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Table 2 Differential methylation in individual biomarkers

From: High performance methylated DNA markers for detection of colon adenocarcinoma

Tissue TMEFF2 GPX7 MAL ARHGEF7 TWIST1
Ca No Ca No Ca No Ca No Ca No
Number of samples 30 23 30 23 30 23 30 23 30 23
%M per sample
 Minimum 0 0 0 0 9 0 0 0 6 1
 25th percentile 40 0 1 0 21 1 0 0 14 3
 Median 59 1 33 0 33 2 8 0 18 4
 75th percentile 75 3 53 0 49 3 33 0 28 6
 Maximum 94 11 72 2 71 7 75 2 50 11
P value (Ca. vs. No.) < 0.0001 < 0.0001 < 0.0001 < 0.0001 < 0.0001
Tissue AKR1B1 HIN1 GAS7C TM6SF1 ZNF671
Ca No Ca No Ca No Ca No Ca No
Number of samples 30 23 30 23 30 23 30 23 30 23
%M per sample
 Minimum 0 0 0 0 0 0 0 1 0 2
 25th percentile 1 0 0 0 6 0 35 5 25 7
 Median 16 0 5 0 9 1 47 10 39 13
 75th percentile 21 0 18 0 12 2 58 15 49 16
 Maximum 52 1 61 0 36 4 70 40 72 20
P value (Ca. vs. No.) < 0.0001 < 0.0001 < 0.0001 < 0.0001 < 0.0001
Tissue COL6A2 APC HIST1H3C
Ca No Ca No Ca No
Number of samples 30 23 30 23 30 23
%M
 Minimum 0 1 0 0 0 0
 25th percentile 12 4 0 1 0 0
 Median 34 8 0 2 1 1
 75th percentile 52 10 58 2 55 3
 Maximum 66 23 92 7 78 8
P value (Ca. vs. No.) < 0.0001 0.2662 0.3959
  1. Ca, Carcinoma; No, adjacent normal tissue; P value for Mann–Whitney test
  2. Methylation levels of 13 individual markers in colon carcinoma lesions – Descriptive Statistics. Fresh frozen tissues in the Training set were assayed for DNA methylation by QM-MSP. Non-parametric analyses of carcinoma (Ca) and adjacent normal (No) tissues indicated the percentiles of methylation and extent of differential methylation (Mann-Whitney P-value) between tissue types. TM6SF1, ZNF671, COL6A2 showed the highest background in adjacent normal colon tissues as observed at the 75th percentile. The other genes were ranked by percent methylation (%M) at the 75th percentile among carcinoma samples: TMEFF2 > GPX7 > MAL > ARHGEF7 > TWIST1 > AKR1B1 > HIN1 > GAS7. Additional file 1: Fig. S1 and Additional file 2: Table S1 show the box whiskers plots and performance analyses for these data