Table 1. Data sets analyzed in this study.

Data source	Data type	Platform	Stage	Treatment	Sample size
Cell line
NCI-60	mRNA	Affymetrix U133 A	—	5-FU	58
CRC tissue
GSE39582	mRNA	Affymetrix U133 Plus 2.0	II–III	5-FU and folinic acid	200
GSE14333a	mRNA	Affymetrix U133 Plus 2.0	II–III	5-FU-based	85
GSE14333a	mRNA	Affymetrix U133 Plus 2.0	I–III	Without 5-FU-based treatment	139
TCGA	mRNA	IlluminaHiSeq_RNASeqV2	II–III	5-FU-based	184
TCGAb	DNA Copy number	Genome-Wide Human SNP Array 6.0	II–III	5-FU-based	183
TCGAb	Somatic mutation	Illumina Genome Analyzer DNA Sequencing	II–III	5-FU-based	143
TCGAb	MSI	Microsatellite Instability Analysis	II–III	5-FU-based	166
TCGAb	DNA methylation	Illumina Infinium Human DNA Methylation 450	II–III	5-FU-based	176

Abbreviations: 5-FU, 5-fluorouracil; MSI, microsatellite instability.

^aIn this data set, there were 85 samples of patients treated with 5-FU-based chemotherapy and 139 samples of patients did not accept 5-FU-based treatment. These two groups of samples were analyzed.

^bAmong the 184 TCGA samples with mRNA-seq profiles, 183, 143, 166 and 176 samples also had copy number, somatic mutation, MSI and DNA methylation data.