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Table 1 TOX3 and LOC643714 mRNA expression compared with clinical and pathological characteristics

From: The risk allele of SNP rs3803662 and the mRNA level of its closest genes TOX3 and LOC643714predict adverse outcome for breast cancer patients

   n TOX3mRNA p-value n LOC643714mRNA p-value
   139 median (25% and 75%)   126 median (25% and 75%)  
Age
  < 50 59 (42%) 1.92 (0.9 - 4.5) 0.89 53 (42%) 3.1 E-4 (5.6 E-6 - 1.5 E-2) 0.07
  ≥ 50 80 (58%) 1.68 (1.1 - 4.0)   73 (58%) 1.7 E-3 (1.1 E-4 - 8.5 E-2)  
Tumour size (mm)
  ≤ 20 42 (31%) 1.5 (1.0 - 4.8) 0.45 39 (31%) 6.4 E-4 (2.7 E-5 - 1.0 E-2) 0.26
  > 20 95 (69%) 2.0 (1.0 - 4.5)   85 (69%) 1.1 E-3 (9.2 E-5 - 8.5 E-2)  
  unknown 2    2   
Estrogen receptor
  negative 44 (33%) 1.3 (0.4 - 3.3) 0.004 41 (34%) 9.3 E-6 (6.4 E-7 - 5.5 E-4) < 0.001
  positive 91 (67%) 2.1 (1.1 - 4.5)   81 (66%) 2.4 E-3 (4.6 E-4 - 9.8 E-2)  
  unknown 4    4   
Progesterone receptor
  negative 65 (49%) 1.4 (0.6 - 4.2) 0.005 59 (50%) 1.9 E-4 (1.4 E-6 - 3.1 E-3) < 0.001
  positive 67 (51%) 2.1 (1.3 - 4.3)   60 (50%) 3.3 E-3 (4.2 E-4 - 0.5)  
  unknown 7    7   
ErbB2 status
  negative 114 (83%) 1.8 (1.0 - 4.2) 0.81 107 (86%) 1.1 E-3 (6.6 E-5 - 7.7 E-2) 0.04
  positive 24 (17%) 1.9 (0.8 - 5.0)   18 (14%) 2.7 E-4 (4.7 E-5 - 9.2 E-4)  
  unknown 1    1   
Nodal status
  negative 56 (44%) 1.3 (0.4 - 3.4) < 0.001 53 (46%) 5.3 E-4 (1.9 E-6 - 2.3E-2) 0.04
  positive 71 (56%) 2.2 (1.2 - 5.3)   62 (54%) 1.4 E-3 (2.0 E-4 - 5.7 E-2)  
  unknown 12    11   
Ki67
  Low 97 (71%) 2.1 (1.1 - 4.4) 0.026 87 (70%) 2.4 E-3 (2.2 E-4 - 9.0 E-2) < 0.001
  High 39 (29%) 1.2 (0.7 - 2.4)   37 (30%) 9.6 E-5 (1.9 E-6 - 9.0 E-4)  
  unknown 3    2   
Histograde
  1 12 (9%) 1.6 (0.8 - 3.5) 0.16 12 (9%) 1.1 E-3 (2.7 E-4 - 3.5 E-2) 0.01
  2 78 (57%) 1.9 (1.1 - 4.4)   69 (56%) 3.5 E-3 (1.9 E-4 - 9.8 E-2)  
  3 47 (34%) 1.6 (0.5 - 4.2)   43 (35%) 2.3 E-4 (3.3 E-6 - 1.5 E-3)  
  unknown 2    2   
Familial status 1
  BRCA2 26 (19%) 2.9 (0.8 - 5.1) 0.90 25 (20%) 6.7 E-4 (1.2 E-4 - 4.2 E-3) 0.40
  Non-BRCA2 112 (81%) 1.6 (1.0 - 4.2)   100 (80%) 1.2 E-3 (6.3 E-5 - 6.4 E-2)  
  unknown 1    1   
Subtype
  Basal 20 (17%) 0.5 (0.1 – 1.3) < 0.001 23 (21%) 3.1 E-6 (2.3 E-7 - 2.0 E-4) < 0.001
  ERBB2 15 (12%) 1.6 (1.2 - 5.0)   9 (8%) 9.7 E-4 (2.7 E-4 - 1.5 E-2)  
  Luminal A 43 (36%) 1.6 (1.1 - 3.1)   38 (35%) 8.9 E-3 (5.0 E-4 - 9.8 E-2)  
  Luminal B 30 (25%) 4.0 (1.6 - 5.4)   28 (26%) 1.2 E-3 (6.7 E-4 – 3.0 E-1)  
  Normal-like 12 (10%) 1.8 (1.2 - 4.4)   10 (9%) 5.8 E-4 (3.4 E-5 - 2.7 E-3)  
  Unclass/unknown 19    18   
Histological type
  Ductal 116 (86%) 2.1 (1.0 - 4.5) 0.12 105 (86%) 1.1 E-3 (9.2 E-5 - 5.2 E-2) 0.91
  Lobular 11 (8%) 1.3 (1.3 - 2.2)   9 (7%) 6.2 E-4 (1.2 E-4 - 7.8 E-3)  
  other 8 (6%) 1.0 (0.6 - 1.5)   8 (7%) 9.8 E-5 (5.2 E-6 - 2.2 E-2)  
  unknown 4    4   
Metastasis
  negative 63 (50%) 1.6 (0.9 - 3.1) 0.18 63 (55%) 6.4 E-4 (6.3 E-6 - 1.9 E-2) 0.16
  positive 63 (50%) 1.9 (1.1 - 4.9)   52 (45%) 1.6 E-3 (1.4 E-4 - 8.1 E-2)  
  unknown 13    11   
  1. The table shows the median and the 25th and 75th percentiles. The p-value is calculated with log2 transformed data using a t-test or ANOVA.
  2. 1 One tumour sample was BRCA1 positive and was not used in familial status calculations.
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