Table 11.

Gene rankings for each method, ordered by pathway number

Extraction		Ranking Numbers
	Gene	Proposed	Co-occurrence	Word2Vec	COALS	Random Indexing	Pathway
PKDE4J	*TNF	361	742	4876	548	851	57
	*EGFR	1468	2063	5550	2391	3381	43
	*GSK3B	990	1374	2341	2119	2349	39
	*CREB1	6298	8240	6792	6468	7460	39
	IL1B	2401	1292	3451	3043	3733	37
	*SRC	3854	8230	3984	4257	5257	36
	*ATF4	2890	6965	4204	3430	4538	32
	MYC	6531	4909	4957	6688	6578	32
	*IGF1	446	463	3410	1940	2040	30
	IGF1R	1868	1397	3697	519	1119	29
SemRep	MAP 2 K1	3466	3462	3433	1.5	1.2	80
	PRKACB	3952	2131	3444	1.5	1.2	67
	*MAPK8	253	1004	3410	1.5	1.2	59
	*TNF	731	3564	2460	1.5	1.2	57
	JUN	2428	1804	2799	1.5	1.2	49
	*TP53	399	724	2492	1.5	1.2	48
	*IL6	925	1012	2816	1.5	1.2	43
	EGFR	3201	3032	2497	1.5	1.2	43
	*BAX	2099	3643	2780	1.5	1.2	41
	IL1B	2264	1910	2246	1.5	1.2	37

The genes with the asterisk (*) symbol indicate that our method generates better ranking than the other methods do