Table 2. Target protein family based drug/compound enrichment analysis results of the large-scale DTI predictions.

Drug sets predicted to	Enriched terms of the predicted drug sets
	ChEBI structure classification (tool: BiNChE)	Chemical structure classification (tool: DrugPattern)	ATC codes (tool: DrugPattern)	Experimentally identified known targets and families (tool: CSgator)	Functions of the experimentally identified known targets (GO) (tool: CSgator)	Disease indications (MeSH) (tool: CSgator)	Disease indications (disease ontology) (tool: CSgator)
Enzymes	CHEBI:133004 – bisbenzylisoquinoline alkaloid	Indoles and derivatives	Antineoplastic agents	Kinase	Phosphorylation (GO:0016310)	Neoplasms (C04 (D009369))	Disease of cellular proliferation (DOID:14566)
	CHEBI:50047 – organic amino compound	Macrolides and Analogues	Antivirals for systemic use	Enzyme	Cellular protein modification process (GO:0006464)	Cardiovascular diseases (C14 (D002318))	Organ system cancer (DOID:0050686)
	CHEBI:24698 – hydroxyflavone		Drugs for obstructive airway diseases	Camk (CAMK protein kinase group)	Receptor signaling protein activity (GO:0005057)	Urologic diseases (C12.777 (D014570))	Kidney disease (DOID:557)
	CHEBI:24921 – isoquinoline alkaloid			Ste (STE protein kinase group)	Transferase activity (GO:0016740)	Kidney diseases (C12.777.419 (D007674))	Urinary system disease (DOID:18)
					Adenyl nucleotide binding (GO:0030554)
GPCRs	CHEBI:33853 – phenols	Morphinans	Psycholeptics	Small molecule receptor (family A GPCR)	Cell–cell signaling (GO:0007267)	Nervous system diseases (C10 (D009422))	Disease of mental health (DOID:150)
	CHEBI:72720 – flavonoid oligomer	Benzofurans	Drugs for obstructive airway diseases	Transporter	Circulatory system process (GO:0003013)	Cardiovascular diseases (C14 (D002318))	Central nervous system disease (DOID:331)
	CHEBI:33822 – organic hydroxy compound	Stilbenes	Bile and liver therapy	7TM1 (family A G protein-coupled receptor)	Plasma membrane region (GO:0098590)	Neurologic manifestations (C23.888.592 (D009461))	Genetic disease (DOID:630)
	CHEBI:33635 – polycyclic compound		Antihistamines for systemic use	Electrochemical transporter	Transmembrane transporter activity (GO:0022857)	Pituitary diseases (C19.700 (D010900))	Disease of metabolism (DOID:0014667)
Nuclear receptors	CHEBI:51958 – organic polycyclic compound	Steroids and steroid derivatives	Antineoplastic agents	Transcription factor	Intracellular receptor signaling pathway (GO:0030522)	Neoplasms (C04 (D009369))	Disease of cellular proliferation (DOID:14566)
	CHEBI:33635 – polycyclic compound	Morphinans	Corticosteroids for systemic use	Nuclear receptor	Nucleic acid binding transcription factor activity (GO:0001071)	Immune system diseases (C20 (D007154))	Cancer (DOID:162)
	CHEBI:36615 – triterpenoid	Prenol lipids	Anti-acne preparations	Cytochrome P450	Programmed cell death (GO:0012501)	Hemic and lymphatic diseases (C15 (D006425))	Immune system disease (DOID:2914)
	CHEBI:25872 – pentacyclic triterpenoid	Stilbenes	Analgesics	AUXTRANS (Auxiliary transport protein)	Positive regulation of apoptotic process (GO:0043065)	Skin and connective tissue diseases (C17 (D017437))	Hypersensitivity reaction disease (DOID:0060056)
			Sex hormones and modulators of the genital system
Ion channels	CHEBI:47916 – flavonoid	Morphinans	Antihistamines for systemic use	Ste (STE protein kinase group)	Phosphorylation (GO:0016310)	Neoplasms (C04 (D009369))	Disease of cellular proliferation (DOID:14566)
	CHEBI:26004 – phenylpropanoid	Benzopyrans	Beta blocking agents	Camk (CAMK protein kinase group)	Receptor signaling protein activity (GO:0005057)	Skin and connective tissue diseases (C17 (D017437))	Organ system cancer (DOID:0050686)
	CHEBI:26195 – polyphenol	Benzene and substituted derivatives	Drugs for obstructive airway diseases	Ion channel	Transmembrane transport (GO:0055085)	Neurologic manifestations (C10.597 (D009461))	Gastrointestinal system disease (DOID:77)
	CHEBI:38443 – 1-benzopyran		Analgesics	Transporter	Cell death (GO:0008219)	Respiratory tract diseases (C08 (D012140))	Cardiovascular system disease (DOID:1287)
Others	CHEBI:33822 – organic hydroxy compound	Macrolactams	Antimycobacterials	Cytosolic other	Proteasome complex (GO:0000502)	Cardiovascular diseases (C14 (D002318))	Disease of anatomical entity (DOID:7)
	CHEBI:26004 – phenylpropanoid	Diazines	Agents acting on the renin–angiotensin system	ATP binding cassette	Ribosome (GO:0005840)	Nervous system diseases (C10 (D009422))	Cardiovascular system disease (DOID:1287)
	CHEBI:47916 – flavonoid	Carboxylic acids and derivatives	Lipid modifying agents	Cytochrome P450	Antigen processing and presentation (GO:0019882)	Vascular diseases (C14.907 (D014652))	Disease of cellular proliferation (DOID:14566)
	CHEBI:25036 – lignan		Antivirals for systemic use	Transporter	Enzyme inhibitor activity (GO:0004857)	Pathological conditions, signs and symptoms (C23 (D013568))	Primary bacterial infectious disease (DOID:0050338)
				Phosphodiesterase
Renin (case study)	CHEBI:35352 – organonitrogen compound	Morphinans	Antineoplastic agents	Kinase	Phosphorylation (GO:0016310)	Neoplasms (C04 (D009369))	Disease of cellular proliferation (DOID:14566)
	CHEBI:26188 – polyketide	Macrolides and analogues	Pituitary and hypothalamic hormones and analogues	Tk (TK protein kinase group)	Receptor signaling protein activity (GO:0005057)	Cardiovascular diseases (C14 (D002318))	Organ system cancer (DOID:0050686)
	CHEBI:46845 – N-alkylpiperazine	Lactams	Endocrine therapy	Cmgc (CMGC protein kinase group)	Adenyl nucleotide binding (GO:0030554)	Vascular diseases (C14.907 (D014652))	Vascular disease (DOID:178)
	CHEBI:37578 – halide	Benzodiazepines		Agc (AGC protein kinase group)	Guanyl-nucleotide exchange factor activity (GO:0005085)	Digestive system diseases (C06 (D004066))	Urinary system disease (DOID:18)