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Documentation

dictyExpres is a Flash-based web application for retrieval and analysis of gene expression profiles from different D. discoideum experiments. The applications consists of components for data retrieval, selection of individual genes or groups of genes, graphic display of gene expression time courses, Gene Ontology term enrichment analysis, display of gene co-expression networks, hierarchical clustering, and expression profile visualization of selected genes in different experiments. The components are connected such that a change in any one of the components (e.g., selection of a gene subset from the hierarchical clustering dendrogram) can propagate to other components and their associated visualizations.

Gene Expression Query

This component supports experiment selection and allows the user to choose a set of genes (up to 30) for viewing in the expression profile window.

The gene selection entry box supports gene name completion.

Use the Up or Down Arrow keys to select the gene from the list of suggestions. Press Enter to add the selected gene to the gene selection list. Alternatively, double-click on the relevant row in the gene selection list. Use the Shift key to select a range of gene names or use the Command key to select multiple individual genes from the list.

Expression Profile

This component displays the expression profiles of a selected set of genes from a selected experiment.

Freehand drawing of an expression profile is invoked by clicking on the "Freehand" button. The button turns grey and cursor changes to a brush:

The "Find similarly expressed genes" button opens a window that lists genes with similar profiles to the selected (target) gene:

Gene Ontology

The set of selected genes (listed in the Gene Expression Query) is used as a cluster (query) set in this gene ontology term enrichment analysis. All the genes from the current experiment are used as the reference set. Enriched terms are reported in the gene ontology tree, displaying one of the three Gene Ontology aspects at a time. If a gene is selected in another dictyExpress component, the Gene Ontology component highlights the corresponding terms.

Hierarchical Clustering

Hierarchical clustering considers a set of selected genes from the Gene Expression Query and displays the results of expression profile-based clustering in a dendrogram. The visualization also includes a heatmap, displaying gene expressions at different time points. The dendrogram is interactive, and may be used to select a target gene or a group of gene.

Coexpression Network

The network considers a single reference gene and displays a neighborhood of the most similar genes. Genes in the network are at most three hops away from the target gene.

Experiment Comparison

This component plots the expression profile of a reference (target) gene in a selected set of experiments.

SCREENSHOT: Comparison ofgeneexpression profile in different experiments.

The Menu Bar

SCREENSHOT: The menu bar

The Toolbox

Quick Tips

References