Regulatory Overview

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Regulatory Overview

Regulatory Overview for
mouse left click highlighted

Pan left/right/up/down the entire diagram by holding the left mouse button, left-click on gene node to open its gene page mouse right click highlighted

Right-click (ctrl-click for Mac) on gene or blank area for menus

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Highlighting by Gene Name Substring

Highlighting by Gene Name or Frame Id

Highlighting by Gene Ontology Terms

Type in or browse to select Gene Ontology term(s) to highlight genes annotated with them

Include Regulatory Arrows Between Genes Found

Highlighting From Gene File

Changing the Network Layout

Regulatory Overview Legend

Regulatory Overview

The Regulatory Overview enables exploration of a cellular regulatory network. Each node in this diagram is one gene. Initially, no regulatory links are shown; use the commands on the right sidebar to find/highlight specific genes. Right click on a gene to show its regulators and its regulatees. Types of regulation captured in this diagram are:

Regulators of transcription including sigma factors
Regulators of translation including small RNAs
Terminators upstream of a gene within its transcription unit

For the default layout (three concentric elipses)

Inner ring: Master regulators and sigma factors
Middle ring: Other regulators
Outer ring: Genes that are not regulators. Genes within the same group share the same regulators.

For the top-to-bottom layout

Genes on the same row do not regulate each other.
The top row contains master regulators.
Genes in the middle rows regulate smaller numbers of genes.
Genes on the bottom row do not regulate other genes.

For both layouts

+ : A gene that has positive regulators only
- : A gene that has negative regulators only
o : A gene that has both positive and negative regulators
oval : A gene for which all of its regulators have an unknown mode of regulation
square : A sigma factor

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Regulatory Overview

For the default layout (three concentric elipses)

For the top-to-bottom layout

For both layouts

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Regulatory Overview

For the default layout (three concentric elipses)

For the top-to-bottom layout

For both layouts