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Table 3 Top unique differentially expressed genes upregulated in lesional skin compared with those in non-lesional skin when ranked according to log2-fold-change in (a) original dataset, (b) predicted dataset with 30 % observability, and (c) sparse known-value (checkpoint) dataset without prediction at 30 % observability

From: Gene expression prediction using low-rank matrix completion

  

Original dataset

   

Recovered dataset (30 %)

   

Checkpoint dataset (30 %)

  

Gene

Probe ID

Symbol

log FC

Adj.

Probe ID

Symbol

log FC

Adj.

Probe ID

Symbol

log FC

Adj.

ranking

   

P-Value ×10−10

   

P-Value ×10−10

   

P-Value

1

205863_at

S100A12

9.79929

< 1

205863_at

S100A12

8.48947

< 1

207367_at

ATP12A

3.17871

0.02

2

211906_s_at

SERPINB4

9.60376

< 1

211906_s_at

SERPINB4

7.98211

< 1

201086_x_at

SON

3.12259

0.17

3

205513_at

TCN1

8.65788

< 1

220664_at

SPRR2C

7.17109

< 1

213356_x_at

NA

3.06212

0.29

4

232220_at

S100A7A

8.21988

< 1

232220_at

S100A7A

6.77508

< 1

209719_x_at

SERPINB3

2.98365

0.15

5

205660_at

OASL

7.94647

< 1

204385_at

KYNU

6.4279

< 1

33322_i_at

SFN

2.89353

0.36

6

220664_at

SPRR2C

7.87929

< 1

207602_at

TMPRSS11D

6.41765

< 1

213523_at

KIAA0368

2.88306

0.29

7

207602_at

TMPRSS11D

7.64471

< 1

207367_at

ATP12A

6.40415

< 1

210413_x_at

CCNE1

2.83059

0.06

8

1569555_at

GDA

7.39506

< 1

210413_x_at

NA

6.39934

< 1

217388_s_at

NA

2.82118

0.19

  1. It is to be noted that the analysis performed solely on known expression values (c) gives incorrect conclusions. However, the results of analysis after low-rank prediction matched with those obtained using original dataset
  2. Abbreviations: logFC log2-fold-change, Ave Expr average log2-expression of the probe over all arrays, Adj. P-Value P-value adjusted from the raw P-value
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BMC Bioinformatics

ISSN: 1471-2105

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