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Por Gary Bader, Ruth Isserlin, Chaitra Sarathy, Veronique Voisin
exercise goal
Create a network and customize it.
The goal of this exercise is to learn how to create a network in Cytoscape and customize the identification. In this example, the proteins are the entities represented as nodes in the network, and the known physical interactions are the connections between the proteins that are represented as edges. We will overlay 2 additional pieces of information about these proteins, mutation information per protein as node color and mutation expression as node size.
Data
- The data used in this exercise is a set of protein-protein interactions and associated attributes.
start the exercise
To begin the hands-on lab section, first create a cytoscape_primer_files directory on your computer and download the files below.
Right click on the link below and select "Save Link As...".
Place it in the appropriate modules directory of your CBW working directory.
Two files are needed for this exercise:
- tablared.txt
- nodoatributo.txt
Exercise 1a: Create a network from a table
- Cytoscape Launch
- Find the top menu bar and selectArchive,–>Matter, –>Network from file....
- Browse your computer and select the filetablared.txt
- AndImport network from tablethe dialog opens. The 3 columns of the table should be set to "source", "interaction" and "target" respectively.
Cytoscape will assume that by default it will search for column names beginning with "source", "interaction" and "target". It will assume that any other column is an interaction attribute (border attribute)
- This is just an example file. You can import files with any number of additional columns and choose to ignore all columns except the ones you want to import or import all. Although Cytoscape tries to guess the data type of each column and the type (that is, whether it is an attribute associated with the source node, destination nodes, or interaction), you can tune everything.
- Click "Open."
- The main Cytoscape window should display a network containing the proteins as blue square nodes and the interaction as edges.
Exercise 1b - Load node attributes
Locate Cytoscape's top menu bar and selectArchive,–>Matter,–>Table from file....
Browse your computer and select the filenodoatributo.txt
click "Open".
An "Import Table from Columns" dialog box appears.
Click "OK."
You should be able to see the imported attributes in the node table.
- The key column is supposed to be the first column of your table.
- The key is the column in the uploaded attribute file that is used to match your attributes to your network.
- key column for networkis the column of the network against which the key is compared. (In this network there is no possibility to set this value because that is the only attribute associated with the nodes in our network, but normally this dropdown box will be selectable)
- The key and the matching column must match perfectly (unless you've specified that case doesn't matter).
similar toImport network from table, everything about the import is customizable. Cytoscape does its best to guess the data types of each column, but you can adjust it.
There are also advanced options if you want to:
- change file delimiter
- skip lines
- specify header column
Exercise 1c: Mapping node attributes to visual style
Go to "Control Panel" on the left side and select the "Style" tab. Make sure you are on the "Node" tab.
Select the "Fill Color" field
expand it by clicking the right arrow.
Set "Column" to "expression" and "Mapping Type" to "Continuous Mapping".
This will change the colors of the nodes to the default color coding.
Double-click the continuous mapping color box to manually adjust color and other settings.
At the bottom of the "Style" tab, check the "Lock width and height of node" box.
Select the "Size" field and
expand it by clicking the right arrow.
Set "Column" to "mutation" and "Mapping type" to "Continuous mapping".
Your resulting network maps the expression to the color of the node and the size of the node to the number of mutations.
- Adjust the settings in the color mapping. Change the color scheme. Change the maximum and minimum values.
- Adjust the settings in the size allocation. Make larger nodes with higher values.
- Although the net is small, play around with the layouts.
Exercise 2 - Working with larger networks
Cytoscape provides some demo networks that you can play around with. When you open cytoscape, you are presented with a Launch Panel where you can choose to reload a previous session or load into one of the sample networks.
You do not need to reopen cytoscape to open the start panel. Locate Cytoscape's top menu bar and selectVista,–>show home panel.
Double click on theaffinity purification networkto open it.
If you are already logged in, you will receive a warning that the current session will be lost. Before continuing, make sure your current session is saved. (Click cancel. Then,Archive–>Save as)
Once the network has loaded, you will see a network of protein interactions derived from an affinity purification experiment. Bait proteins are represented as pink hexagons and their corresponding blue boxes of prey proteins.
