Figure 2.
Identifying topic-relevant significant proteins using normalized copublication distance (NCD). (A) The multiplicity of occurrence of the top 50 proteins in each of the six examined systems is shown. Proteins with a multiplicity of six (e.g., TP53) are found in the top 50 most published proteins in all six examined systems and are colored in dark brown. Proteins with a multiplicity of one (e.g., BDNF in the cerebral system) are in the top 50 in only one of the six organ systems queried. (B) NCD normalizes the number of referenced publications in a particular topic for a particular protein by the total number of referenced publications of that protein to any topic. In contrast with ranking proteins by total publication count, normalized copublication distance down-ranks proteins that are of general interest with large numbers of publications in multiple fields (e.g., certain proteins in tumorigenesis pathways) and promotes query-specific proteins, such that top-ranked proteins by NCD (right) are mostly organ-specific. (C) The distribution of NCD values for proteins in a query (black line) follows a normal Gaussian distribution (red line), with a mean of 1.0 and standard deviation (sd) of 0.1. (D) The graphs show the number of publications for each protein referenced in a queried tissue (ordinates), plotted against the NCD between the protein and the tissue (abscissae). Line and shade: locally weighted scatterplot smoothing regression and 95% confidence interval thereof, respectively. Proteins with significant NCD (Z ≤ −1.96) are colored in blue. The top protein in each query is labeled in red text.