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: A typical query is shown in Figure 1 where we can investigate differences in specimen histological types using the transcriptomics profiling module. Here we investigate the differences between Invasive Lobular Carcinoma (ILC) and normal lobular cells and obtain a list of 175 transcripts of significance and related pathways (Figure 1). The portal allows multiple further filtering to enhance this initial query if required. For example, we can intersect this output to see if any of these genes appear in the Parker PAM 50 gene set (17) and extract related upstream sequences (Supplementary Figure S1).
Affiliation: Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.