The demonstration cases described below feature published microarray gene-expression data. They were converted to ranked lists by calculating t-test P-values between the relevant sample types (classes) for each probe, that were log10-transformed and signed to indicate direction of change (positive for increased in Class B, negative for increased in Class A or decreased in Class B). Probes were annotated with current mouse or human UniGene identifiers and homologs were identified using HomoloGene; only the probe with the highest absolute signed t-test P-value within those with matching UniGene identifiers was kept in the collapsing step. Data downloaded from Gene-expression Omnibus (GEO) (19 (link)): MPAKT prostate cancer mouse model, GSE1413; breast tumors with ER, PR and HER2 status, GSE2603; MMTV-HER2/neu mouse model, GSE2528; BCR-ABL transfected cell line, GSE10912; mammary stem cell, GSE3711; KRAS2 overexpression cell line, GSE3151; lung tumors with KRAS2 status, GSE3141; imatinib treatment in leukemia patients, GSE2535; dasatinib treatment in cell lines, GSE9633 and GSE6569; castration and testosterone treatment in mice, GSE5901; gedunin treatment in prostate cancer cell line, GSE5506. Data downloaded from Array Express (20 (link)): imatinib treatment in leukemia patients, E-MEXP-433 (21 (link)). Data downloaded from an individual lab website: KRAS2 lung tumors and mouse model (1 (link)), Cmap database (10 (link)). Data communicated by collaborators: PTEN knockout prostate cancer mouse model, Dr Shunyou Wang, laboratory of Dr Hong Wu, UCLA (22 (link)).