Gene expression analysis in bladder cancer cells lines

We have previously characterized two groups of bladder cancer cell lines based on their dependence on Hedgehog signaling for survival. Here, we examined the global gene expression in these cells. By comparing the gene expression profile within and between these two groups of cells, we identified list of genes and pathways that potentially account for their dependence on Hedgehog signaling, and specifically a gene signature for those cells more dependent to HH signaling for proliferation. We analized four different bladder cancer cell lines: J82, HT1376, T24, and Vmcub1. We performed triplicates of each sample, and completed a Hierarchical Condition Clustering, a Principal Component Analysis, and we also applied statistical analysis to identify genes that are differentially expressed between the different cell lines. We also put these lists of statistically significant genes into a biological context by performing Pathway Analysis.