Median and 95% confidence interval (CI) estimates of the rate of change of marginal effect of benzene exposure below 1 ppm (/ – see equations (9) and (12)) and above 1 ppm (/ - see equations (10) and (13)) and the change in absolute rate of change of the marginal effects from below 1 ppm to above 1 ppm (/ – see equations (11) and (14)) for the first two principal components of the Acute Myeloid Leukemia pathway and six chosen genes of interest.

<p>Median and 95% confidence interval (CI) estimates of the rate of change of marginal effect of benzene exposure below 1 ppm (/ – see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091828#pone.0091828.e050" target="_blank">equations (9</a>) and (12)) and above 1 ppm (/ - see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091828#pone.0091828.e051" target="_blank">equations (10</a>) and (13)) and the change in absolute rate of change of the marginal effects from below 1 ppm to above 1 ppm (/ – see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091828#pone.0091828.e055" target="_blank">equations (11</a>) and (14)) for the first two principal components of the Acute Myeloid Leukemia pathway and six chosen genes of interest.</p

Overlapping sets of genes determined by two linear models.

<p>Two linear mixed models were used, a published model <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091828#pone.0091828-McHale2" target="_blank">[13]</a> (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091828#pone.0091828.e019" target="_blank">Equation (2</a>)) and a modified version including counts of different blood cell types as potential confounders of gene expression (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091828#pone.0091828.e012" target="_blank">Equation (1</a>)). Differential expression was determined based on altered fold changes in at least one of the four previously chosen dose ranges of benzene exposure, with an FDR-adjusted <i>p</i>-value<0.05.</p

Responses of selected genes associated with the leukemia disease process.

<p>Non-parametric model fits to the expression response of the probes corresponding to six genes known to be associated with AML, with air-benzene concentrations in parts per million. Note the responses here are log fold-changes in expression. The dot-dashed horizontal line at a log fold change value equal to zero indicates the no-effect response. The gene names along with the corresponding probe id number on the microarray in parentheses are provided for each gene. The small vertical ticks on the x-axis denote doses to which one or more subjects in the study were exposed and consequently the doses for which data for all covariates under consideration were available. The three red ‘x’s above these ticks indicate the doses that there used to compare the rate of change of the marginal effect of benzene exposure from 0.001 to 1 ppm air benzene to the corresponding rate from 1 to 10 ppm air benzene.</p

Overview of methods and analyses.

<p>Overview of methods and analyses.</p

AML pathway-Clusters of probes/genes.

<p>Hierarchical cluster of the probes in the AML pathway. The probes are clustered based on the distance between the corresponding rows of the matrix, given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091828#pone.0091828.e038" target="_blank">Equation (6</a>). The figure is a visual representation of the distance matrix between all the probes/genes in the pathway. The color of the <i>(i,j)^th</i> position of the distance matrix is a measure of how close probes <i>i</i> and <i>j</i> are to each other based on their response across the dose range. The color ranges from white to red. The closer the pair of probes is two each other, the greater the intensity of red at the corresponding position. The dashed black lines correspond to boundaries of clusters of probes as determined by the HOPACH algorithm <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091828#pone.0091828-vanderLaan1" target="_blank">[47]</a>.</p

Response of two Cytochrome p450 genes associated with benzene metabolism.

<p>Non-parametric model fits to the expression response of the probes corresponding to two genes known to be associated with the metabolism of benzene, CYP2E1 and CYP2F1, with air-benzene concentrations in parts per million. Note the responses here are log fold-changes in expression. The dot-dashed horizontal line at a log fold change value equal of zero indicates the no-effect response. The gene names along with the corresponding probe id number on the microarray in parentheses are provided for each gene. The small vertical ticks on the x-axis denote doses to which one or more subjects in the study were exposed and consequently the doses for which data for all covariates under consideration were available. The three red ‘x’s above these ticks indicate the doses that there used to compare the rate of change of the marginal effect of benzene exposure from 0.001 to 1 ppm air benzene to the corresponding rate from 1 to 10 ppm air benzene.</p

AML pathway-Principal Components-based response.

<p>The continuous fits in the two subplots use the first and second eigenvectors (that are slightly modified, see Material and Methods section) respectively from the eigenvector matrix, given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091828#pone.0091828.e037" target="_blank">Equation (5</a>). The elements of the individual eigenvectors are treated as the pathway response at the corresponding dose. The subscript <i>p</i> corresponds to the pathway under consideration and superscript <i>s</i> to a given bootstrap sample. The bold red line correspond the mean parameter estimates across the bootstrap samples and the bold black lines represent the corresponding 95% confidence intervals for the mean parameter estimates. The small vertical ticks on the x-axis denote doses to which one or more subjects in the study were exposed and consequently the doses for which data for all covariates under consideration were available. The three red ‘x’s above these ticks indicate the doses that there used to compare the rate of change of the marginal effect of benzene exposure from 0.001 to 1 ppm air benzene to the corresponding rate from 1 to 10 ppm air benzene.</p