Significant pathway enrichment of transcripts with outlier gene expression. The heatmap in the top panel provides the pathway enrichment scores for representative canonical pathways in each tumor sample and benign tissue showing that outlier transcript sets from different tumors converge on distinct cellular functions (pathway score = -log10(Benjamini-Hochberg adjusted P value); only pathway scores >1 (that is, B-H <0.1) are shown). Note pathway names truncated from 1Role of CHK Proteins in Cell Cycle Checkpoint Control, 2Cell Cycle: G2/M DNA Damage Checkpoint Regulation, 3Role of Pattern Recognition Receptors in Recognition of Bacteria and Viruses, 4Altered T Cell and B Cell Signaling in Rheumatoid Arthritis. The bottom panel provides explorations of several key pathways, highlighting the expression distribution of representative genes within those pathways across the entire tumor cohort (full list of outlier gene sets within enriched pathways in Additional file 1: Table S8). Tumors with outlier gene enrichment within a given pathway are represented by colored circles. Immunohistochemistry images show high Ki67 indices in three tumors reflecting the probable high proliferation rate of tumors with outlier gene enrichment within cell cycle-related pathways (for additional images with larger fields see Additional file 2: Figure S3).