Cytoscape

The official version of Cytoscape is a professional and efficient bioinformatics analysis software. The latest version of Cytoscape software is powerful and can help users build networks. Users can easily integrate modular networks and draw biological science connection network diagrams. Cytoscape official version can achieve the purpose of analyzing networks by integrating, analyzing and visualizing data. Friends who like Cytoscape, come to Huajun Software Park to download and experience it!

Cytoscape software features

Supports multiple standards

Cytoscape supports many standard network and annotation file formats, including: SIF (Simple Interaction Format), GML, XGMML, BioPAX, PSI-MI, GraphML, KGML (KEGG XML), SBML, OBO, and Gene Association. SIF (Simple Interaction Format), GML, XGMML, BioPAX, PSI-MI, GraphML, KGML (KEGG XML), SBML, OBO, and Gene Association. Also supports qualified text files and MS Excel? Workbook lets you import data files generated by other applications or spreadsheet programs, such as expression profiles or GO annotations. Using this feature, you can load and save arbitrary attributes on nodes, edges, and networks. For example, enter a custom set of annotation terms for your protein to create a set of confidence values ​​for your protein-protein interactions.

​ ​ Public database client

​​Cytoscape works as a network service client, which means that Cytoscape can directly connect to external public databases and import network and annotation data. This means Cytoscape can connect directly to external public databases and import network and annotation data. Currently, we support Pathway Commons, IntAct, BioMart and NCBI Entrez Gene. We will also continue to develop new service clients for popular databases.

Interoperability

Since Cytoscape supports import/export of standard file formats, you can easily fit Cytoscape into your workflow. For example, if you have a graph created by igraph or Network data generated by Bioconductor, Cytoscape can load the file as a text table and display it as PSI-MI Format export for use by other bioinformatics tools or your own applications/scripts.

Starting from version 3.3, Cytoscape supports RESTful API programmatic access. You can use the programming language of your choice to access Cytoscape's core functionality, such as creating networks, applying layouts, or image exporting.

Session file

You can save your work with one click. All settings, data files and visualizations are packaged in a session file. It's called a Cytoscape session (.cys) file. Cytoscape Session files include network, properties (nodes/edges/networks), desktop state (select/hide nodes and edges, window size), properties, some plugin states, and visualization styles.

Layout

        Layout the network in two-dimensional space. There are a variety of layout algorithms to choose from, including loop, tree, force-directed, edge-weighted, and yFiles organic layout. You can also use manual layout tools similar to other graphical application user interfaces.

Image export

You can export your web as a high-quality, publishable image. Supports PDF, PS, SVG, PNG, JPEG and bmp files. Vector images (PDF and PS) can be processed through other applications such as Adobe **)Modified for further enhancement.

VizMapper

Use powerful VisualStyles to customize network data display. View the overlay of gene expression ratios and p-values ​​on the web. Representation data can be mapped to node colors, labels, boundary thickness, or boundary color, etc., based on user-configured color and visualization schemes.

Filter

​​Filter the network to select a subset of nodes and/or interactions based on the current data. For example, users can select a threshold number of nodes that participate in interactions, nodes that share a specific GO annotation, or nodes that experience significant changes in gene expression levels under one or more conditions based on the p-value of the gene expression data load. You can create new networks from filtered results.

Search

Search for target nodes and edges from the search window. Lucene syntax supports arbitrarily complex queries.

Browse

​​Zoom in/out and pan to browse the web. Use Network Manager to easily organize multiple networks. And this structure can be saved in the session file. Easily navigate large networks using a bird's eye view. Easily navigate large networks (100,000+ nodes and edges) with an efficient rendering engine.

Find modules/clusters

Find active subnetwork/pathway modules. The network is screened based on gene expression data to identify sets of interacting connections, i.e., interacting subnetworks, whose genes show particularly high levels of differential expression. The interactions contained within each subnetwork provide hypotheses for the regulatory and signaling interactions that control the observed expression changes. Find clusters (highly interconnected regions) in any network loaded into Cytoscape. Depending on the type of network, the meaning of clusters may differ. For example, clusters in protein-protein interaction networks have been shown to be part of protein complexes and pathways. Clusters in a protein similarity network represent protein families.

