ORTHOLOG LAYOUT IN CYTOSCAPE FOR MAC OS X
ORTHOLOG LAYOUT IN CYTOSCAPE MANUAL
ORTHOLOG LAYOUT IN CYTOSCAPE MAC

Remove Nested Network: Removes the currently associated nested network from a node. If the current node already has a nested network it will be replaced. These additions usually appear in the Apps section of the context menu.Īdd Nested Network: Lets the user select any network in Cytoscape as the current node's nested network. For nodes, it typically shows:Īpps can contribute their own items into node and edge context menus. This menu can change based on the current context. You can hold down the Shift key (or Ctrl key on PCs) to select more than one node/edge or you can hold down the left mouse button and drag the mouse to select groups of nodes/edges.Ĭlick the right mouse button (or Ctrl+left mouse button on Macs) on a node/edge to launch a context-sensitive menu with additional information about the node/edge.

ORTHOLOG LAYOUT IN CYTOSCAPE MAC

Command Key + Drag (Mac only) - If you use Mac without middle button, you can pan the view by holding down Command key and then drag.ĭragging Box on Network Overview - You can also pan the image by holding down the left mouse button over the blue box in the overview panel in the lower part of the Network tab in the Control Panel.Ĭlick the left mouse button on a node or edge to select that object.

Middle Click and Drag - You can pan the network image by holding down the middle mouse button and moving the mouse.There are several ways to pan the network:

ORTHOLOG LAYOUT IN CYTOSCAPE FOR MAC OS X

These directions are reversed on Macs with natural scrolling enabled (the default for Mac OS X Lion and newer versions). Using the scroll wheel, you can zoom in by scrolling up and zoom out by scrolling downwards. Zoom Out to Display all of Current Network.Use the zooming buttons located on the toolbar to zoom in and out of the interaction network shown in the current network display. Panning allows users to move the focus of a screen to different parts of a view.Ĭytoscape provides two mechanisms for zooming: toolbar buttons and the scroll wheel. Zooming increases or decreases the magnification of a view based on how much or how little a user wants to see. ZUIs use two mechanisms for navigation: zooming and panning.

ORTHOLOG LAYOUT IN CYTOSCAPE MANUAL

The current version of the Cytoscape manual can be found at Basic Network NavigationĬytoscape uses a Zoomable User Interface for navigating and viewing networks. We present this interactome, and an online Web interface the Arabidopsis Interactions Viewer, as a first step toward understanding global signaling in Arabidopsis, and to whet the appetite for those who are awaiting results from high-throughput experimental approaches.This page has been deprecated and is no longer updated. In addition we have predicted interactions for many previously unknown proteins in known pathways and complexes. These predictions can aid researchers by extending known complexes and pathways with candidate proteins.

A notable exception was that proteins located in the Golgi were more likely to interact with Golgi, vacuolar, or endoplasmic reticulum sorted proteins, indicating possible docking or trafficking interactions. Interacting proteins were also significantly more likely to be found within the same subcellular location, and significantly less likely to be found in conflicting localizations than randomly paired proteins. There was significant coexpression of genes whose proteins were predicted to interact, even among low confidence interactions.

A total of 1,159 high confidence, 5,913 medium confidence, and 12,907 low confidence interactions were identified for 3,617 conserved Arabidopsis proteins. As an internal quality control, a confidence value was generated based on the amount of supporting evidence for each interaction. We present an interactome for Arabidopsis (Arabidopsis thaliana) predicted from interacting orthologs in yeast (Saccharomyces cerevisiae), nematode worm (Caenorhabditis elegans), fruitfly (Drosophila melanogaster), and human (Homo sapiens). A map of all protein-protein interactions, an interactome, is thus an invaluable tool.

The complex cellular functions of an organism frequently rely on physical interactions between proteins.

Ortholog layout in cytoscape