BCCTBbp: the Breast Cancer Campaign Tissue Bank bioinformatics portal.
Bottom Line: By recording a large number of annotations on samples and studies, and linking to other databases, such as NCBI, Ensembl and Reactome, a wide variety of different investigations can be carried out.Additionally, BCCTBbp has a dedicated analytical layer allowing researchers to further analyse stored datasets.A future important role for BCCTBbp is to make available all data generated on BCCTB tissues thus building a valuable resource of information on the tissues in BCCTB that will save repetition of experiments and expand scientific knowledge.
Affiliation: Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.Show MeSH
Related in: MedlinePlus
Mentions: Four analysis categories can be performed: Molecular Classification; Tumour Purity; Gene Expression; and Survival. Each of the included dataset samples can be classified based on the PAM50 set of markers (15) or the hormonal receptor status can be inferred from the transcriptome using the MCLUST R package (http://cran.r-project.org/web/packages/mclust/). Cancer samples frequently contain a small proportion of normal adjacent tissue that might confuse sample analysis. A method to infer sample cancer purity is implemented using ESTIMATE (16). Gene expression plots can be obtained for a gene of interest (Figure 3). Finally, for datasets that contain patient survival information, survival analysis can be performed using the ‘survival’ package in R (http://cran.r-project.org/web/packages/survival/). Two modes are available, survival based on sample sub-groups within the dataset or survival based on the expression value of a gene of interest. In the gene-based survival analysis, two classes of gene expression values (high and low) are determined based on the median expression value (Figure 3).
Affiliation: Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.