SANTA: Quantifying the Functional Content of Molecular Networks
Figure 2
Application of the Knet-function to two gene sets.
Example input: (A) S. cerevisiae GI map and (B) gene sets obtained from GO (‘GO:0044451: nucleoplasm part’ and ‘GO:0070011: peptidase activity’). (C, D) Network annotated with each gene set. From visual inspection, it appears that the gene set in (C) clusters more significantly than the gene set in (D). SANTA allows us to assess this clustering objectively. (E, F) The K net-function is computed for the observed gene sets (red and blue lines) and for a large number of permutations (yellow area). (G, H) In order to quantify the significance of the clustering, the area under the Knet-function curve (AUK) is computed for the observed gene set (red and blue lines) and for each permutation (grey histogram). An empirical p-value is calculated using a Z-test. For GO:0044451, p = 5.680×10−30 and for GO:0070011, p = 0.174, demonstrating objectively that the gene set in (C) does cluster more significantly.