Primers and restriction enzymes used to investigate polymorphisms in the <i>PTEN</i>, <i>AKT1</i> and <i>p53</i> genes.

a<p>Italicized lowercase letters indicate base mismatches.</p>b<p>Designated rs2498799 in previous literature.</p

Combined effects of the genetic variants in the <i>PTEN</i>, <i>AKT1</i>, <i>MDM2</i> and <i>p53</i> genes on the risk of nasopharyngeal carcinoma.

<p>Abbreviations: OR, odds ratio; CI, confidence interval.</p>a<p><i>χ²</i> test for the distribution of genotypes between patients and control subjects.</p>b<p><i>P</i> values were calculated by multivariate logistic regression, adjusted for age, sex, smoking and drinking status, smoking level, and nationality.</p>c<p><i>χ</i>² test for the <i>P</i>_trend value of genotypes between patients and control subjects.</p>d<p>Low-risk group, individuals carrying 0–2 risk genotypes; high-risk group, individuals carrying 3-4 risk genotypes.</p><p>*<i>P</i> value remained significant after c°rrection for multiple comparisons (<i>P</i> = 0.048).</p

Haplotypes of <i>AKT1</i> polymorphisms and the risk of nasopharyngeal carcinoma.

<p>(<i>a</i>) Genomic structure of the <i>AKT1</i> locus and the polymorphic sites used. Exons (boxes) and introns are not drawn to scale; open boxes represent noncoding sequences, and filled boxes represent coding sequences. The physical distance between SNPs is shown in nucleotides. (<i>b</i>) Linkage disequilibrium (LD) map of SNPs based on <i>D</i> ´. (<i>c</i>) LD map of SNPs based on <i>r</i>². (<i>d</i>) Global <i>P</i> values from single-locus and multi-locus (two to five) based association analysis. (<i>e</i>) Haplotypes showing significant genetic associations with the risk of nasopharyngeal carcinoma. The two-SNP core haplotype is highlighted in gray.</p

Stratification analysis of the combined genotypes of the <i>PTEN</i>, <i>AKT1</i>, <i>MDM2</i> and <i>p53</i> polymorphisms and risk of nasopharyngeal carcinoma.

<p>Abbreviations: OR, odds ratio; CI, confidence interval.</p>a<p>ORs and <i>P</i> values were calculated by multivariate logistic regression, adjusted for age, sex, smoking and drinking status, smoking level and nationality when appropriate within the strata.</p>b<p>For differences in ORs within each stratum.</p>c<p>Low-risk group, individuals carrying 0–2 risk genotypes; high-risk group, individuals carrying 3–4 risk genotypes.</p

Transcription Factor Response Elements on Tip: A Sensitive Approach for Large-Scale Endogenous Transcription Factor Quantitative Identification

The ability to map endogenous transcription factors (TFs) DNA binding activity at the proteome scale will greatly enhance our understanding of various biological processes. Here we report a highly sensitive, rapid, and high-throughput approach, transcription factor response elements on tip-mass spectrometry (TOT-MS), that allows for quantitative measurement of endogenous TFs. A total of 150 TFs from 1 μg of nuclear extracts can be quantified with single shot mass spectrometry detection in 1 h of machine time. Up to 755 TFs, which is comparable to the depth of RNA-seq, were identified by TOT coupled with on-tip small size reverse-phase liquid chromatography. We further demonstrated the capability of TOT-MS by interrogating the dynamic change of TFs in the epidermal growth factor (EGF) signaling pathway. This approach should find broad applications in elucidating the TF landscape from limited amounts of biological materials