Skip to main content

Table 3 BAC clones with significant frequency differences between SCC and AC subtypes of NSCLC

From: Identification of novel candidate target genes, including EPHB3, MASP1 and SSTat 3q26.2–q29 in squamous cell carcinoma of the lung

BAC clone Regions Gene contained in clones % of gain in SCCs % of gain in AC p-value*
Gains      
   BAC13_I04 2q14.2   55 7 0.046
   BAC215_M07 3q26.2 EVI1 77 29 0.007
   BAC28_H10 3q26.2 MDS1 45 7 0.034
   BAC127_C12 3q26.32 PIK3CA, KCNMB3 50 14 0.050
   BAC78_P09 3q26.2 LOC389174 45 7 0.034
   BAC97_L20 3q27.1 EPHB3 32 0 0.039
   BAC187_G13 3q27.3 MASP1 45 7 0.034
   BAC195_F06 3q27.3 SST 32 0 0.039
   BAC62_G09 3q28   64 7 0.002
   BAC29_O18 3q28 TP73L 45 7 0.034
   BAC74_E06 3q28   50 7 0.015
   BAC143_F11 3q28 FGF12 45 7 0.034
   BAC144_N20 3q28 LPP 48 0 0.032
   BAC95_M19 3q29 OPA1 55 7 0.046
   BAC96_C05 3q29 KIAA0226, LOC220729, LOC440996, LOC440997, LOC440998 45 7 0.034
   BAC42_D19 7q22.1 TRRAP 0 29 0.023
   BAC141_P01 7q22.1 ZKSCAN1, ZNF38, ZNF3 0 29 0.023
   BAC118_C23 12p13.2 CDKN1B, DKFZP434F0318 50 0 0.003
   BAC26_P09 12p13.32 TSPAN9, LOC399986, LOC441627 59 7 0.001
   BAC159_B18 12p13.33 LOC440123, SLC6A12, SLC6A13 45 0 0.002
   BAC179_J19 12p13.33 SLC6A12, SLC6A13 32 0 0.003
   BAC18_B14 19p13.3 SCHC2, C19orf19, MADCAM1,
C19orf20, CDC34, GZMM, BSG
41 0 0.008
Losses §      
   BAC83_J18 3p26.2 LOC440943 36 0 0.018
   BAC229_D19 3p26.3 CCR2, CCRL2, APOD 45 0 0.005
   BAC57_A15 15q22.2 RORA 5 36 0.033
   BAC175_C05 15q25.2 DNM1DN11-6, LOC388160, LOC440300, LOC388152, LOC161527, LOC440301, LOC159170 5 36 0.033
   BAC169_L10 16p13.11   55 7 0.046
   BAC130_G23 17p11.2   64 36 0.039
  1. Abbreviations: AC, Adenocarcinoma; SCC, Squamous cell carcinoma; * P values from Fisher's exact test on categorized log2 ratio values. Alterations were defined by log2 ratio thresholds of 0.25 for copy number gain. Using this threshold, we generated a frequency table. §Alterations were defined by log2 ratio thresholds of – 0.25 for copy number loss. Using this threshold, we generated a frequency table.
\