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Viewing Location and eQTL

The location graphic allows you to investigate and use expression QTL (eQTL) datasets. By default, only the physical locations are shown on the graphic. You can click the "Show locations of transcription control in brain" check box to display the locations of transcription control. These green arrows represent the genomic position(s) that control transcription of the candidate genes in the gene list (expression QTLs, or eQTLs).You can also change the significance level for displaying eQTLs

You can view the location and eQTL data for a gene list in two ways:

Gene List Analysis Tools

1. Choose Genes List Analysis Tools in the main menu.
2. Click Analyze a gene list. A page displays the gene lists to which you have access.
3. Click the gene list for which you want to view location and eQTL.
4. Click the Location (eQTL) tab. The Location page displays.

QTL Tools:

1. Choose QTL Tools in the main menu.
2. Click View physical location and eQTL information about specific genes from a gene list. A page displays the gene lists to which you have access.
3. Click the gene list for which you want to view location and eQTL. The Location and eQTL page displays.

Take a look

The data on the page looks the same, regardless of the way you access the page. You can:

• Click the View in table form link to see a table of all of the genes currently displayed on the graphic. If any of the probe sets for a given gene have a significant eQTL, all of the probe sets for that gene are displayed in the table, but only the most significant eQTL position ("Max LOD") and the associated marker locations are shown on the graphic.
• Click the View link in the gene table to display individual LOD plots for each probe set. Copy these by right-clicking on the image.
• Click the Download button to download the table into a tab-delimited text file.
• Click the Customize this view button to change the default view of the table, which includes all probe sets for a given gene.
• Choose Genes (and all associated probesets) from the [selected] list that meet the restriction criteria to restrict the list to those with eQTLs (probe sets) that overlap the selected bQTL intervals.
• Select Probesets that are in the [selected] gene list to restrict the list to probe sets (as opposed to genes) whose expression values are significantly correlated with the phenotype. These probe sets are also identified by the asterisk in the first column of the table.
• Selelct Probesets that have eQTL p-value < [selected value] to restrict the list to only the probe sets passing the desired threshold.
• Choose Genes (and all associated probesets) from the [selected] list with probesets that did not meet the restriction criteria or were not considered in eQTL to restrict the list to those that were not considered in eQTL.
• Click the Download icon to download the chromosome map as a JPEG graphic.
• Click the Save displayed genes link to save the displayed genes as a gene list.
• Click the Magnify icon in the graphic to expand the graphic to the full page.
• Click a chromosome in the graphic to show an expanded view. See "Expanded Chromosomal View".
• Set the Gene Graphic Settings:
• Show physical location of genes - Choose this option to mark the physical location of genes with a red arrow.
• Show genomic locations of transcription control in...Choose this option to mark the transcription control locations with a green arrow, and choose a corresponding eQTL p-value. For mouse, only brain is available. For rat, options are brain, heart, liver, and brown adipose.
• Click Advanced Settings to enter user-defined regions, such as QTLs. You can also:
• Click View to see details about the specific region.
• Click the Delete icon beside the region you want to delete.

Take a look

Expanded Chromosomal View

The expanded chromosomal view zooms in on the specific location you choose in the graphic, shows the zoom location, and allows you to set basepair start (left) and end (right) positions.

Take a look