Table 2 |
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|
Top prostate cancer marker candidates selected by both t-test and SVM-RFE. |
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|
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 |
|
|
||||
|
¶ detail information of each isoform, such as the exon junction and probe design, can be accessed at the MAASE database [48]; # FDR is calculated using all 38 samples; §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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|
Zhang et al. BMC Bioinformatics 2006 7:202 doi:10.1186/1471-2105-7-202 |
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