Microarray analysis demonstrates differences in gene expression associated with tumor behavior. Serous tumors (28 invasive, 7 low malignant potential (LMP) and 7 benign) were compared with four normal whole ovaries. (A) Unsupervised hierarchical clustering analysis of 3,197 transcripts exhibiting highest variance (SD ≥ 0.5) shows similar gene expression levels in low malignant potential and invasive tumors compared with differential expression in normal ovarian and benign tumor tissues (blue = normal ovaries; yellow = benign; green = low malignant potential; red = invasive). (B) Hierarchical clustering of 456 transcripts selected from ANOVA analysis (p < 0.01, Benjamini and Hochberg FDR multiple testing correction applied, Additional file 3 for genes and details) further illustrates similar gene expression profiles exhibited by low malignant potential and invasive tumors as compared with normal ovaries and benign tumors. (C) Pair-wise comparisons between invasive tumors and low malignant potential or benign tumors (p < 0.01, Benjamini and Hochberg FDR multiple testing correction applied) identified 20 differentially expressed genes between invasive and low malignant potential tumors and 311 genes that differed in expression between invasive and benign tumors. (D) Differential expression as detected by microarrays is demonstrated for six selected genes in serous tumors exhibiting differences in behavior. Box and whisker plots depict the median (line), interquartile range (box) and error bars demonstrate the full range of the data, excluding outliers and extreme values which are represented individually.