RegulonDB RegulonDB 11.2: Gene local context Help
Gene local context Help

Image of the gene local context
The figure Gene Local Context shows the genomic region surrounding the query gene. The coordinates of this region are displayed at the ends of the figure. The image shows all RegulonDB objects contained within this region; the meaning of all graphic features can be found at:
Graphic code for objects and colors.

Object properties in the image:
a) Orientation. The objects are drawn depending on their strand orientation: on the top of the line, elements in forward, and on the bottom to elements in reverse.
b) Relationship to the query gene. Objects relating to the query gene are displayed in color or in black, while for that unrelated are displayed in light gray.
c) Confidence. Objects with strong evidence are plotted with solid lines, whereas those with weak evidence are shown with dashed lines.
d) Information of the object. All the objects have a tooltip by rolling the mouse over the graphic element, by means of which a brief description is displayed.
e) Navigation. Clicking on a gene that is displayed in the figure, the user can navigate to the page describing the selected gene.

Three buttons allow you to zoom in (+), zoom out (-), and expand 5? region (<<>>).

The + and - buttons allow you to zoom in and zoom out, respectively by clicking on the button located above the image of the gene local context.

The <<>> button displays 500bp upstream of query gene to 200bp inside of query gene; although, in the case that the query gene is less than 200bp, the graph displays just until its end. The displayed region is amplified; each object position is multiplied by two, doubling the size of each of them. Incomplete objects contained within those 700bp are indicated by a zig-zag line.

The >><< button reset to the gene local context image.

Furthermore, the help button (?) provides a window designed to present a description of the graphic code for each displayed element in the image, as well as, the color code used.