3.2.2. Pathways that Are Differentially Expressed between Normal Lung Tissue and Adenocarcinoma
Three datasets have a comparison between normal lung tissue and adenocarcinoma: E-GEOD-6044, E-GEOD-40725 and E-GEOD-43458. Of these the E-GEOD-43458 dataset is the largest and it is the only one that was specifically targeted to adenocarcinoma.
The smallest of these datasets is E-GEOD-6044. This array also used the hgfocus gene array and not the more complete hgu133a array. From the rma and farms normalized data less than 10 pathways were identified and these were: biological oxidation; axon guidance; hemostasis; platelet activation, signaling and aggregation; platelet degranulation; translation of GLUT4 to the plasma membrane; response to elevated platelet cytosolic Ca2+; L1CAM interactions; phase 1-functionalisation of compounds; membrane trafficking and extracellular matrix organization. It is noteworthy that none of these pathways were amongst those identified as differences between the normal and tumor tissues and that they are not involved in cell cycle or DNA regulation. Phase 1-functionalisation is the processing and export of proteins from the endoplasmic reticulum and the reactions involve cytochrome P-450. Sugar transporters have previously been identified as having a role in cancer [37]. The L1 cell adhesion molecule L1CAM is associated with invasive tumors and metastasis [38,39]. After gcrma normalization pathway analysis identifies over 40 significant pathways (Supplementary Figure S1). These include the DNA regulation, mitotic pathways and cell cycle pathways previously identified in the normal-tumor comparisons. It also includes the meiosis pathways, negative regulation of rRNA expression and amyloids.
The E-GEOD-40275 dataset uses an exon array and so it can only be normalized using rma. The results of pathway analysis are very different from those for the E-GEOD-6044 dataset and the normal‑tumor analysis. These include a number of cancer specific pathways involving mutants and also a group of pathways involved in mRNA regulation and processing (Figure 5).
Figure 5  Pathway Analysis for E-GEOD-40275, Normal-Adenocarcinoma.   The E-GEOD-43458 dataset could only be normalized with rma and farms as gcrma is incompatible with the array type used. The results from the pathway analysis have been shown in Figure 2. As stated above there is a large difference in the number of pathways identified between the two analyses, with many more differentially expressed pathways after farms normalization. Many of them are previously identified pathways involved in cell cycle regulation and mitosis. Amyloids appear in both of the pathway analyses and they were identified in the gcrma normalized pathway analysis of E-GEOD-6044. Serum amyloid a protein has been known for some time to be a biomarker for lung cancer and nasopharyngeal cancer [40,41]. Signaling pathways including the Rho GTPases, Wnt and TCF are also present in the post-farms pathway analysis. These signaling pathways have previously been associated with cancer, although TCF has mainly been associated with colorectal cancers [42,43,44,45,46]. The L1CAM pathway is also identified as being significant in agreement with the results from E-GEOD-6044.