PMC

Integrative visualization of GO annotation and user-mined or -specified networks. Note that YGR119C is annotated using two selected GO branches only: molecular function and metabolic process (indicated by the selected checkbox of the tree node; only the checkbox for metabolic processes is visible in the figure).

Visualization of NMEA of p53 mutation data on the cell-cycle pathway. The color of each node is in proportion to the density score according to the same color map of the expression shown in the VisANT toolbar, nodes with darker green have more contribution to the enrichment score.

Illustration of the multi-scale network found by integrating the Y2h protein–protein interaction network of yeast and GO hierarchies. Y2h interaction network with 4872 nodes and 13 514 edges, part of the branch for GO term binding and multi-scale network resulted from the integration of y2h network and binding branch. Note that in C, the metanode contains genes annotated under nucleic acid binding (green nodes in circle), and three of its sub-terms. Only 1842 genes in the Y2H network are annotated under the GO branch binding.

Different roles of GO annotation in two different workflows designed for VisANT 3.5. The solid red lines represent the workflow of functional profiling where GO annotations are used to interpret the roles of a given gene set. The dashed blue lines represent the workflow of the gene set/network module enrichment analysis, where GO terms and associated genes are used to construct the functional modules.