I would appreciate if someone can help me understand the TCGA. I recently read a paper in PNAS (2015) where the authors used the TCGA database to report that a low expression of a particular gene in breast cancer was associated to poor survival.
Does anyone know:
1. how do such database gather data on genetic differences in cancer vs normal tissues. Do they conduct genetic experiments on thousands of cancer tissues vs normal tissues and make the data pubically available. Who funds these projects? The TCGA has data describing tumor tissue and matched normal tissues from more than 11,000 patients.
2. how to use the TCGA. Do we need computational biology knowledge to dig out data from the database. Example, how can I dig out expression and survival data of my gene of interest.