Table 1:

Equations for ranking GeneID-MeSH co-occurrences.

Equation	Description
C = {c1, …cn }	a set of co-occurrences, where c is a GeneID-MeSH term co-occurrence that is unique by PMID and n is the total number of co-occurrences
G(g)	the number of co-occurrences of C that contain gene, g
M(m)	the number of co-occurrences of C that contain MeSH term, m
M(m′)	the number of co-occurrences of C that contain m and all the descendants of m
T(g; m)	the subset of C that contains co-occurrences with both g and m
$p(g)=\frac{|G(g)|}{n}$	the probability of g occurring
$p(m)=\frac{|M(m)|}{n}$	the probability of m occurring based on frequencies before MeSH term frequency normalization
$p\left(m^{\prime }\right)=\frac{\left|M\left(m^{\prime }\right)\right|}{n}$	the probability of m and all the descendants of m occurring based on frequencies after MeSH term frequency normalization
$p(g;m)=\frac{|T(g;m)|}{n}$	the probability of g and m co-occurring
$pmi(g;m)=log\left(\frac{p(g;m)}{p(g)p\left(m^{\prime }\right)}\right)$	pointwise mutual information for a given g and m
$npmi(g;m)=\frac{pmi(g;m)}{-log(p(g,m))}$	normalized pointwise mutual information for a given g and m