Using this larger grid, play around with the different layouts
- Look for the “VPR” node
- select all prey proteins associated with "VPR"
Exercise 3: Perform a basic enrichment analysis with EnrichmentTable
In Module 2, we performed a detailed enrichment analysis with g:profiler and GSEA. We provide gene lists and ranked expression sets for analysis. What if you want to run a quick enrichment analysis with a given network or a given subset of the network? The easiest way to do this is to use cytoscape's EnrichmentTable app. EnrichmentTable will query g:profiler directly with the given network or subnet. Not all of the parameters that are available in the web version can be modified from the enrichment map table application, but it can be an easy way to quickly see the results of the enrichment.
We will select the VPR bait protein and all of its associated prey proteins for use in an enrichment assay.
bait protein- It is the protein labeled in an affinity purification experiment that is removed.
prey protein- are the proteins that associate with the bait protein when pulled down and are supposed to interact with the bait protein.
first neighbor- are all nodes that are directly connected to the given node
1. In the search bar enter “VPR”. press enter.
- VPR is now the only highlighted node in the network. To select all its associated dams, we need to select all the nodes that are connected to VPR, all the first neighbors of VPR. There are two ways to select the first neighbors:
- On the top menu bar, clickSelect–>nodes–>First neighbors of selected nodes–>not directed
- Click on thefirst neighborbutton,, in the set of quick links buttons.
, in the set of quick links buttons.- Click on the "Enrichment Table" in the table pane.
- Click the gear icon in the upper right corner of the Enrichment Table panel
- This will open a panel with the adjustable settings. There are only 5 adjustable parameters-
- Body- This displays a list of organisms that are available on the g:Profiler site.
- Gene ID column- the column in the current network that you want to use to search g:Profiler with. Ideally this should be a column specifying the gene name or some other identifier.
- Multiple test correction- switch to fdr.
- Adjusted p-value threshold (min 0 max 1)- leave as 0.05. If you get too many results, you can lower this value.
- Include Inferred GO Annotations (IEA)- by default, the search will exclude GO terms inferred from the electronic annotation. If you want to include them, select this option.
By default, EnrichmentTable automatically uses all the databases available on the g:Profiler site. There is no way to filter before running the analysis. You must filter the results after running the analysis. Thiswillpowerchange the results because you end up filtering the results after multiple correction and multiple correction depends on the number of gene sets you are testing against.
- Filter the EnrichmentTable results to show only GO:BP, Reactome, and Wikipathway, similar to what we used in Module 2.
- Click the filter icon in the upper left corner of the enrichment table results.
- Next toselect categoriesselectGene ontology biological process,reactoma,Roads Wiki. To select multiple options, click and holddomainkey on Mac orChangeand Windows
- click onOK
- The enrichment table will be updated to include only the sets ofGene ontology biological process,reactoma,Roads Wiki.
Exercise 3B: Creating Enrichment Map Nodes and Enhanced Graphs from EnrichmentTable
- To create an enrichment map from the enrichment table results, click the EM logo in the upper left bar of the enrichment table panel.
- This will open an EM options panel with very limited parameter settings. You can only change the network name and connectivity threshold. You already specified the p-value threshold when you originally performed the analysis. If you want to create your network with a more permissive q value, you need to go back to the EnrichmentTable lookup panel. Click onOK
- This will create an Enrichment Map on a new network and represents all theGene ontology biological process,reactoma,Roads Wikienriched terms for the VPR and its set of prey proteins.
- To annotate the original PPI network with the top 5 enriched terms, you can use the improved graphical integration in the EnrichmentTable.You must have the EnhancedGraphics app installed to use this feature. To install it, go to Applications -> Application Manager... and install the EnhancedGraphics application
- Navigate back to the original PPI network. Click on theRedtab on thecontrol Panel. select networkHIV - human - PPI
- Select Enrichment Table in the Table Panel
- Unfortunately, you won't have remembered your filter settings, so you'll need to filter your results again.
- Filter the EnrichmentTable results to show only GO:BP, Reactome, and Wikipathway, similar to what we used in Module 2.
- Click the filter icon in the upper left corner of the enrichment table results.
- Next toselect categoriesselectGene ontology biological process,reactoma,Roads Wiki. To select multiple options, click and holddomainkey on Mac orChangeand Windows
- click onOK
- The enrichment table will be updated to include only the sets ofGene ontology biological process,reactoma,Roads Wiki.
- Click the Enhanced Charts icon in the top left bar of the Enrichment Table panel
- This will associate your top five enriched terms with a color.
- This will also update the graphs in the nodes associated with that term to include a ring with that color. Nodes that are not associated with any of the five terms will not have a ring.
