Figure 2
From: Discovery of biological networks from diverse functional genomic data
bioPIXIE query-driven context illustration. Nodes represent proteins, and edges represent functional links between them. Edge color indicates the confidence of the links ordered by color from red (highest confidence), orange, yellow, to green (lowest confidence). Query proteins are indicated by gray nodes. Rad23 is known to form a complex with Rad4 (NEF2) and participate in nucleotide excision repair and has also been implicated in inhibiting the degradation of specific substrates in response to DNA damage. (a) Rad23 was entered with Rad4, Rad3, and Rad24 and the resulting network is enriched (22 of 44, P value < 10-22) for DNA repair proteins (GO:0006281). (b) Rad23 was entered with proteasome components Pup1, Pre6, Rpn12 and the recovered network is enriched (36 of 44, P value < 10-55) for ubiquitin-dependent catabolism proteins (GO:0006511) and only contains 2 DNA repair proteins (Rad6 and Rad23). Rad23 has high-confidence relationships with several proteins in both processes, but the network recovery algorithm is dependent on the context of the query, which results in two different views of Rad23 and its neighbors.