Finding biological process modifications in cancer tissues by mining gene expression correlations

Additional File 3: This .csv file contains data for Table 5 – Relations in HCC. In this table are reported all the well-correlated gene pairs found for each GO term in HCC samples. The table presents: in the first column, the name of the GO term; in the second and third column, the CloneIDs of the two correlated genes.

Additional File 4: This .csv file contains data for Table 6 – Relations in LIV. In this table are reported all the well-correlated gene pairs found for each GO term in LIV samples. The table presents: in the first column, the name of the GO term; in the second and third column, the CloneIDs of the two correlated genes.

Additional File 1: This .csv file contains data for Table 3 – Bootstrap with random GO term annotation. In this table are reported complete results for our first bootstrap analysis (shuffling GO term annotation). The table presents: in the first column, the name of the GO term; in the second (pairs HCC) the number of correlations present in the cancer samples; in the third (pairs LIV), the number of correlations found in the normal tissues; in the fourth and fifth column the mean and the standard deviation as computed by bootstrap analysis for HCC samples; in the sixth and seventh column, the mean and the standard deviation as computed by bootstrap analysis for LIV samples.

Additional File 2: This .csv file contains data for Table 4 – Bootstrap with random HCC/LIV assignment. In this table are reported complete results for our second bootstrap analysis (random assignment to HCC/LIV class). The table presents: in the first column, the name of the GO term; in the second (pairs HCC) the number of correlations present in the cancer samples; in the third (pairs LIV), the number of correlations found in the normal tissues; in the fourth and fifth column the mean and the standard deviation as computed by bootstrap analysis for HCC samples; in the sixth and seventh column, the mean and the standard deviation as computed by bootstrap analysis for LIV samples.