Figure 1.
A PPI page showing annotations about the proteins and about the interaction. URL: http://severus.dbmi.pitt.edu/wiki-pi/index.php/pair/view/466/672.
Figure 2.
The homepage gives a search box, and also shows a shortlist of interactions some of which are populated randomly from the database while others are those that are most-frequently searched on Wiki-Pi. URL: http://severus.dbmi.pitt.edu/wiki-pi/.
Table 1.
Data sources.
Figure 3.
Concept diagram of GO term enrichment calculation.
Gene a interacts with genes ,-. GO terms ti of each interacting partner are shown to its right. BiNGO computes the statistically enriched GO terms (functional categories that the genes are enriched in, and find that the statistically enriched GO terms are t20, t30, and t12.See methods in [24] for details of computation.
Figure 4.
Image shows the results of the search where one gene is involved in the immunity pathway, while the other gene contains the term cancer anywhere in its annotation but not the word immunity. Note that the results can be sorted by number of pathways, diseases or drugs associated with the genes (counts of each gene are considered individually). URL: http://severus.dbmi.pitt.edu/wiki-pi/index.php/search/adv?a-all=pathway%3Aimmunity&b-any=cancer&b-none=immunity.
Figure 5.
PPIs retrieved when searched by gene symbol.
In these search results also, similar to those in Figure 3, the results can be sorted by number of pathways, diseases or drugs associated with the genes (counts of each gene are considered individually). URL: http://severus.dbmi.pitt.edu/wiki-pi/index.php/search?q=brca1.
Figure 6.
PPIs retrieved when searched by disease.
In these search results also, similar to those in Figure 3, the results can be sorted by number of pathways, diseases or drugs associated with the genes (counts of each gene are considered individually). URL: http://severus.dbmi.pitt.edu/wiki-pi/index.php/search?q=alzheimers.
Table 2.
Comparison of functionality of Wiki-Pi with other PPI databases.
Figure 7.
Statistically enriched Gene Ontology biological process terms of PPIs of IGSF21.
Wiki-Pi website makes available only a list and not an image of enriched GO biological process terms. For clarification, this network diagram has been generated with BiNGO Cytoscape Plugin [24], for GO biological process terms, with the hypergeometric statistical test of significance, and a Benjamini & Hochberg False Discovery Rate (FDR) correction at a significance level of 0.05, by pasting the list of interacting partners (gene symbols) from Wiki-Pi. Statistical significance of the node (GO term) is shown in color, with the darker color indicating stronger significance. High-resolution image with labels of the nodes is available as File S1.