Skip to main content

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.