This tutorial serves as a basic introduction to finding the approximate location of a gene on a chromosome map using NCBI Map Viewer.

Contents of this tutorial:

• Accessing a chromosome map
• Modifying display options

Tutorial Tips

One option for following along with the steps described in this tutorial is to open two browser windows at once (one for the tutorial and one for NCBI Map Viewer) and toggle between these two windows as needed. Another option would be to print this tutorial out and then go to NCBI Map Viewer.

NCBI Map Viewer is a Web resource that anyone can use to view and search an organism's complete genome. Users can also view maps of individual chromosomes and zoom into specific regions within chromosomes to explore the genome at the sequence level. Map Viewer provides access to several different types of maps for different organisms. Many of these maps are meaningful only to scientific researchers. A discussion of all the different types of maps and genomic data is beyond the scope of this tutorial, which will focus only on how to locate a specific gene on a chromosome map.

For demonstration purposes, we will search for the chromosomal location of the hereditary hemochromatosis gene, HFE. The same process can be carried out for any gene.

Before you begin to explore Map Viewer or other molecular databases to retrieve information about a particular gene, you should know the official symbol for your gene and the number of the chromosome on which it resides. One resource for finding this information about a gene is Online Mendelian Inheritance in Man (OMIM). For tips on searching OMIM see our tutorial.

Accessing a Chromosome Map

To begin, go to the NCBI Map Viewer home page

http://www.ncbi.nlm.nih.gov/mapview/static/MVstart.html

To access the genome view for humans, select Homo sapiens (humans) from the Search drop down box and click Go!, or simply click on Homo sapiens (humans) under Mammals in the tree structure on the home page. The Homo sapiens genome view is shown in the following screenshot.

After using OMIM, we determined that the gene for the most common form of hereditary hemochromatosis resides on chromosome 6 and that the symbol for this gene is HFE. In the Search for box at the top of the page, enter the gene symbol HFE and, in the on chromosome(s) box, enter 6 as demonstrated below. The Search for and on chromosome(s) links take you to the section of the Entrez Map Viewer Help Document that describes these search features. Click to submit your query.

This search returned one hit on chromosome 6 (as indicated by the red number 1 listed below the chromosome number). The genome view now displays one red mark on chromosome 6 marking the approximate location of the HFE gene.

Below the genome view is a table describing the match to your query.

The maps and map element, which also serve as links to maps of regions on chromosome 6, are described below. Due to differences in map and display settings, the view of the chromosome associated with each link will vary.

Map element

HFE - the gene symbol serves as a map element identifier on the Genes_ cyto and Genes_seq maps.

Maps

Two different types of maps contain a match for the search term:

Genes_cyto - Genes on the Cytogenetic Map gives cytogenetic locations of genes as reported in NCBI's LocusLink database.

Genes_seq - Genes on the Sequence Map gives cytogenetic locations of genes that have been annotated on genomic contigs (copied segments of DNA from a particular chromosome).

To access a map of chromosome 6, click on the the Genes_cyto link. This opens a view of Chromosome 6 that should resemble the following screenshot.

Take some time to explore the different features of this Chromosome View. The particular type of map displayed in this view is the Genes on Cytogenetic map. Note that you can directly link to maps of other chromosomes by simply clicking on a chromosome number. Each chromosome view gives the total number of genes that have been mapped to that chromosome and identifies the specific region of the chromosome displayed in the view.

For this view, the region between 6p22.3 and 6p21.1 is shown. The small chromosome image in the blue column on the left shows where this region is located on the chromosome. Both 6p22.3 and 6p21.1 are cytogenetic map locations. For the location 6p21.1, 6 is the chromosome number, p indicates the short arm of the chromosome, and 21.1 is the number assigned to a particular band on a chromosome. When chromosomes are stained in the lab, light and dark bands appear, and each band is numbered. The higher the number, the farther away the band is from the centromere.

More information about display options and map views is provided in the next section of this tutorial.

Modifying Display Options

Users can zoom in on a particular region of a chromosome, select a particular map type to serve as the Master Map, and adjust other display options by clicking on the link. This will open the Maps & Options window in your browser.

Select the following options to modify the map display:

Delete 6p22.3 and 6p21.1 from the Region Shown: boxes. This tells Map Viewer to display the map of the entire chromosome instead of zooming in on a particular region of the chromosome.

Under Available Maps: scroll down until you find Ideogram. Select Ideogram and click ADD to move the ideogram map into the Maps Displayed box.

In the Maps Displayed box, select Gene_Cytogenetic and then click the Make Master/Move to Bottom button. This will make the Gene_Cytogenetic map the master map. The master map is always displayed on the rightmost side of the chromosome view and may include links and descriptive text.

Under More Options, leave the Verbose Mode and Compress Map boxes checked. The Verbose Mode controls whether or not labels and descriptive text are displayed on the master map. Change Page Length from 20 to 15, which will list 15 gene labels on the master map. Unfortunately, the size of the ideogram map (or any map) is proportional to page length. The smaller the page length, the smaller and more distorted the ideogram map will be. The larger the page size is, the more scrolling required to view the entire map. A page length of 15 should generate an ideogram map that can be printed on a single page and yet is not too distorted.

The Maps & Options window should now look like the following screenshot.

Select , then close the Maps & Options window to generate your new map display:

The red marks on the ideogram and Genes_cyto maps show where the HFE gene can be found.

The Genes_cyto map, which displays the cytogenetic locations of genes listed in NCBI's LocusLink, is our master map. The HFE gene is highlighted in pink because it matched our query term, HFE. The HFE map element in the Genes_cyto map includes the following links to additional information:

HFE - Links to the HFE entry in NCBI's LocusLink Database.

sv - Links to Sequence Viewer, which graphically shows where the HFE gene lies within a particular region of genomic sequence. A graphic representation of the gene's sequence shows where the gene, mRNA, coding sequence (CDS), and other annotated features are located. For more information about this feature, see the Sequence View section in the Map Viewer Help document.

ev - Links to Evidence Viewer, which displays biological evidence that supports a particular gene model, in this case the HFE gene model. It provides a graphic representation of the genomic region containing the gene and other mRNA models or potential transcripts that align to the area of interest. In addition to graphic gene depictions, it also shows an exon-by-exon alignment of all mRNA sequences with the genomic sequence. For more information about this feature, see Evidence Viewer Help.

To learn more about what you can do with Map Viewer, experiment with different features on your own or see Map Viewer Help, Human Maps Help or Using the Map Viewer to Explore Genomes, a chapter in The NCBI Handbook.

Acknowledgments

Source for screenshots used in this tutorial:

"NCBI Map Viewer." <http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/map_search>, National Center for Biotechnology Information (January 2, 2003).

Continue with other tutorials:

Searching OMIM: Finding information about genes, traits, and disorders

Accessing records in NCBI's sequence databases

Sequence similarity searching using NCBI BLAST

Examining protein structures from the Protein Data Bank