Contingency table for probeset <i>g_ij</i> at age <i>a = δ_j</i> where <i>j≤m</i> samples (<i>m = 1, 2, …n-1</i>).

<p>Contingency table for probeset <i>g_ij</i> at age <i>a = δ_j</i> where <i>j≤m</i> samples (<i>m = 1, 2, …n-1</i>).</p

Functional annotation analysis summary.

<p>Functional annotation analysis summary.</p

Histograms of genes with age-regulated transition points within each decade between 25 and 95 years (p-value≤0.005) in three brain regions.

<p>The distribution of age-regulated genes is very different in BA10 compared to BA9 and BA47.</p

Performance of age estimation using the proposed naïve Bayes method and other methods.

<p>The five-fold cross validation results showed age estimation errors of the naïve Bayes model to be 0.14∼4.38 years smaller than in other tested models, thus reducing error by 34%.</p

Best number of genes (<i>N</i>) used in age estimation and the difference of median of age is the absolute difference between the median of estimated age and the median of chronological age.

<p>The significance of the error was determined by obtaining 1,000 randomized cross-validation errors with age information randomly shuffled; the significance of the prediction error is the fraction of the 1,000 randomized errors lower than the actual cross-validation error. The best <i>N</i> varies across regions.</p

Characteristics Path Length in-between Groups of age-correlated genes.

<p>The size of each region shows the number of genes having overlap between the protein-protein interaction network and our age-regulated gene study. Size of Y(young) vs. M (middle-aged), M vs. O (old), and O vs. Y showed the union gene number of each group each brain region.</p

Additional file 1 of McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes

Supplementary figures. (PDF 9185 kb

Additional file 3 of McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes

McEnhancer predicted DHSs for each cluster. This table shows the predicted DHSs for each cluster, along with its associated gene. Columns represent DHS coordinates (chr, start, end), DHS ID linked to its associated gene, and number of times each DHS was selected in the model’s pairwise comparisons against other clusters. (TXT 778 kb