Table 1.

Frequency of increased mRNA expression in SSA/P signature genes in 30 hypermutated and 165 nonhypermutated colon cancers from TCGA

Hypermutated CCNonhypermutated CCFisher exact
Gene symbolGene descriptionIncidence (%)Incidence (%)P
FSCN1Fascin actin-binding protein 19 (30)3 (2)<0.001
ZIC5Zic family member 57 (23)5 (3)<0.001
CRYBA2Crystallin, β A25 (17)0 (0)<0.001
SEMG1Semenogelin4 (13)0 (0)<0.001
ZIC2Zic family member 26 (20)4 (2)0.001
TRNP1TMF1-regulated nuclear protein 16 (20)5 (3)0.002
MUC6Mucin 64 (13)1 (1)0.002
FOSL1FOS-like antigen 13 (10)1 (1)0.012
ALDH1L1Aldehyde dehydrogenase 1 family member L15 (17)7 (4)0.022
KLK10Kallikrein-related peptidase 103 (10)4 (2)0.075
SLC18A1Solute carrier family 18, member 13 (10)4 (2)0.075
VNN1Vanin 13 (10)4 (2)0.075
MUC17Mucin 173 (10)13 (8)0.717
ANXA10Annexin A101 (3)2 (1)0.396
CLDN1Claudin 11 (3)11 (7)0.696
  • NOTE: Incidence of increased mRNA in 195 colon cancers (30 hypermutated and 165 nonhypermutated) was obtained using TCGA data available in the cBioPortal for Cancer Genomics, Memorial Sloan-Kettering Cancer Center. Table lists 13 of 51 signature genes that show frequent (≥10%) increased mRNA expression in hypermutated colon cancers. Incidence of increased mRNA expression is also shown for two previously developed SSA/P gene markers, Annexin A10 (ANXA10) and claudin 1 (CLDN1). Changes in mRNA expression were obtained by comparing normalized read counts (RPKM) for each gene across colon cancers diploid for each gene. Statistical significant differences between incidence of increased mRNA expression between hypermutated and nonhypermutated were determined using a Fisher exact test. Nine genes showed statistically significant increased incidence of mRNA overexpression in hypermutated colon cancers.

  • Abbreviation: CC, colon cancer.