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Table 2 Clusters with focal aberrations in lung cancer.

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

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
  1. 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.
  2. §Gene annotations are based on hg18 human genome assembly.
  3. †MDM2 is located at chr12:67,488-67,520 KB and CCNE1 at chr19:34,500 KB.
  4. ‡Cancer related genes identified using the proposed method, not GISTIC.