Exercise 4 - Load network from NDex
Ndexis an open source repository where scientists can store, share, manipulate, and publish biological network data. The networks can be viewed on the web via their web application, but can also be downloaded directly into cytoscape so they can search, manipulate, integrate and analyze the given network themselves.
For the purposes of this exercise we will load into a network the publicationA protein overview of breast cancer. This post is associated with several networks that the authors of this article created and shared on NDex:https://www.ndexbio.org/index.html#/networkset/4423340d-e8e3-11eb-b666-0ac135e8bacf
- Start a new session.Archive–>Fence
- In the network search bar (located at the top of the control panel), make sure that the search provider is set to NDex.
It should be set to NDex by default, but click the down arrow to see the different data sources you can search for. Later in the workshop we will use this bar to query GeneMania.
- Get intoMCF7_All_PPI >= 0.9in the search box, click the search icon.
- A search results box will appear. HeMCF7_All_PPI >= 0.9network is just one of the networks associated with this post. Even though you are searching for this specific network, other networks associated with the original article will also appear in the search results, as well as others.
- Click the green down arrow next toMCF7_All_PPI >= 0.9, the network will begin to import.
- Once the network is loaded, clickclose dialog
- Resulting network loaded into cytoccape.
Description taken fromNdexrecord
- Baits are shown as yellow box, and
- prey as gray circle.
- The size of each node represents the number of patients with alterations in each protein.
- The dotted line represents the physical protein-protein association (validated in other studies) with a high integrated association stringency score.
- Change the width of the border to reflect the number of patients in which the associations are found instead of the PPI score.
- Change the default node color to blue.
FAQs
How do I analyze a network in cytoscape? ›
To run NetworkAnalyzer, select Tools → NetworkAnalyzer → Network Analysis → Analyze Network. The NetworkAnalyzer will determine whether your network contains directed or undirected edges. At this point, you can choose to ignore edge direction information.
What are the new features of Cytoscape 2.8 for data integration and network visualization? ›Version 2.8 of Cytoscape has introduced two significant new features that improve its ability to integrate and visualize complex datasets. The first feature allows non-programmers to map graphical images onto nodes, which greatly increases the power and flexibility with which integrated data can be visualized.
What is the function of the cytoscape? ›Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
How do I visualize network connections? ›To visualize your network, you must use a network map, diagram, or drawing. Good network visualization tools will allow you to clearly understand, update, and share information relative to your network.
How do I analyze my network connection? ›- Step 1: Identify Your Data Sources. ...
- Step 2: Determine the Best Way to Collect from Data Sources. ...
- Step 3: Determine Any Collection Restrictions. ...
- Step 4: Start a Small and Diverse Data Collection. ...
- Step 5: Determine the Data Collection Destination.
Cytoscape can read network/pathway files written in the following formats: Simple interaction file (SIF or . sif format) Graph Markup Language (GML or .
How do I import data from CSV to access? ›- In Access, open a new database file.
- Name the new database and place it in an appropriate directory.
- Select File, Get External Data, Import from the menu bar.
- Select the directory in which you saved the *. ...
- Highlight the file name and click Import.
Adding an Edge
To add an edge to connect nodes, right-click on the source node. Select Edit → Add Edge from the pop-up menu. Next, click on the target node. The Images below show the two steps for drawing an edge between two nodes.
One thing to add: Gephi is a smaller, simpler, perhaps less "mature" project than Cytoscape. Therefore, if you just want a quick and dirty network visualizer to get a feel for the basics, Gephi may be a good place to start, because it is less complicated and not as confusing the first time you use it.
Who uses Cytoscape? ›Social Science. Cytoscape is used by social scientists to: Visualize and analyze large social networks of interpersonal relationships.
What are the advantages of Cytoscape? ›
It provides 2D representations and is suitable for large-scale network analysis with thousands of nodes and edges. Multiple networks can be organized easily with the help of network manager. Cytoscape does not provide 3D representations which is one of the drawbacks of this tool.
What is the protocol of Cytoscape? ›Cytoscape is an open source software platform for integrating, visualizing, and analyzing measurement data in the context of networks. This protocol describes a network analysis workflow in Cytoscape for a set of differentially expressed genes. Points covered: Retrieving relevant networks from public databases.
How do you color nodes in Cytoscape? ›Select the node or nodes which you want to change color. Go to Node tab and Select>Style>Fill... click on 3rd box (bypass (Byp.)) and change color.
