PMC

Curation of gene signatures in GeneSigDB. (A) GeneSigDB hierarchical file structure SigID.txt, SigID-mapping.txt, SigID-maptrace.txt, SigID-standardized.txt and SigID-index.xml. These files are respectively, the original gene signature, the mappable gene identifiers from SigID.txt, the mapping-trace showing how each gene was mapped, a list of EnsEMBL gene identifiers that correspond to genes in SigID.txt, and xml annotation of SigID.txt. (B) An example xml gene signature annotation file.

Visualization of gene overlap in gene signatures. In this example, we searched for Fanconi anemia-related genes by performing a gene search for FANC* which returned 12 human genes and 2 mouse genes. This screen shows the overlap between gene signatures in which these 12 genes are present in at least 2/12. Red and grey boxes indicate presence or absence, respectively.

Overlap in gene signatures across tumor types. (A) Heatmap-style representation of gene overlap. Each row is a gene and each column is a tissue type. Presence of a gene is indicated by a black line, and absence is white. It can be seen that some gene maybe linked to phenotypic subclasses in many tumors, but there are generally many more tumor-specific genes, likely indicating the effect of the tissue of origin. (B) Dendrogram of hierarchical cluster analysis that was performed using a Sorensen's coefficient asymmetrical measure of binary distance and joined using Ward's minimum variance method.