Table 1.
Mappings between cancer tissues and normal tissues.
Figure 1.
Procedure for determining the score of an antibody in relation to a mapping of interest.
(A) Initially, the protein expression levels and the expression difference (ED) between cancer tissue and normal tissue for all antibodies covering all mappings are calculated. (B) The significance of the target ED with respect to the mapping of interest is determined by a cumulative z distribution. (C) The specificity of the target ED with respect to the mapping of interest is determined by another cumulative z distribution. (D) The final score of the antibody with respect to the mapping of interest is determined on the basis of its protein expression level in cancer tissue and the significance and specificity of its ED.
Figure 2.
The HPA Scoring web server (http://bal.ym.edu.tw/hpa/).
(A) The result of querying by gene name. (B) The result of querying by the mapping of a cancer type.
Table 2.
The statistical significance of the EiC mean differences between the top 100 antibodies and all the tested antibodies.
Table 3.
The statistical significance of the ED mean differences between the top 100 antibodies and all the tested antibodies.
Figure 3.
Specificity of the average ED of the top 100 antibodies selected for each mapping.
In this heat map, large ED values are colored dark blue and small ED values are colored light blue. The entry (i, j) on the heat map represents the average ED of the top 100 antibodies of the j-th mapping calculated for the i-th mapping. The rightmost column, All, lists the average ED of all the tested antibodies calculated for each of the 27 mappings.
Figure 4.
The results of various combinations of filtering criteria when applied to a cohort of 1482 membrane proteins.
(A) The rules that are used to screen genes are marked with a plus sign and otherwise there is a minus sign. For each combination, the numbers of filtered genes, genes with biomarker annotation, and genes with disease annotation are listed. (B) The proportions of annotated biomarkers and disease-related genes to filtered genes of each combination are shown. (C) The proportion of the filtering results to our sample population is shown. This figure is a panel chart that has two panels; the upper one has an axis that covers the full range of data, while the lower one has an axis that focuses on data within the range 0%–25%.
Table 4.
The four filtered genes obtained by applying Combination 8.