How do I create an enrichment map in Cytoscape? ›Open EnrichmentMap
To create an Enrichment Map network go to the Cytoscape main menu and select Apps > EnrichmentMap. This will show the EnrichmentMap panels and open the Create EnrichmentMap Dialog. If the Create EnrichmentMap Dialog does not appear then click the (+) icon at the top of the EnrichmentMap Main Panel.
Windows 10:
In the lower-right corner of your screen, click the WiFi icon. Click Network Settings > Wi-Fi > Hidden Network > Connect.
The best data visualization tools include Google Charts, Tableau, Grafana, Chartist. js, FusionCharts, Datawrapper, Infogram, ChartBlocks, and D3. js. The best tools offer a variety of visualization styles, are easy to use, and can handle large data sets.
Can I see what websites have been visited on my Wi-Fi? ›No. Wi-Fi bills only show the devices that accessed the internet and how much data they used, not the websites that were visited. That said, if a Wi-Fi admin wanted to see the activity on their network, they could check the router logs at any time.
Can you see activity on your Wi-Fi? ›Can Someone See My Internet History On Their WIFI? Yes. The WiFi owner has access to the admin panel from the WiFi router, meaning they can see the browsing information performed on their WiFi network. In addition, routers see log information, including when and what you did on your computer.
Can I track internet activity in my house? ›Using your wifi router's settings online, you can see what IP addresses logged into your network connection and when, and many routers can also give details as to which websites were accessed by each IP address that was connected to it.
How do I merge two networks in cytoscape? ›- Select either Union, Intersection or Difference.
- Networks available for merge are listed under Networks to merge. Select a network from the list and click the right arrow to transfer the network to Selected networks. Click Merge to continue.
What is the most common file format used for 3D modeling information? ›
Ever since its invention, the STL file format has been readily adopted by the rapid prototyping, 3D printing, and computer-aided manufacturing industries. It's still the most widely used file format in 3D printing.
How do I link a text file in Access? ›Access opens the Get External Data – Text File dialog box. In the Get External Data - Text File dialog box, specify the name of the text file that contains the data to which you want to link in the File name box. Select Link to the data source by creating a linked table and then click OK.
Can you import multiple text files into access at once? ›The short answer, of course, is yes you can do that.
How do I select nodes and edges in Cytoscape? ›Cytoscape allows you to select nodes and edges in sophisticated ways. To begin using these capabilities, choose the Select pane on the left-hand control panel, and then click the + sign to indicate that you'll choose an attribute that you'll use to select nodes.
What are nodes and edges in Cytoscape? ›Interaction networks are useful as stand-alone models. However, they are most powerful for answering scientific questions when integrated with additional information. Cytoscape allows the user to add arbitrary node, edge and network information to Cytoscape as node/edge/network data columns.
How do I add nodes in Cytoscape? ›To add a node as a source or a sink, first select it in the current network and then press the + button next to the appropriate box. The node IDs for selected nodes will be added to the list in the box. To remove nodes from a list, select them and press the - button next to the box they are in.
What is the alternative to Cytoscape? ›- Databox. Compare.
- Grafana. Compare.
- Looker Studio. Compare.
- Sigma. Compare. Free 2-Week Trial.
- JMP Statistical Discovery Software from SAS. Compare.
- Kibana. Compare.
- Chartio (discontinued) Compare.
- Sisense for Cloud Data Teams. Compare.
- Gephi. Gephi is the leading visualization and exploration software for all kinds of graphs and networks. ...
- Cytoscape. Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data.
- GraphVis. ...
- igraph. ...
- UCINET. ...
- SocNetV. ...
- Pajek.
- In Gephi, there's really not a great export feature for the map you've created. ...
- All the interactivity is lost if not using the Gephi file itself.
The Social Network Cytoscape app creates a visual summary of how individuals are connected. Biological networks can be visualized and analyzed using Cytoscape. Often researchers want to go beyond the network of proteins or genes and also look at the inter-connectedness between colleagues and institutions.
Which software helps in network Visualisation? ›
Best Network Virtualization Software include:
VMware NSX, VMware Anywhere from Claranet, and Lumen Cloud Connect.
| Cytoscape home page | |
|---|---|
| Original author(s) | Institute for Systems Biology |
| Developer(s) | Cytoscape Team |
| Initial release | July 2002 |
| Stable release | 3.8.2 / 29 October 2020 |
CytoHubba provides 11 topological analysis methods including Degree, Edge Percolated Component, Maximum Neighborhood Component, Density of Maximum Neighborhood Component, Maximal Clique Centrality and six centralities (Bottleneck, EcCentricity, Closeness, Radiality, Betweenness, and Stress) based on shortest paths.
