Table 3.

Simplified relationship themes derived from the clusters shown in Figure 3a–d

Type	Symbol	Theme	Relevant figure	Supporting cluster(s)
Chemical-gene	A+	Agonism, activation	3a	6+
	A−	Antagonism, blocking		6–
	B	Binding, ligand (esp. receptors)		14–16
	E+	Increases expression/production		8+, 9+
	E−	Decreases expression/production		8–, 9–, 10
	E	Affects expression/production (neutral)		8, 9, 11a
	N	Inhibits		3
Gene-chemical	O	Transport, channels	3a	19, 21
	K	Metabolism, pharmacokinetics		11c
	Z	Enzyme activity		20
Chemical-disease	T	Treatment/therapy (incl. investigatory)	3b	8g, 8h, 9
	C	Inhibits cell growth (esp. cancers)		2, 3
	Sa	Side effect/adverse event		6, 15, 16
	Pr	Prevents, suppresses		1, 9, 21, 24, 28
	Pa	Alleviates, reduces		26, 30
	J	Role in pathogenesis		20
Disease-chemical	Mp	Biomarkers (progression)	3b	18, 19
gene-disease	U	Causal mutations	3c	14
	Ud	Mutations affect disease course		13
	D	Drug targets		10, 12
	J	Role in pathogenesis		2h, 4, 6, 8, 9
	Te	Possible therapeutic effect		2j, 3
	Y	Polymorphisms alter risk		22, 26, 27
	G	Promotes progression		29
Disease-gene	Md	Biomarkers (diagnostic)	3c	5, 7
	X	Overexpression in disease		15, 17, 30
	L	Improper regulation linked to disease		18, 19, 21
Gene–gene	B	Binding, ligand (esp. receptors)	3d	10
	W	Enhances response		13
	V+	Activates, stimulates		14, 16
	E+	Increases expression/production		21, 22
	E	Affects expression/production (neutral)		7, 17
	I	Signaling pathway		24
	H	Same protein or complex		25
	Rg	Regulation		28, 30
	Q	Production by cell population		1, 2, 6

Note: A symbol is bolded if it refers to a theme that appears in multiple dendrograms. Complete descriptions of the individual clusters can be found in the Discussion. Examples of dependency paths from each cluster are in the Supplementary Material for this article.