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Table 11 Gene rankings for each method, ordered by pathway number

From: Combining entity co-occurrence with specialized word embeddings to measure entity relation in Alzheimer’s disease

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

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