Table 1

Testing SBS frequency equality in healthy (H) and cancer (C) cells for the 17 mRNA selected by Brulliard, M. et al. (2007)
Gene COSMIC L-SAGE Tag-seq Brulliard, M. et al. TI study using EST
GAPDH 0 C > H (3.67×10-115) C > H (~0) C > H
VIM 13 C = H C > H (2.32×10-78) C > H
ENO1 7 C > H (3.48×10-3) C < H (0.76×10-2) C > H
HSPA8 10 RT C > H (9×10-9) C > H
TPT1 0 C > H (4.05×10-4) C > H (~0) C > H
ATP5A1 5 C > H (1.51×10-15) C > H (1.35x10-83) C > H
FTL 0 RT C > H (1.5×10 -7) C > H
TPI1 3 C > H (1.14×10-52) C > H (~0) C > H
ALDOA 4 C = H C < H (5.55×10-23) C > H
LDHA 4 C > H (6.98×10-14) C > H (1.84×10-3) C > H
FTH1 5 RT RT C > H
RPS4X 2 RT RT C > H
RPL7A 1 3’ polyadenylated RNA record not available C > H
RPS6 0 RT RT C > H
CALM2 1 RT RT C > H
TMSB4X 1 RT RT C < H
ALB 17 RT RT C < H

C > H: greater SBS frequency in cancer. C < H: greater SBS frequency in healthy. C = N: SBS frequencies are not significantly different between H and C. RT: the 17 base NlaIII tag associated with this transcript was not present in either L-SAGE or Tag-seq lists of RT and therefore equality between SBS frequencies in H and C could not be tested. COSMIC: number of cancer related somatic mutations recorded by the COSMIC database. 3’ polyadenylated RNA record not available: the sequence recorded in RefSeq-rna does not have a 3’ polyadenylated boundary, therefore NlaIII tag cannot be determined.

Bianchetti et al.

Bianchetti et al. BMC Cancer 2012 12:509   doi:10.1186/1471-2407-12-509

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