Expression array Analysis

 

Main Display

The expression analysis module of GenomeMTV is used for a gene-centric analysis of microarray data. The analysis is compatible with both standard gene expression microarray designs, with multiple probes per gene, and tiling designs, with probes targeting the entire genome including in gene regions. After loading your microarray data, genomeMTV scores each gene on each chip using the standard MAS 5.0 analysis routines to compute gene intensity values. The Main window of the analysis is a window listing all CEL files, and a toolbar launching different views and analyses. It also has a signal intensity filter to hide genes with low signal intensity.

Chip Display

Contents

- Chip Display

- Bar Plot

- Heatmap

  1. -Different Plot

  2. -Parallel Coordiantes

  3. -Spreadsheets

Chip Display

Bar Plot

Heatmap

Difference Plot

Parallel Coords

Bar Plot

Heatmap

Difference Plot

Parallel Coordinates

The chip display lets you visually inspect the microarray quality by displaying the probe intensities   by their spatial positions on the microarray. Chips with spatial artifacts (cracks, smears, distortions), should be removed from the analysis. The side menu allows you to select between the different CEL files.

The bar plot displays the gene intensities on a single microarray experiment using a bar for each gene. Tooltips display the name and the signal value intensity. Click and drag to select genes for further analysis.

The heatmap displays the signal intensity for each gene (by row) and for each microarray (by column). It can also computes hierarchical clustering of the genes and/or experiments to help identify trends in the intensity values. GenomeMTV uses the C Clustering Library to compute the clusters, which supports several distance metrics (Euclidean, Pearsons, etc) and several linkage methods (Single Link, Complete, etc). The clustering can take a long time to compute if there are many genes to cluster. Use the signal intensity filter to exclude the low intensity genes from the analysis.

The difference plot compares the gene intensity values in a pair of experiments. The red bars show the intensity values for the individual chips, and the white overlay shows the difference between the two intensities. Use the side control panel to select which microarrays to compare, the first will use positive bars (up), and the second uses negative bars (down). “Show Relative Intensity” normalizes the individual gene intensity values by the maximum of the pair.

The parallel coordinates plot displays the change in intensity over the chips, such as in a time series analysis. Each gene is drawn as a polyline, and each microarray is represented by equally spaced vertical lines shown in white. The polyline coordinates on the vertical lines indicate the intensity of that gene in that microarray.

In the display menu from the main window, there are also options for displaying the “Chip Design”, “Probe Values”, and “Gene Results”. These options display a sortable and seachable spreadsheet of the information. The Chip Design spreadsheet has probe specific information, such as the location of the probe on the microarray, and the gene target. The Probe Values spreadsheet displays the probe intensity values after normalization. The Gene Results spreadsheet shows the intensity for each gene. The file menu has options for saving the entire spreadsheet or selected portions of the table to a tab-deliminated text file.

Spreadsheets

Signal Intensity Filter