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ALL Methylation Supplementary Table 5A

Correlation between downregulated and hypermethylated genes.

The first 8 data rows of the table represent data for genes downregulated in each subgroup of ALL (e.g. CRLF2, ETV6-RUNX1 etc) compared to the comparison group (e.g. non-CRLF2r B-ALL, or non-ETV6-RUNX1 ALL).

The second 8 rows show data for genes downregulated in the comparison group compared to each specific subtype. Significant Fisher P values are highlighted in pink

Downregulated, hypermethylated (A) Downregulated FDR<0.1 and hypermethylated FDR<0.1 (B) Downregulated FDR>0.1 and hypermethylated FDR<0.1 (C) Downregulated FDR<0.1 and hypermethylated FDR>0.1 (D) Downregulated FDR>0.1 and hypermethylated FDR>0.1 Fisher P Fraction of all hypermethylated genes that are downregulated (A/A+B) Fraction of all downregulated genes that are hypermethylated (A/A+C)
CRLF2r vs nonCRLF2r_B 0 52 17 12855 1 0 0
ETV6 vs nonETV6_B 232 1336 1563 9793 0.28 0.15 0.13
Hyper vs nonHyper_B 1363 5146 968 5447 4.63E-18 0.21 0.58
MLLr vs nonMLLr_B 276 1656 881 10111 5.86E-17 0.14 0.24
ERGr vs nonERGr_B 201 1204 1032 10487 1.10E-09 0.14 0.16
BCRABL1 vs nonBCRABL1_B 163 1720 1001 10040 0.6 0.09 0.14
TCF3 vs nonTCF3_B 87 175 1999 10663 6.25E-12 0.33 0.04
T-ALL v B-ALL 629 2190 1248 8857 4.89E-37 0.22 0.34
               
nonCRLF2r_B vs CRLF2r 1 57 14 12852 0.07 0.02 0.07
nonETV6_B vs ETV6 614 2432 1366 8512 1.53E-16 0.2 0.31
nonHyper_B vs Hyper 433 2383 1446 8662 0.16 0.15 0.23
nonMLLr_B vs MLLr 474 2957 1117 8376 0.002 0.14 0.3
nonERGr_B vs ERGr 161 1140 1119 10504 0.002 0.12 0.13
nonBCRABL1_B vs BCRABL1 315 2408 791 9410 9.83E-10 0.12 0.28
nonTCF3_B vs TCF3 25 162 1364 11373 0.23 0.13 0.02
B-ALL v T-ALL 1102 3779 1451 6592 4.78E-10 0.23 0.43