, including Galaxy, a web application that enables researchers to carry out their own analyses and the Core to deploy analysis and visualization tools developed in-house.

Finally, in 2010 the Core ran training courses on functional and network analysis, motif searching, and microarray analysis, and a seminar series on next generation sequencing.

Facility manager
Matthew Eldridge is head of the Bioinformatics core facility.