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Table 2 Genes directly and indirectly associated with the Reelin signal pathway. The cosine similarities between RELN and genes in the full space and the reduced dimensional space obtained from NMF are also presented. (n/a: not applicable)

From: Extracting unrecognized gene relationships from the biomedical literature via matrix factorizations

Gene

PubMed co-citation

Symbol match

Full space

NMF (k = 3)

 

# co-citation

Rank

# match

Rank

cos θ

Rank

cos θ

Rank

Genes directly associated with the Reelin signaling (five genes)

RELN

n/a

-

n/a

-

1.0000

1

1.0000

1

DAB1

9

1

47

1

0.7349

2

0.9964

3

LRP8

2

2

1

7

0.4955

4

0.9854

6

FYN

1

5

4

4

0.2887

9

0.9811

7

VLDLR

2

2

9

2

0.5223

3

0.9463

8

Genes indirectly associated with the Reelin signaling (six genes)

CDK5R1

1

5

0

-

0.2893

7

0.9966

2

CDK5

2

2

3

6

0.2903

6

0.9964

3

CDK5R2

1

5

0

-

0.3228

5

0.9962

5

SRC

1

5

5

3

0.2889

8

0.8433

9

MAPT

0

-

0

-

0.2147

29

0.7630

10

APOE

0

-

0

-

0.2151

28

0.6059

11