FIG 3.

Exploring OncoMX for an individual gene biomarker: Findings for PCA3 in prostate cancer. (A) The OncoMX landing page provides quick access to the search bar. Entering “PCA3” will redirect the user to the search results page. (B) The default open tab of the top viewer in the search results page shows mRNA differential expression results for the queried gene across all cancers. PCA3 is shown to be upregulated in 94% of prostate cancer tumor samples compared with the corresponding adjacent normal samples. (C) Tabular and text details are also available in the lower viewer on the search result pages. Exploring the quantitative information shows that 49 of 52 samples have a logtwo-fold change increase of expression in tumor samples compared with the adjacent normal, and that the overexpression reported for prostate cancer is statistically significant. (D) Text details, including a list of biomarker aliases, a brief description, and a list of links to publications reported by Early Detection Research Network (EDRN), are available from the Biomarkers tab in the lower viewer. (E) Healthy expression of PCA3 is found to be “MEDIUM” in earlier human adult stages but “HIGH” in the 65- to 79-year-old human stage. (F) Automatic literature mining finds 16 unique sentences from 15 unique publications reporting overexpression of PCA3 in prostate cancer and another sentence reporting overexpression of PCA3 in leiomyosarcoma. FDA, US Food and Drug Administration; PSA, prostate-specific antigen; RNA-seq, RNA sequencing; TCGA, The Cancer Genome Atlas.