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Table 2 Top prostate cancer marker candidates selected by both t-test and SVM-RFE.

From: Profiling alternatively spliced mRNA isoforms for prostate cancer classification

Isoform ID¶

Normalized log2 expr

FDR# (q-value)

SVM-RFE freq.*

Protein Name§

ALDH1A2-0004

-1.21

1.3E-04

35

Aldehyde dehydrogenase 1A2

AMACR-2094

1.41

6.7E-05

38

Alpha-methylacyl-CoA racemase

AMACR-2097

1.08

9.2E-04

38

 

AMACR-2098

0.99

1.8E-03

17

 

ANXA2-0914

-1.04

1.8E-03

36

Annexin A2

APBB3-0185

1.01

1.5E-03

38

Amyloid beta (A4) precursor protein-binding family B member 3

BC008967-0877

-1.38

7.9E-05

26

 

C21ORF5-0239

1.24

6.0E-04

35

Chromosome 21 open reading frame 5

C7ORF24-0062

1.30

8.4E-05

17

 

CALCR-1180

1.05

5.2E-04

37

Calcitonin receptor

CCT8-0334

1.21

1.5E-04

32

Protein with high similarity to C. elegans Y55F3AR.3

CDC42BPA-1048

-1.19

6.0E-04

38

CDC42 binding protein kinase alpha

CDK7-0899

1.35

8.4E-05

37

Cyclin-dependent protein kinase 7

CES1-0937

-1.34

7.9E-05

32

Cat eye syndrome chromosome region candidate 1

CLU-0197

-1.11

1.2E-03

38

Clusterin (apolipoprotein J)

EDNRB-1187

-1.24

4.7E-04

26

Endothelin type B receptor

FGFR2-0094

-1.13

4.0E-04

19

Fibroblast growth factor receptor 2

FGFR2-0099

-1.03

7.7E-04

28

 

HEBP2-0472

1.08

7.8E-04

24

Heme binding protein 2 (placental protein 23)

HSPD1-0152

1.10

1.8E-03

37

Chaperonin 60

HSPD1-0154

1.17

2.8E-04

31

 

IGSF4-0722

0.72

2.1E-03

38

Immunoglobulin superfamily member 4

IMPDH2-0144

1.25

1.3E-04

34

Inosine monophosphate dehydrogenase type 2

IQGAP2-0234

1.17

5.6E-04

22

IQ motif containing GTPase activating protein 2

LAMR1-0523

1.20

1.3E-04

38

Laminin receptor 1

LTBP4-0746

-1.27

1.5E-04

33

Latent transforming growth factor beta binding protein 4

LTBP4-0748

-1.10

1.4E-03

38

 

LYPLA1-0860

1.38

7.9E-05

35

Lysophospholipase 1

NELL2-0805

-1.10

1.2E-03

24

Nel-like 2

PGR-1166

-1.16

4.0E-04

32

Progesterone receptor

PGR-1555

0.85

7.5E-04

38

 

PPIB-0969

0.94

2.2E-03

34

Cyclophilin B

PTS-0059

-1.07

2.2E-03

31

6-pyruvoyltetrahydropterin synthase

PYCR1-0058

1.28

4.1E-04

38

Pyrroline-5-carboxylate reductase 1

RING1-0217

-0.93

1.7E-03

22

Ring finger protein 1

SFRS10-1126

0.95

2.0E-03

34

Splicing factor arginine/serine rich 10

SMPDL3B-2030

1.09

2.2E-04

38

Protein containing a calcineurin-like phosphoesterase domain

STAC-1044

-1.31

7.9E-05

34

Src homology three and cysteine rich domain

TGFB2-0085

-1.11

6.5E-04

38

Transforming growth factor beta 2

TRIM29-1350

-1.29

1.5E-04

35

Ataxia telangiectasia mutated

TRIM29-1353

-1.20

1.7E-04

34

 

TXNIP-1116

1.09

1.3E-03

38

Thioredoxin interacting protein

  1. ¶ detail information of each isoform, such as the exon junction and probe design, can be accessed at the MAASE database [48];
  2. # FDR is calculated using all 38 samples;
  3. §SVM-RFE freq.: the number of times that an isoform is included in 38 selected subsets in leave-one-out cross validation.
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BMC Bioinformatics

ISSN: 1471-2105

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