SNP Table View

Step 1: Introduction

This tutorial was prepared using Genome Workbench version 2.7.0

The purpose of this tutorial is to acquaint you with the newly redesigned SNP Table view which is the place where you can work with SNPs from a sequence (or a range thereof) in a tabular format.

Step 2: Opening the SNP Table view

Let us suppose that we want to see a list all SNPs placed in the range covered by the LPL gene on human chromosome 8.

Finding the LPL gene

Loading Chromosome 8

First of all we need to add chromosome 8 to the Genome Workbench. For this we use the File => Open dialog, select the Data from GenBank item and type in "NC_000008".

Load chromosome 8

Clicking Next and then Finish in the next dialog will add the latest version of chromosome 8 (NC_000008.10 at the time of writing) to the Project Tree View.

Opening Chromosome 8 in the Graphical View

Now that the chromosome is added to the project, we can take a look at it in the Graphical view. For this double click on NC_000008.10, select Graphical View and allow some time for all tracks to load. You should see the following screen.

Chromosome 8 in graphical view

Note that there is Genes track. It has many genes, so how would we find our gene of interest, LPL? The Search View will help us with that.

Searching for the gene

In the Search View select:

  • "Feature Search" as the Search Tool
  • "NC_000008.10 (Graphical View)" as the Search Context
  • "Exact Match" as the Search Type
  • "Gene..." as the Feature Type (Click on the link and check the Gene box only)

Type "LPL" in the Search Expression box. Make sure that the Start button is enabled

Gene search setup

Clicking on the Start button will commence the search which should not normally take more than a few seconds. Select the line with Label "LPL" and switch back to the NC_000008.10 Graphical View. Your search result selection should have been broadcasted and the view zoomed to the LPL gene.

Gene search results

Opening the SNP table view for the gene

Now that we have found the gene, it is easy to open the SNP table that corresponds to it. Right click on NC_000008.10, select Open new view from the pop-up menu and you will see the Open View dialog. Make sure that the Show only compatible views checkbox is unchecked and select SNP Table View from the list.

Opening SNP table-view for gene

The SNP Table View will open and in a few seconds load the SNP information for the LPL gene.

Step 3: Working with the SNP Table view

The SNP Table View gives you a way to see the most important SNP characteristics like alleles, locations, variation classes, etc. in a tabular way.

Working with SNP table view

Besides visually browsing the list of SNPs there are other useful things that you can do, like:

  • Following the links to other SNP-related resources
  • Searching and selecting SNPs with specific characteristics
  • Exporting the table to a CSV format and then importing it into Excel or another application that can read CSV files

Browsing the table

The SNP table view has the usual properties you can expect from a tabular view – sorting by data in a specific column, resizing the columns, etc. By default, the SNP table is sorted by Location, but this can be changed by clicking on the column caption, for example, you can sort by Weight by clicking on the Weight name og fthe column.

SNP table sorted by weight

You can get more information on a particular SNP by clicking the underlined values. This will open your default browser with the referenced web resource. The link you are about to open is always shown in the status line when you hover your mouse pointer over the value. For example, if you hover over RS ID 78643820 in the first row of the table, you will see the link http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=78643820 to the NCBI dbSNP Reference SNP page for that particular RS ID.

Following outside links

Clicking on the link will take you to the actual page.

Searching for SNPs in the table

If you are looking for SNPs with particular characteristics, you can use the search functionality of the SNP table view. Search is done by building search expressions and then executing them. The easiest way to start building a search expression is to right-click on a value in a column that interests you and select Filter Include This Value or Filter Exclude This Value.

For example let us suppose we want to find all SNPs that have a FXN (Function) class of "Intron". For this right-click on any "Intron" value in the FXN class column and select Filter Include This Value. You will see that the Search box on top of the table is filled with the expression "(FXN Class = Intron)".

Set search criteria

Once the expression is prepared, the Start button becomes enabled and you can click on it to perform a search. By default a completed search operation selects all rows that satisfy the search expression.

Search results highlighted

Instead of just selecting, you can choose only the results to be shown by checking the Filter checkbox.

Search results filtered

You can build more complicated search expressions. For example if in addition to FXN class being "Intron" you want to find only those of them that are not true SNPs, right-click on the "SNP" value and select Filter Exclude This Value. You will notice that the search expression has changed to "(FXN Class = Intron) AND (Variation Class != SNP)" and clicking onto Start shows only intronic SNPs that are at the same time not true SNPs.

Complex search results filtered

Besides using the menu you can edit the search expression directly. For example if you want to change the logic of the previous expression and find SNPs that are "Missense" and true SNP, just go the Search box and directly edit the search expression to "(FXN Class = Missense) AND (Variation Class = SNP)". Clicking on Start button will again show the changed result.

Direct edited search

Exporting the SNP table

The SNP table can be exported into a CSV format file, which can be imported into other application. Export works with the currently shown SNPs, so you can export search results as well.

Exporting the whole SNP table

Make sure that the Filter box is unchecked, so you see all SNPs again. Right-click anywhere in the table and select Export to CSV. Input a file name in the dialog box shown (if you want to specify location different from the default use the ... button located to the right from the file name box). Click OK button. You will find that a file has been created in you file system that you can use for importing to Excel or any other application that supports the CSV format. For a quick check, we can just open it in the Windows Notepad.

Whole SNP export table

Exporting the filtered SNP table

To export the part of the SNP that satisfies the search expression, check Filter checkbox again and repeat the export operation to a different file. A check in the Notepad shows that only the filtered SNPs have indeed been exported.

Filtered SNP export table

Step 4: Conclusion

In this tutorial we have demonstrated how you can open a SNP table for a given gene and a typical scenario of how you could use the view. This demonstration could not show all of the ways in which you could use the view, so please explore and discover further ways of how you can use it. Please let us know on how we could improve the SNP table view by using the feedback feature in the Help menu of Genome Workbench.

Write to the Help Desk

Last updated: 2013-03-19T14:27:37-04:00