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Table 1 The 38 lung-specific TFs in LungNet and their differential activity characteristics

From: Systems-epigenomics inference of transcription factor activity implicates aryl-hydrocarbon-receptor inactivation as a key event in lung cancer development

LungNet TF LSCC (RNA-seq) LSCC (DNAm) LCIS (mRNA) LCIS (DNAm) Smoking (DNAm) Smokinga (mRNA-Affy)
TFEC –24.14 18.61 2.9 5.16 –4.58 UP
TBX2 –33.08 –18.69 –5.52 –1.16 –6.55 DN
FOXA2 –22.01 –17.57 –1.43 –7.91 1.41 NA
TAL1 –40.65 -18.45 –2.28 –0.87 –5.33 DN
TBX4 –44.91 –7 –1.68 –4.45 1.61 DN
NKX2-1 –34.8 –2.76 1.73 –2.63 5.18 NA
GATA2 –40.81 –11.36 –2.47 –1.53 –5.26 NA
EPAS1 –35.72 –32.7 –3.28 –5.25 –1.69 DN
FOXJ1 –9.44 –16.65 –1.73 –6.94 –1.86 NA
LDB2 –44.35 –11.99 –3.16 2.14 –5.32 DN
ETS1 –32.67 –5.25 0.15 –3.42 –5.37 NA
ETV1 –33.76 –9.3 –5.97 0.25 –2.66 NA
ERG –33.38 –23.56 –3.16 –2.76 –5.23 DN
ELF3 3.56 10.57 1.96 –4.44 5.73 NA
SOX13 –30.47 15.77 –7.33 –1.8 1.13 NA
AHR –21.6 –0.61 –2.67 –2.98 1.7 NA
PML –9.33 –7.3 2.82 –1.56 –2.06 NA
FOXA1 –9.57 11.95 –0.21 –5.57 5.51 NA
MLLT4 –1.28 –12.25 2.53 2.16 1.52 DN
BGN –9.85 –24.23 –4 –6.12 3.08 NA
ZFP36 –11.43 –7.05 2.9 1.05 2.62 NA
TNXB –27.31 –12.72 –4.44 –3.58 4.19 NA
SOX18 –39.37 –13.51 –3 1.23 –4.88 NA
TEAD2 –19.59 –32.39 –3.26 –4.49 –2.64 NA
XBP1 5.66 –6.78 –0.54 1.69 –0.07 NA
MEOX2 –40.54 –3.58 –4.73 –1.6 1.28 NA
KLF4 –14.85 2.89 4.05 –0.33 5.44 NA
HIF3A –36.97 –9.37 –5.85 3.44 3.65 NA
LSR 9.53 4.06 2.51 –4.1 5.27 NA
KLF9 –29.79 –21.26 –5.49 1 –5.1 NA
STON1 –36.61 –7.75 –4.79 –3.04 1.9 NA
PPARG –25.61 –19.38 –0.45 –4.53 –5.77 UP
ZFP36L2 –29.34 –4.42 –3.63 1.66 –3.36 NA
CEBPD –15.4 –0.86 –0.07 –0.14 –4.08 NA
TRIP10 0.09 –5.79 –3.52 –1.22 3.94 NA
NR2F2 –20.82 –8.14 –6.41 –7.52 3.61 NA
TGFB1I1 –15.65 –25.46 –4.86 –4.96 1.52 NA
EHF 6.17 25.89 2.3 –3.08 5.98 NA
  1. Table lists for each of the 38 lung-specific TFs, the t-statistics of differential activity in five different studies. In LSCC (RNA-seq), t-statistic reflects differential activity of LSCC relative to NADJ tissue as measured using RNA-seq of the predicted TF targets; in LSCC (DNAm) t-statistics of differential activity are shown but as inferred using promoter DNAm levels of targets, in LCIS (messenger RNA [mRNA]) and LCIS (DNAm) t-stats reflect differential activity between LCIS and NADJ tissue as assessed using gene expression and promoter DNAm levels of targets, respectively (expression and DNAm are from unmatched cases and cohorts); and finally, in Smoking (DNAm) we give the t-statistics of differential activity between buccal samples of heavy smokers compared to non-smokers (measured in smoking pack-years) and as assessed using promoter DNAm levels of targets. Numbers in italic represent cases of significant inactivation
  2. aA gene expression study comparing NADJ lung tissue of smokers to non-smokers and which only provided a table of differentially expressed genes
  3. DN TFs that were reported in this study to be underexpressed in the normal lung tissue of smokers, UP TFs reported to be overexpressed, NA not reported to be consistently differentially expressed across three independent studies