Wavelet-based identification of DNA focal genomic aberrations from single nucleotide polymorphism arrays

BMC Bioinformatics

Table 2 Clusters with focal aberrations in lung cancer.

Score	P _cluster	Cytoband	Start (KB)	End (KB)	# of PA	Gene Symbol§
118	0	14q13.2 q13.3	35,467	36,690	10	MBIP,NKX2-1
107	0	12p11.23 p12.1	24,055	26,685	4	KRAS
84	0	18q11.2 q12.1	20,300	23,537	4	SS18
62	0	7p11.2 p12.1	53,796	55,553	3	EGFR
54	0.006	18q21.1	43,971	45,322	2	SMAD7 ‡
51	0.064	12q15	67,983	69,669	4	MDM2 †
47	0.006	19q12	35,835	36,303	2	CCNE1 †
47	0	11q13.2 q13.3	68,164	69,500	3	CCND1
42	0.012	19q13.11 q13.12	37,716	41,040	5
35	0	22q11.21	19,057	19,785	2
33	0	17q12 q21.1	33,845	35,540	4	ERBB2
26	0.018	8p11.23 p12	38,417	39,171	2	FGFR1
24	0	10p11.21	37,594	38,717	2
22	0	6p21.33	30,143	30,911	2
15	0.023	6p22.1 p22.2	26,089	26,937	2
14	0.007	5p12	42,982	44,452	2	FGF10 ‡
10	0.064	6p21.1	43,240	44,227	2	VEGFA
10	0.019	10q11.21	42,184	43,133	2
9	0	9p21.3	24,546	25,375	2
-3	0	9p21.3	21,181	22,194	2	CDKN2A

When M = 11, 20 statistically significant clusters are shown. These clusters contain known lung cancer genes or cancer related genes in other cancer types. All genes contained in the 20 clusters are described in Additional File 6. Columns are as described in Table 1.
§Gene annotations are based on hg18 human genome assembly.
†MDM2 is located at chr12:67,488-67,520 KB and CCNE1 at chr19:34,500 KB.
‡Cancer related genes identified using the proposed method, not GISTIC.

ISSN: 1471-2105