Chromosome view

This function is for visualizing SNP LOH or copy number data or expression data of genes according to their relative chromosome positions, thus the relationship between gene expression changes and their physical locations can be investigated in a greater detail than the “Analysis/Genome” function.
 
At “Analysis/Open group”, specify a sample info file with a “Ploidy(numeric)” column to specify the reference samples. Samples with “Ploidy(numeric)” column as 2 are regarded as reference samples and are used to compute the mean signal of normal expression level or 2 copy. Select the menu “Analysis/Chromosome” and provide a “Genome information file” and optional “RefGene file”, cytoband file and gene list file in the dialog, select the analysis method as “Expression” (for expression data) or "LOH and copy number analysis" (for SNP data), and then click “OK”. If there is multiple chromosomal mapping for a probe set in the genome info file, dChip will use the last one (row). A “Chromosome” icon will be added in the left panel and the “Chromosome View” displays the expression or SNP data across samples along the chromosome (data from Janne et al. 2004):

 

Displayed on columns are the ordered samples in the currently used “Tools/Array list file”, and genes are displayed in rows according to their relative chromosomal positions. In the log2 data view, the red and blue colors represent the log2 ratios between a sample and the mean signal of the reference samples for a gene. In the “Copy number” view, the raw copy number is computed as the ratio between a sample and the reference mean multiplied by 2 and is displayed. The color range can be adjusted by “Tools/Options/Clustering/Display range of standardized values”. The presence or absence calls can also be displayed, by using “Chromosome/Next Data Type” or key “D, S” to toggle between the expression values and the presence calls. In this display, light red color represents “Present” calls and light blue color “Absent” or “Marginal” calls. Cytoband information is display on the left side, and gene names are displayed on the right side.

Navigate the chromsome view
 
Use “Home” and “End” keys to view other chromosomes, and “Chromosome/Show All” or key “A” to display genes on all chromosomes in a single picture. For SNP arrays the chromosome Y may not be available since there are no probe sets on the array for chromosome Y markers. Mouse-over the colored data point area to display information such as the expression values (and standardized values) or presence calls. Mouse-overing a refgene name on the left will display its transcription start and end site by a vertical bar, and clicking the gene name can bring you to the NCBI website for this gene.

Use “Chromosome/Proportional Distance” or key “P” to toggle between the “Natural order” and the “Proportional distance” displays. In the “Natural order” display, genes are ordered according to their order in the chromosome, but their relative distances are not reflected. In the “Proportional distance” display, the genes are displayed with their relative screen distances proportional to real physical chromosomal distance. The cytoband and reference gene names will also be display when available. In this display, since the data points or gene names occupy a certain screen height, for some genes there is not enough space to display their data and names, and they are represented by small blue dots on the left margin of the gene name display region.

If “RefGene file” or Cytoband file are specified at “Analysis/Chromosome”, the “Proportional distance” display will display the cytoband information and reference gene names on the left side. If cytoband information is not available, a ruler is displayed on the left of the refGene names, with space between horizontal lines representing 1 megabase distance. One can use “Chromosome/Find refGene” or “Chromosome/Find Next” to find a gene in the refGene list by keyword, or click a “refGene” name on the left side will start the LocusLink webpage for this gene.

A gene list containing a set of interesting genes (may be obtained by “Analysis/Filter genes”, “Analysis/Filter SNPs” or “Analysis/Compare samples” functions) can be specified in the “Analysis/Chromosome” dialog to display only these interesting genes.
 
Adjust the chromosome view

Use Arrow keys to zoom the data figure, and Control+Arrow keys to adjust the width of the cytoband information area and height of the sample name area. Click a colored data point in the figure to select a “Current” data point and “ESC” to dismiss it. When a “Current” data point is selected, it will always be displayed in the viewable region of the picture when zooming the figure by the arrow keys. For example, a data point in a peak score region can be clicked and then use the Down arrow to zoom in this region.

When “Chromosome/Proportional distance” is unchecked, use Up and Down arrows to adjust the height of the data point and gene/SNP names, Left or Right arrow to adjust the width of the figure, and Shift+Up or Shift+Down arrow and to adjust the height of the sample information rows on the top and the color legend on the bottom. When “Chromosome/Proportional distance” is checked, use Shift+Up and Shift+Down keys to adjust the height of the data point and gene/SNP names, but the height of the sample information rows cannot be adjusted.

The displaying range of the score curve (e.g. LOH prevalence score) on the right side can be adjusted at “Tools/Options/Chromosome/Curve along chromosome”. The red threshold line can also be adjusted directly by Shift+Left and Shift+Right keys, with the SNPs, genes and cytoband names shown as blue for the regions with the score exceeding the threshold.

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