Disease Portals

RGD has numerous disease portals, where relationships between diseases and genes, QTLs and strains can be explored in human, rat and mouse. The Disease Portals entry page can be accessed either via the tab on the top banner of the home page, or the center panel.

Jump to information about the:

Disease Portal Entry Page

Term Selection and Summary

Gviewer

Object Lists and Term Usage

Click here to view the Disease Portal Video Tutorial

 

Disease Portal Entry Page

The Disease Portal entry page lists all the portals with brief descriptions.

1. One can access complete sets of annotations from the RGD ftp site via the link at the top of the page.

2. Each portal is accessed by clicking the icon or titles.

 

3. One may also directly access sub-categories (phenotypes, pathways, biological processes) or tools, related links and rat strain models by clicking the appropriate links in each portal description.

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Term Selection and Summary

 

1. Across the top of the disease portal main page, one can select diseases, phenotypes, biological processes or pathways as areas of interest.

2. The two pull-down menus are used to select a category and subcategory of the area of interest.


3. The Summary section gives counts of all the rat, human and mouse genes, rat and human QTLs, and rat strains annotated to the portal (default) or to the categories and subcategories as they are chosen.

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Gviewer

The Gviewer window displays a genome-wide view of the chromosomes with associated genes (triangles) and QTLs (bars) annotated to the selected categories.

1. The species displayed is selected in the upper left and is presented in black and white.

2. Colored syntenies (shown) for the other two species can be selected at the right. Mousing over a gene or QTL marker will display its name. Shift+clicking on them links out to the report page for that object in a new tab.

3. Mousing over a chromosome gives the chromosome number, cursor position base pair coordinates, and p or q arm coordinates.  In synteny displays (shown), the last value is replaced by the chromosome to which that region is syntenic.

4. Clicking on a chromosome isolates it in the field. Mousing over gene and QTL markers now gives coordinates as well as name. Right clicking on the ideogram above the chromosome allows zooming in or out. Reclicking the chromosome returns to the full genome display.

5. Region handles to the left of the chromosome can be dragged to select a desired region.  Clicking on the green bracketed bar will display that region in the rat Gbrowse tool in a new tab.

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Object Lists and Term Usage

1. The next section alphabetically lists the genes (rat, human and mouse), QTLs (rat and human) and strains (rat) annotated to the terms selected at the top of the page. Each name links to the appropriate report page, displayed in a new tab.


2. The last section displays the annotation frequencies of selected Gene Ontology (GO) terms to the genes listed in the previous section. For each of the three GO categories, frequencies for ten terms are shown, with the first five listed. The remaining five can be viewed by clicking the triangle (circled) at the lower right of each list.

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