Table 3.

Explanation of the scoring functions evaluated

Scoring method	Description
Cosine distance of term frequency-inverse document frequency	$\sum _{j\in M}\left(g_i\left(j\right)d_i\left(j\right)\right)\left./\right)\left(\sqrt{\sum _{j\in M}{\left(g_i\left(j\right)\right)}^2}\sqrt{\sum _{j\in M}{\left(d_i\left(j\right)\right)}^2}\right)$
Cosine distance of P-values	$\sum _{i\in M}\left(g_p\left(i\right)d_p\left(i\right)\right)\left./\right)\left(\sqrt{\sum _{i\in M}{\left(g_p\left(i\right)\right)}^2}\sqrt{\sum _{i\in M}{\left(d_p\left(i\right)\right)}^2}\right)$
Cosine distance of term fractions	$\sum _{i\in M}\left(g_f\left(i\right)d_f\left(i\right)\right)\left./\right)\left(\sqrt{\sum _{i\in M}{\left(g_f\left(i\right)\right)}^2}\sqrt{\sum _{i\in M}{\left(d_f\left(i\right)\right)}^2}\right)$
Sum of the log of combined P-values	$\sum _{i\in M}\mathsf{\text{log}}\left(g_p\left(i\right)+d_p\left(i\right)-g_p\left(i\right)d_p\left(i\right)\right)$
Sum of the differences of log P-values	$\sum _{i\in M}\left|\mathsf{\text{log}}\left(\frac{g_p\left(i\right)}{d_p\left(i\right)}\right)\right|=\sum _{i\in M}\left|\mathsf{\text{log}}\left(g_p\left(i\right)\right)-\mathsf{\text{log}}\left(d_p\left(i\right)\right)\right|$
L2 of log-p of overlapping terms only	$\sqrt{\sum _{i\in \left(G\cap D\right)}{\left(\mathsf{\text{log}}\left(g_p\left(i\right)\right)-\mathsf{\text{log}}\left(d_p\left(i\right)\right)\right)}^2}$
L2 of term fractions of overlapping terms only	$\sqrt{\sum _{i\in \left(G\cap D\right)}{\left(g_f\left(i\right)-d_f\left(i\right)\right)}^2}$
L2 of log of P-values	$\sqrt{\sum _{i\in M}{\left(\mathsf{\text{log}}\left(\frac{g_p\left(i\right)}{d_p\left(i\right)}\right)\right)}^2}=\sqrt{\sum _{i\in M}{\left(\mathsf{\text{log}}\left(g_p\left(i\right)\right)-\mathsf{\text{log}}\left(d_p\left(i\right)\right)\right)}^2}$
L2 of P-values	$\sqrt{\sum _{i\in M}{\left(g_p\left(i\right)-d_p\left(i\right)\right)}^2}$
L2 of term fractions	$\sqrt{\sum _{i\in M}{\left(g_f\left(i\right)-d_f\left(i\right)\right)}^2}$
L2 of term frequency	$\sqrt{\sum _{i\in M}{\left(g\left(i\right)-d\left(i\right)\right)}^2}$
Term coverage	|G∪D|
Term overlap	|G∩D|
Number of gene MeSH terms	|G|
Number of disease MeSH terms	|D|
Gene ID	Entrez Gene ID of the gene

M refers to the set of all MeSH terms, G and D to the MeSH terms for the gene and disease profile, respectively. g(i), g_f(i), g_p(i) and g_i(i) refer to the frequency, term fraction, hypergeometric P-value and term frequency-inverse document frequency for the MeSH term i of the gene profile. d(i), d_f(i), d_p(i) and d_i(i) refer to the frequency, term fraction, hypergeometric P-value and term frequency-inverse document frequency for the MeSH term i of the disease profile.