Pan-cancer analysis of TCGA data reveals notable signaling pathways

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" The second interesting relationship is that the Calcium pathway hardly overlaps with the other six pathways. This is shown in Fig. 1b. The Calcium pathway was found to be notable in only ovarian and uterine cancer (Table 1). This result indicates that there might be a common region of aberrant signaling in these two cancers, which does not overlap with regions of aberrant signaling in other cancers."

Background

A signal transduction pathway (STP) is a network of intercellular information flow initiated when extracellular signaling molecules bind to cell-surface receptors. Many aberrant STPs have been associated with various cancers. To develop optimal treatments for cancer patients, it is important to discover which STPs are implicated in a cancer or cancer-subtype. The Cancer Genome Atlas (TCGA) makes available gene expression level data on cases and controls in ten different types of cancer including breast cancer, colon adenocarcinoma, glioblastoma, kidney renal papillary cell carcinoma, low grade glioma, lung adenocarcinoma, lung squamous cell carcinoma, ovarian carcinoma, rectum adenocarcinoma, and uterine corpus endometriod carcinoma.

Signaling Pathway Impact Analysis (SPIA) is a software package that analyzes gene expression data to identify whether a pathway is relevant in a given condition.......

..... To investigate this question of whether we could obtain meaningful results using large-scale gene expression data, Neapolitan et al. [14] analyzed the ovarian cancer TCGA data using both SPIA and CASA. In their analysis, they investigated 20 signaling pathways believed to be implicated in cancer and 6 randomly chosen pathways. They obtained significant results that the cancers believed to be implicated in cancer are the ones most likely to be implicated in ovarian carcinoma.

The study in [14] was only a proof of principle study. In this paper we present the results of a study that uses SPIA to investigate all 157 signaling pathways in the KEGG PATHWAY database.....