Colon cancer associated genes exhibit signatures of positive selection at functionally significant positions

Morgan, Claire C; Shakya, Kabita; Webb, Andrew; Walsh, Thomas A; Lynch, Mark; Loscher, Christine E; Ruskin, Heather J; O’Connell, Mary J

doi:10.1186/1471-2148-12-114

BMC Ecology and Evolution

Table 1 Colon Cancer Gene Set analyzed in this study

From: Colon cancer associated genes exhibit signatures of positive selection at functionally significant positions

Gene (HGNC code)	Ensembl Identifier	Taxa Number²	Alignment Length³	Syndrome	Tumor Types Observed	Pathway(s)	References⁴
APC	ENSG00000134982	20	9177	Familial adenomatous polyposis (FAP)	Colon, thyroid, stomach, intestine	APC	[19, 24]
ATM	ENSG00000149311	18	9189	Ataxia telangiectasia (A-T)	Leukemia, lymphoma, colorectal	CIN	[24], [17]
BHD	ENSG00000154803	20	1737	Birt-Hogg-Dube syndrome	Renal, colon	AMPK, mTOR, STAT	[24]
BMPR1A	ENSG00000107779	19	1596	Juvenile polyposis	Gastrointestinal	SMAD	[24]
CDH1	ENSG00000039068	15	2649	Familial gastric carcinoma	Stomach	AP	[[24, 28] (E-cadherin)]
MADH4	ENSG00000141646	16	1656	Juvenile polyposis	Gastrointestinal	SMAD	[[24], (SMAD4)]
MET	ENSG00000105976	21	4146	Hereditary papillary renal cell carcinoma (HPRCC)	Kidney, colorectal	RAS, PI3K, STAT, Beta-catenin, Notch	[24]
MLH1	ENSG00000076242	19	2274	Hereditary non-polyposis colon cancer (HNPCC)	Colon, uterus	MMR	[24]
MSH2	ENSG00000095002	18	2802	Hereditary non-polyposis colon cancer (HNPCC)	Colon, uterus	MMR	[24]
MSH6	ENSG00000116062	19	4101	Hereditary non-polyposis colon cancer (HNPCC)	Colon, uterus	MMR	[24]
MUTYH	ENSG00000132781	21	1569	Attenuated Polyposis	Colon	BER	[24]
NF1	ENSG00000196712	17	8523	Neurofibromatosis type I	Neurofibroma, colon	RTK	[24]
PMS1	ENSG00000064933	20	2799	Hereditary non-polyposis colon cancer (HNPCC)	Colon, uterus	MMR
PMS2	ENSG00000122512	21	2592	Hereditary non-polyposis colon cancer (HNPCC)	Colon, uterus	MMR	[24]
PTEN	ENSG00000171862	18	1209	Cowden syndrome	Hamartoma, glioma, colorectum	PI3K	[24], [17]
SDHB	ENSG00000117118	18	840	Hereditary paraganglioma, Carney–Stratakis	Paragangliomas, pheochromocytomas, gastrointestinal	HIF1	[24]
SDHC	ENSG00000143252	16	507	Hereditary paraganglioma, Carney–Stratakis	Paragangliomas, pheochromocytomas, gastrointestinal	HIF1	[24]
STK11	ENSG00000118046	18	1320	Peutz-Jeghers syndrome	Intestinal, ovarian, pancreatic, colorectal	PI3K	[24, 29]
TP53	ENSG00000141510	16	1185	Li-Fraumeni syndrome/sarcoma	Breast, sarcoma, adrenal, brain, colorectal	p53	[24, 29]
TSC1	ENSG00000165699	18	3495	Tuberous sclerosis	Hamartoma, kidney, colorectal	PI3K	[24, 29]
TSC2	ENSG00000103197	19	5436	Tuberous sclerosis	Hamartoma, kidney, colorectal	PI3K	[24, 29]
VHL	ENSG00000134086	18	639	Von Hippel-Lindau syndrom	Kidney, colorectal	HIF1	[24]

Each of the 22 genes analyzed in this study are detailed, including their HGNC approved gene symbols, and Ensembl gene IDs. The total number of species analyzed for each gene and the overall length of alignment in base pairs are also given. The syndrome, tumor type observed and pathway involved are detailed. References citing alternative gene names are identified using rounded parentheses.

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ISSN: 2730-7182

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