                          App Manager and App Store

​ ​ ​Apps for network and molecular profiling analysis. Cytoscape is a software written in Java. You can write your own App for data analysis, import and visualization by writing Java code. More Apps are available in Cytoscape Found in the App Store. You can install most apps with one click in the App Manager, or directly from the App Store (this is Cytoscape 3).

Cytoscape software features

​​​Cytoscape software uses a scalable user interface to navigate and view the network. ZUIs use two navigation mechanisms: zooming and panning. Zoom increases or decreases the magnification of the view depending on how much or how little of the content the user wants to see

Node and edge column data

Interaction networks are useful as stand-alone models. However, they are most effective for answering scientific questions when combined with other information. Cytoscape allows users to add arbitrary node, edge and network information into Cytoscape as node/edge/network data columns

​ ​ Cytoscape functionality is not fixed. They can be extended via apps. They can extend Cytoscape in various ways. An application can import data from an online database. Another application could provide a new way to analyze networks. You can install the application after installing Cytoscape. Most applications are developed by Cytoscape users like you.

If you are familiar with Cytoscape2. You may know that fine Cytoscape applications are called plug-ins. Starting from Cytoscape3.0, we call it application.

Cytoscape Instructions for Use

1. Input file

Supports multiple input formats, can save project files, supports multiple layout methods, supports exporting images, can make rich adjustments to styles, and intelligently selects and filters.

1. edge file format:

tsv (tab-delimited txt is the same), csv (comma-delimited), xls, xlsx files, etc. Generally, two tsv files are enough for us to use. The following is a typical three-column tsv format file example. The first column is the original node, the third column is the target node, and the second column is the interaction relationship between the two. The interaction relationship here indicates different types. In the following You can see the beauty of it in the network settings, and the source and target here are both numbers. How to convert it into the gene name we want to see? Here is a question first, which will be explained later.

​ ​ 2. node properties file

It can be imported and can be used to solve our above problem by replacing the numbers in the edge file with simple visual gene names.

2. Import data

You can click on the species name above to select an example to study, or you can directly select an empty network to import data. For example, if I selected Arabidopsis, the following interface will appear. The diagram shows an example of a completed network:

user interface

1. Import data

2. Import the properties file

3. Layout

3. Advanced functions

1. Adjust the style

(1)Basic style

(2)Node style

(3) Side style

2. Change the node name

3. Change the color of the edge

4. Statistics on various indicators of the control network

The result will appear in a new panel:

5. Change node size

An important point to emphasize here is that before changing the node size here, if you want to set the gradient through the number of edges connected by the node, you must perform the statistical analysis in the fourth step above, otherwise No Degree option appears:

​ ​Double-click the gradient setting area above to bring up the control panel for modification:

4. Select filter

1. Selection of nodes

2. Selection and separation of subnetworks

6. Export pictures

The export of data can be a network file, a table file or an image file. Image files include a variety of image formats and pdf formats. Comparing the shapes of icons, the two left icons shown in the figure below are icons for quickly importing files:

​​Biological information analysis software (Cytoscape) 7. Expression analysis

Cytoscape can also import the expression values ​​of genes and display different expression values ​​in color gradients. Since my analysis does not have this part of the data, I made a few screenshots of the pictures I learned on the Internet:

8. Others

Cytoscape provides many external databases. Right-click on the corresponding node and select externallinks from the options that appear. There are the following connected databases:

In addition, based on the development of a large number of powerful plug-ins, the following functions are also very comprehensive:

​ GO analysis: BiNGO

Pathway analysis: CytoKegg, KEGGscape, etc.

​​Module and complex analysis: jActiveModules+BiNGO

FAQ

Problem description:

An error occurred while importing data, such as an unrecognized file format or incomplete data.

Solution:

Make sure that the downloaded document data format meets the requirements of CiteSpace. It is usually a txt file in Refworks, EndNote and other formats, and the file name must start with a specific prefix (such as "download_").

Check whether the data file is complete, including necessary fields such as author, title, abstract, keywords, year of publication, etc.

If you use a database such as Web of Science or CNKI to export data, be sure to follow CiteSpace's requirements for format selection and export.

Cytoscape update log

​ 1. Optimized some functions

​ 2. Solved many unbearable bugs