Main Functions
Dynamic Heatmap Viewer is a powerful and versatile tool to help scientists to interactively visualize the microarray gene expression data. This guide provides a summary of options in the graphical user interface.
- Gene ID/Array Label
- The drop-down list displays the gene id (array label) from mouse-over gene (array).
- Value
- This shows the gene expression of the mouse-over array and gene combination.If centering and scaling option is checked in the main dialog, it will be applied on this value.
- Class
- A color bar representing different classes in arrays by different colors can be shown with this option.
- Color Pref
- Several predefined color preferences representing the expression data are available for users to select. Gray color represents missing values.
- Color Scheme
- Two color schemes are provided. The Saturated method will truncate gene expression at color limits in heatmap while Quantile method will use expression data quantiles as bins to represent the colors. Gray color represents missing values.
- Color Limit
- If Saturated method was selected (default), the heatmap displays gene expression data by truncating theexpression at lower and upper thresholds. Users can adjust the upper/lower threshold by clickingthe +/- buttons. The color legend on the right hand side of heatmap shows the current threshold values. By default, if the minimum value of expression is less than 0, the limit is determined by the data; otherwise [max(-2, smallest data value), min(2, largest data value)] will be used. Summary Statistics: These statistics provide basic information about the data which could be useful for the selection of thresholds if ‘Saturated’ color scheme is used. The gene distance information is useful when cutting gene tree is performed.
- Link to GeneCards
- Right click on the heatmap, a browser will be opened and connected to GeneCards that contains more relevant information about the gene.
- Zoom In
- To zoom-in to a subset of genes, users can left click mouse button and select an area on the heatmap. The heatmap will be re-drawn the desired region after the mouse is released. If the plot was zoomed in to show less than 50 genes, gene symbols or unique IDs will be shown along the plot on the right hand side.
- Reset Zoom-In
- The heatmap will be re-drawn using all genes. The keyboard shortcut is Alt+R.
- Zoom Out
- To go back to the heatmap before zooming in, click on the Zoom Out button.
- Print to PDF
- This function allows users to save the plot in a high-quality Portable Document Format (PDF) format. Alternatively, users can use Windows keyboard shortcut Alt + PrtSc to copy the current heatmap to a clipboard. Then the graph in the clipboard can be pasted to a MS-WORD document or other image processing software.
- Highlight Genes
- To highlight genes in the heatmap, users can choose from one of three options (the selected gene identifier will be used to match the gene labels if users choose the option #1).
- Enter gene labels to search for. The comma sign can be used to separate multiple genes.
- Browse a genelist file. The first column in the genelist file will be used to match.
- Browse a Biocarta/KEGG pathway.
After clicking the OK button, genes containing the desired labels will be highlighted using purple circle dots located on the right hand side of the heatmap. To erase the dots, select either option 1 or 2. Then press the Clear and then the OK button.
- Cut Gene Tree
- This will cut gene dendrogram and save the gene IDs in each individual cluster to a text file. For example, if users select 3 clusters or a distance which results in 3 clusters, there will be 3 tab-delimited text files generated (cluster1.txt, cluster2.txt and cluster3.txt) under the output folder where each text file contains gene IDs from each individual cluster. This function will be disabled if the zoom-in has been applied.
- Save Genes
- This will save the gene IDs from currently selected genes to a text file.
- Options
Show gene dendrogram: check/uncheck the box to show/hide the gene dendrogram.
Save color preference and scheme: check the box to save the color preference and scheme for the next launch.
Choice of Y label: which gene label will be used on the Y-axis.
Choice of X label: which array ID will be shown on the X-axis.
- Tips
The heatmap displays array IDs at the bottom of the heatmap. The array IDs are obtained from the first column of the Experiment Descriptor (this can be changed from the Options dialog). They are displayed only if the total number of arrays is less than or equal to 200.
The heatmap displays gene symbol at the right hand side of the heatmap. If gene symbols are not available, the first column of gene identifiers worksheet will be used (this can be changed from the Options dialog). The gene symbols are only displayed if the number of genes is less than or equal to 100.
If the number of classes is more than 10, the colors for the class color bar will be re-used.
The executable program Qheatmap.exe can be used as a stand alone application. When users run the program without specifying a working directory, the program will pop up a dialog asking the working directory. The working directory should contain input files expression.txt (gene expression), GeneIDs.txt (gene annotation), ExpDescWkSht.txt (experiment descriptor), options.txt (options such as linkage method and distance), order.txt (orderGene.txt), merge.txt (mergeGene.txt), and height.txt (heightGene.txt) for plotting array and gene dendrograms.