3.2.3. Pathways that Are Differentially Expressed between Normal Lung Tissue and Squamous Cell Carcinoma
Two datasets are available to compare the transcriptomes of normal lung tissue and squamous cell carcinoma, E-GEOD-6044 and E-GEOD-40275. The E-GEOD-6044 data shows a similar profile to the normal-adenocarcinoma pathway profile for E-GEOD-40275 including the TCF dependent signaling in response to Wnt (Supplementary Figures S2–S4). There are also shared pathways with the normal-adenocarcinoma analysis of the same dataset. The results suggest that squamous cell carcinoma has an affect on a more diverse range of pathways than adenocarcinoma.
The E-GEOD-40275 normal-squamous cell carcinoma comparison identifies platelet associated pathways as well as RNA processing as the most important groups of differentiated pathways (Figure 6). These overlap with the pathways identified in the normal-adenocarcinoma comparison carried out with the same dataset and also the normal-adenocarcinoma pathway differences identified using the E-GEOD-6044 data.
Figure 6  Pathway analysis for E-GEOD-40275, Normal-Squamous Cell Carcinoma.

3