SIGnAL/CCSB Cytoscape Web||Beta 1.0|
Welcome to the SIGnAL/CCSB Arabidopsis Interactome network visualization website
This website is intended for the interactive online exploration of the Plant-Pathogen Immune Network (PPIN-1) and the Arabidopsis Interactome (AI-1).
The PPIN-1 network contains 3,148 interactions among 926 immune related proteins. These 926 immune related proteins include 83 combined effectors from the bacterium Pseudomonas syringae (gold nodes) and obligate biotrophic oomycete Hyaloperonospora arabidopsidis (purple nodes), 170 known Arabidopsis immune receptors and response proteins (N-termini of NB-LRR disease resistance proteins, cytoplasmic domains of LRR-RLKs and other known defense proteins; red, pink, and blue nodes respectively) and 673 newly identified interacting Arabidopsis proteins (grey nodes). Direct interactions derived from the PPIN-1 screen are shown as grey lines (immune edges). Interactions between the 926 immune proteins and Arabidopsis proteins identified in an independent screen (AI1) are shown as green edges. Interactions between proteins found in the literature (LCI) are shown as blue edges. Interactions identified in multiple datasets are indicated by different colored edges as marked.
The AI-1 network contains 6,205 interactions among 2,774 Arabidopsis proteins. Arabidopsis proteins are shown as grey nodes, protein interactions detected in the CCSB-Y2H screen are shown as green lines (edges) and protein interactions detected in both the CCSB-Y2H screen and the literature (LCI) are shown as black edges.
To navigate through the network, use the zoom and pan buttons located in the lower right box. Node positions can be adjusted by simply dragging them to the desired location. To reload the entire PPIN-1 node network, click the PPIN1 box in the upper right. To visualize all nodes and edges in PPIN-1, check the boxes of the desired edge type and click the Update Interactions button. Reloading the entire network may take up to 10 seconds.
To view direct protein interactions for a gene of interest, enter an Arabidopsis locus ID (i.e. At5g43700) or pathogen effector ID (i.e. HopC1_Pto DC3000) into the search field in the upper right-hand corner and click GO. A new network displaying all direct interactions will appear. Clicking on individual nodes will display gene descriptions in the upper right panel (selected nodes are highlighted in black). Please be patient after clicking as processing speeds may vary.
To browse the network, click on any node to select it and view gene description information (selected nodes will be highlighted in black). Double clicking on a selected node will open a new window displaying all the direct interactors of that protein. Clicking on the ID number link displayed below the search field will open a new tab showing all direct interactors of that protein. Please be patient after clicking as processing speeds may vary.
To build a sub-network module starting from a gene of interest: Ensure the entire PPIN-1 network is displayed, then enter an AT ID or effector ID into the Filter & Search field in the lower right-hand panel. Click the boxes corresponding to the edge type you would like to view (i.e. LCI, Immune, etc). Next, move the slider bar (located directly below the Filter & Search field) stepwise to the right. A number 1 will display all direct interactors of the protein, a 2 will display all direct interactors of the proteins shown in 1, a 3 will display all direct interactors of the proteins shown in 2, etc. Please be patient after moving the slider as processing speeds vary depending on the number of interactions. Typical wait times are 1-10 seconds. You may also launch this function by selecting a node in the main network. Once the node is highlighted in black, the AT ID number will appear in the Filter & Search field. Move the slider to the right as explained above.
To order SALK homozygous knock-out lines for a set of interacting proteins, select the nodes of interest (AtIDs will appear in the Request List box) and click the 'order SALK homozygotes' button.
The CCSB/SIGnAL Cytoscape Web visualization of the PPIN-1 network was generated by Lantian Gai using Cytoscape Web (Lopes et al, 2010).