Populations of human hematopoietic cells.

<p>38 hematopoietic cell populations are shown with their respective positions in hematopoiesis. Cells called as “progenitors” in the analysis are marked by a red box, “non-progenitor” cells are marked by a gray box. Figure adapted from Novershtern et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039148#pone.0039148-Barrett1" target="_blank">[9]</a>.</p

Overview of the LGA architecture.

<p>Data is imported from several online repositories and the medical literature into the LGA database. An analysis module processes the molecular data. The application server handles data transfer between database and analysis module and can be accessed through a web interface. It executes queries and forwards data and analysis results to the client.</p

Usage of the LGA web interface. (Above)

<p>Experiment view with information on the integrated study <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039148#pone.0039148-Robinson1" target="_blank">[15]</a> (above), sample characteristics (hidden, in the middle) and stored result tables (below). Genes with <i>RUNX1</i> binding sites are copied from a table of peak annotations and stored as a gene list. <b>(Middle)</b> Groups of samples from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039148#pone.0039148-Benjamini1" target="_blank">[14]</a> are defined in the analysis tab. <b>(Below)</b> Selecting the stored gene list (genes with <i>RUNX1</i> binding sites) and performing principle component analysis on the selected groups of samples from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039148#pone.0039148-Benjamini1" target="_blank">[14]</a>.</p

Overview of data in the LGA.

<p>Overview of data in the LGA.</p

The role of <i>RUNX1</i> and its binding sites in leukemias.

<p>(<b>A</b>) Screenshot of a t-test result table with the 33 most differentially expressed genes with <i>RUNX1</i> binding sites in progenitor and non-progenitor cells. (<b>B</b>) Distribution of <i>RUNX1</i> expression for different leukemic disease states. (<b>C</b>) Heat map and hierarchical clustering of patients with acute lymphoblastic leukemia and non-leukemia samples with healthy bone marrows for gene expression of genes with RUNX1 binding sites and highest variances over all samples. The phenotype color grid at the top represents the sample characteristics. (<b>D</b>) Kaplan Meier curves of event-free survival for patients with acute myeloid leukemia with low (≤33% quantile), median (>33% quantile and ≤66% quantile), and high <i>RUNX1</i> expression (>66% quantile).</p