Errors in CGAP xProfiler and cDNA DGED: the importance of library parsing and gene selection algorithms

Background: The Cancer Genome Anatomy Project (CGAP) xProfiler and cDNA Digital Gene Expression Displayer (DGED) have been made available to the scientific community over a decade ago and since then were used widely to find genes which are differentially expressed between cancer and normal tissues. The tissue types are usually chosen according to the ontology hierarchy developed by NCBI. The xProfiler uses an internally available flat file database to determine the presence or absence of genes in the chosen libraries, while cDNA DGED uses the publicly available UniGene Expression and Gene relational databases to count the sequences found for each gene in the presented libraries. Results: We discovered that the CGAP approach often includes libraries from dependent or irrelevant tissues (one third of libraries were incorrect on average, with some tissue searches no correct libraries being selected at all). We also discovered that the CGAP approach reported genes from outside the selecte...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Andrew T. Milnthorpe, Mikhail Soloviev
• Keywords: Artificial Intelligence, BMCBI 2011, CGAP, Gene Expression, Libraries