How do I find nodes in Cytoscape? ›You can search for nodes and edges by column value directly through Cytoscape's tool bar. For example, to select nodes or edges with a column value that starts with STE, type ste* in the search bar. The search is case-insensitive. The * is a wildcard character that matches zero or more characters, while ?
Which protocol is used for network monitoring? ›Internet Control Message Protocol (ICMP)
ICMP a network monitoring protocol that's designed specifically for error reporting. Network devices rely on ICMP to transmit error messages.
When connected to the internet or intranet, the nodes are referred to as internet nodes. These nodes are identified by their IP addresses. Some Data Link layer devices(switches, bridges, WLAN access points, etc.) do not have an IP address.
What is passthrough mapping in cytoscape? ›Cytoscape currently supports three different types of mappings: Passthrough Mapping. The values of network column data are passed directly through to properties. A passthrough mapping is typically used to specify node/edge labels. For example, a passthrough mapping can label all nodes with their common gene names.
How do I hide nodes in cytoscape? ›Hide (but do not delete) the specified node or nodes, by setting the Visible property bypass value to false.
How to do network analysis in Cytoscape? ›By default, Cytoscape uses a plugin called NetworkAnalyzer. To use it click Tools > NetworkAnalyzer > Network Analysis > Analyze Network. A dialogue box will appear that asks you whether the network is directed or undirected. Select directed for this specific network.
How do you use BiNGO in Cytoscape? ›- Start Cytoscape and load the network galFiltered. ...
- The BiNGO Settings panel pops up. ...
- The program will inform you of its progress while parsing the annotations and calculating the tests, corrections and layout. ...
- Select some interesting GO categories by checking the boxes on the left side of the BiNGO output window.
How do I import data into Cytoscape? ›
- Via the File menu: Load the galExpData. csv file under File menu, select Import → Table from File....
- Drag and drop: Drag and drop the galExpData. csv file onto the Node Table .
Check for local connectivity issues: The first step in troubleshooting network errors is to check cables, devices, switches, and routers for proper functioning. Teams can also try restarting devices such as the modem, PC, and router to resolve simple network issues. Another issue could be LAN connectivity.
How do you draw a network analysis? ›- Select a network diagram template. ...
- Name the network diagram. ...
- Remove existing elements that you don't need on your diagram. ...
- Add network components to the diagram. ...
- Name the items in your network diagram. ...
- Draw connections between components. ...
- Add a title and share your network diagram.
The tail of the arrow represents the start of the activity and the head represents the finish. The length of the arrow typically denotes the duration of the activity. Each arrow connects two boxes, known as “nodes.” The nodes are used to represent the start or end of an activity in a sequence.
What are the five 5 network diagnostic utilities? ›- PING.
- Traceroute.
- PathPing.
- Nmap.
- Netstat.
- ARP.
- Ipconfig.
- Nslookup.
Traffic spikes. Perhaps the most common cause of network failure apart from human error, spikes in traffic can overwhelm a network that isn't prepared or scalable. These network errors can disrupt business across multiple sites if the failure hits a critical location or network.
What are the best network analysis techniques? ›...
There are four main stages in network analysis:
- Network generation.
- Network evaluation.
- Network monitoring.
- Network modification.
Rules for constructing network
(i.e) only one activity can connect any two nodes. (ii) No two activities can be identified by the same head and tail events. (iii) Nodes are numbered to identify an activity uniquely. Tail node (starting point) should be lower than the head node (end point) of an activity.
- All program activities must be clearly defined, including identifiable start and completion points.
- A logic diagram showing the sequence and interrelationships of activities must be developed.
- The time to complete each activity must be estimated as accurately as possible.
A network diagram is a visual representation of a computer or telecommunications network. It shows the components that make up a network and how they interact, including routers, devices, hubs, firewalls, etc.
What is the difference between Gantt chart and network diagram? ›
Like PERT charts, network diagrams are a flowchart that show the sequential workflow of project tasks, whereas a Gantt is a bar chart that shows the project schedule in a graphic representation. Gantts tend to focus on tasks and time management while the project is ongoing.
What is the purpose of a Gantt chart? ›A Gantt chart is a project management tool that illustrates work completed over a period of time in relation to the time planned for the work. It typically includes two sections: the left side outlines a list of tasks, while the right side has a timeline with schedule bars that visualize work.