SNPExpress user manual
Quick start-up guide
Follow these steps to take a ride on the SNPExpress.
1. Prepare files identical to the sample files found at http://www.erasmusmc.nl/47396/emcw_SNPExpress. A genotype file is compulsory, copy number and gene expression files are optional. It is critical that all files contain the same samples as recognized by their unique sample ID. Various annotation files, i.e., Affymetrix 250K NspI DNA Mapping array, Affymetrix 250K StyI DNA Mapping array, Affymetrix 500K NspI/StyI DNA Mapping array, Affymetrix SNP 6.0 array, Illumina human610-quad array, Affymetrix U133Plus2.0 GeneChip and GeneChip Human Exon 1.0 ST Array, can be downloaded from http://www.erasmusmc.nl/47396/emcw_SNPExpress.
2. Go to http://www.erasmusmc.nl/hematologie/ and start the application by clicking on the SNPExpress link (Software Links – upper right corner).
Files can be optionally uploaded as tab- or comma-delimited .txt files or binary files. The menu item ‘convert data source’ can create these binary files.
3. Load the files.
4. A pop-up box appears; drag and drop samples to be visualized from the left panel to the right panel.
5. Depending on which input files have been specified, genotypes of chromosome 1 are shown in combination with copy number and/or gene expression (additional info in the extended user guide).
Extended user guide
I. Default settings
Figure: SNPExpress Screenshot displaying two samples. The copy numbers (n=0, 1, 2, 3, 4) are shown for each individual patient by horizontal lines and copy number n=2 is depicted by a green line (A). The SNP genotypes are aligned sequentially along the chromosome (default: AA: red; BB: yellow; AB: blue, noCall: white). LOH is indicated by a magenta horizontal bar (B), gains (default: n>2.5) by a pink (C1) and losses (default: n<1.5) by a turquoise background (C2). The chromosome selector (D; where 23 is the X chromosome), the mouse-over function showing info of each SNP or probe set (E), full chromosome view (F), zoom function (G), gene search function (H), the links to external databases (I), display CNVs (J) and export selected data (K) are indicated.
II. Customization
SNPExpress can be customized in several ways.
1. Visualization options
General
Zoom in on a particular region of interest using the left mouse button; zoom out to a larger region by using your right mouse button. Use the slider at the bottom to move around the chromosome. Depending on the input files, genotypes, copy number and gene expression are being displayed. A red rectangle on the chromosome bar indicates which region is being shown.
Customization
- Genotype colours
By default, AA calls are red, BB calls are yellow and heterozygous calls are blue. The colours can be adjusted through the menu option ‘change colours’.
- Gene expression
By default, the height of the expression bars is capped at 500. This can be adjusted through the menu option ‘set parameters’, which can be useful for instance when log transformed data is being presented. Three types of gene expression bars are shown. The size of a grey bar indicates the expression level of one probe set. Red bars indicate that more probe sets overlap at that locus. Green bars indicate negative values, e.g. in case log transformed data is plotted. The height of the bar on such loci is determined by the highest expresser. The ‘Show details on mouseOver’ checkbox can be used to establish individual expression levels.
- Chromosome gains/losses
Gains and losses are visualized using a threshold on the copy number, which is +/- 0.5 by default. This can be adjusted through the menu. The colours can be adjusted through the menu option ‘change colours’.
- HMM copy numbers
This option enables the user to display (or remove) the results of a novel analytical method that infers the copy number of each SNP based on a HMM model (Zhao X, Li C, Paez JG, Chin K, Janne PA, Chen TH, Girard L, Minna J, Christiani D, Leo C, Gray JW, Sellers WR, Meyerson M: An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res. 2004: 64(9), 3060-71). The HMM copy number results should be uploaded before starting SNPExpress (together with genotype-, copy number- and expression files) and HMM copy numbers of the individual SNPs are indicated as a thin magenta line across the chromosome.
2. Panel options
Chromosome selector (D)
Switch to a different chromosome by sliding the chromosome selector to the chromosome of interest.
Show details on mouse-over (E)
This shows detailed information when the mouse is pointed to a particular locus on the chromosome. The items shown in the ‘Show details’ box can be set through the menu option ‘Change mouse items’; default are Sample ID/SNP ID/call/copy number/cytoband/probe set id/expression level/gene ID.
Full chromosome view (F)
Switch to full chromosome view of all selected samples.
Select region (G)
This function can be used to get a detailed visualization of a chromosomal region. After selecting it, draw a square on the chromosome panel and the tool will zoom into the selected region. Choose ‘zoom out’ to return to normal status.
Search genes (H)
The gene names as provided by Illumina or Affymetrix are being used for this function. Enter the name of a gene of interest and SNPExpress will locate it on the genome and indicate the associated SNPs with an orange background. Use ‘show detail on mouse over (H)’ to get detailed information on this locus.
External links (I)
This function enables a link towards external databases. Hold Ctrl, go to a particular SNP (left mouse button), click on external link in upper right window.
Display CNVs (J)
This option enables the user to display (or remove) the CNVs cataloged in the Database of Genome Variants (http://projects.tcag.ca/variation). In the event that multiple CNVs span the same region in the chromosome-wide view the background is violet, whereas single CNV are indicated with a rosy brown background.
Export data (K)
This function enables the export of relevant data, i.e., Sample, Probe_set_id, Chromosome, Location (bp), Cytoband, Associated gene, Genotype, Copy number, Inferred LOH, of the selected region. Clicking this button and selecting the region of interest can download the relevant data.
3. Menu options
Open data source
Open a new set of sample files.
Convert data source
Option to convert .txt files to binary files.
Save image
Save an image of the current visualization in the Portable Network Graphics (.png) format.
Exit
The SNPExpress has reached its destination.
Select samples
Displays a box with the sample IDs in which the samples that are currently being visualized are in the right panel while the remaining samples present in the source files are in the left panel. Drag and drop samples between the panels to change the samples to be shown.
Draw complete sample
Select a sample to display chromosomes 1 to 22 and the X chromosome.
Set parameters
Settings for threshold of chromosomal gains and losses, and expression levels can be changed through this menu option.
Change colors
The colors of all items are adaptable to the users’ preferences.
Change mouse items
All items displayed on the mouse-over are adaptable to the users’ preferences.
Help index
User manual SNPExpress.