Systematic genomic identification of colorectal cancer genes delineating advanced from early clinical stage and metastasis

Table 1 Top 10 genes associated with MSI

	Mutation alone		Methylation alone		Integrated data
Rank	Gene	Sign	Gene	Sign	Gene	Sign
1	TGFBR2	↑	MLH1	↑	MLH1 (methyl)	↑
2	CASP8	↑	FLVCR2	↑	PDE6B (mut)	↑
3	ACVR2A	↑	EFNA1	↓	POLR1D (mut)	↑
4	MSH3	↑	CDK12	↑	FLVCR2 (methyl)	↑
5	MAP3K6	↑	HOXC11	↓	DAK (mRNA)	↑
6	GATA2	↑	ZNF318	↑	TGFBR2 (mut)	↑
7	MACF1	↑	SEPT5	↑	SEPT5 (methyl)	↑
8	BRAF	↑	MIER3	↑	EFNA1 (methyl)	↓
9	GPHN	↑	ELK4	↓	MLH1 (mRNA)	↓
10	MAEA	↑	SDHD	↓	STK32B (mut)	↑

Gene ranking is based on the regression coefficient (see Methods). Genomic assay and associated feature is indicated in parentheses for integrative analysis of the combined genomic data. The symbol ↑ indicates increased frequency (mutation) or level (methylation) in MSI. The symbol ↓ indicates decreased frequency (mutation) or level (methylation, gene expression) in MSI.

ISSN: 1755-8794