Strand MK, Stuart GR, Longley MJ, Graziewicz MA, Dominick OC, Copeland WC.
#Cytoscape linux software
Cytoscape: a software environment for integrated models of biomolecular interaction networks. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. In each of the Cytoscape displays in this article, up-regulated genes (nodes) are colored red, while down-regulated genes are colored green, with the extent of shading proportional to the level of expression as indicated in an expanded view in the image in the lower part of this panel. ( B) The ‘Gradient Editor for Node Color’ editor from the Cytoscape VizMapper tool. heavier edges indicate more (multiple) interactions, of the indicated type, between two nodes, as described in the Materials and Methods section. The thickness of the edges represent weights, i.e. Nodes in which the blue edge loops back on itself indicate self-regulated genes. synthetic lethality-the loss of viability when both alleles are inactivated.
Node–node interactions (edges) are color-coded with blue edges indicating protein–protein interactions, gold edges indicating transcription factors with the arrow pointing from the transcription factor toward the regulated gene, and broken red edges indicating genetic (rather than physical) interactions, e.g.
Mitochondrial-associated nodes are shown as rectangles, and nodes associated with the response to stress are drawn with emphasized, blue borders with the gene names also displayed in blue text. Also illustrated is a a box containing the SGD gene description, that automatically pops up when the cursor is placed on top of a gene description, here showing the complete SGD gene description for Hal9. In this example, transcription factor Hal9 is a mitochondrial stress response gene that was up-regulated 1.7-fold in wild-type diauxic-shifted cells. The data panel at the lower right of the image displays information associated with each of these nodes, imported from various user-defined annotation files, including (as shown) common gene names, the expression values, genes associated with the mitochondrion and the response to stress, descriptions of the genes from SGD and genes encoding transcription factors. regulated by) transcription factor Rpn4 are selected and shown in yellow (these selections are made from the Select menu). In this example, genes directly associated with (i.e. The upper left frame contains a list of the subnetworks arising from various analyses within Cytoscape, including the numbers of nodes and edges, and the number of these currently selected, that are highlighted in yellow in the displayed subnetworks. The main, upper right frame displays a close-up view of some of the genes present in this subnetwork, while the lower left frame shows an overview of the entire subnetwork, with the part shown in the main frame indicated by the shaded region. ( A) This panel illustrates part of the subnetwork identified by the jActiveModules plugin, as described in the text and summarized in Table 1.
Selected illustration from the yeast interactome, using a screen capture from a Cytoscape ‘session’ (Cytoscape sessions can be saved, preserving the work for future use). These cells are thus able to sensitively regulate cellular metabolism in response to changes in genetic or environmental conditions through relatively small changes in the expression of large numbers of genes, affecting the entire yeast metabolome. We also report and briefly describe the complex associations among transcription factors that result in the regulation of thousands of genes through coordinated changes in expression of dozens of transcription factors. Using Cytoscape, we illustrate the use of this interactome through the analysis of expression data from a recent yeast diauxic shift experiment. The methods described for the construction of this yeast interactome are generally applicable to the construction of any interactome.
To facilitate the analysis of yeast microarray data using Cytoscape, we constructed an interaction network (interactome) using the curated interaction data available from the Saccharomyces Genome Database (and the database of yeast transcription factors at YEASTRACT (These data were formatted and imported into Cytoscape using semi-automated methods, including Linux-based scripts, that simplified the process while minimizing the introduction of processing errors. Cytoscape is a bioinformatic data analysis and visualization platform that is well-suited to the analysis of gene expression data.
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