ConceptGen: A gene set enrichment and gene set relation mapping tool Concept Building

Gene Ontology, KEGG pathway, Biocarta Pathway, Panther Pathway, and Pfam information were downloaded from their respective sources. For Pfam, Uniprot IDs were mapped to Entrez Gene IDs, thus resulting in all transcripts for a gene being mapped to the same Pfam terms. Chromosomal location was determined by NCBI cytoband assignment, and gene expression signatures were defined as detailed below. Testing cytobands allows one to identify differential expression clustered in a particular location, possibly indicating copy number change in that cytoband. Testing gene expression signatures enables one to identify combinations of processes/pathways that are not will characterized by any other concept type. The additional concept types were built as detailed here.