Quick Start Guide demonstrates:
- Queryign Data in BiologicalNetworks, Section 3.0
- Quick Search, Section 3.1
- Save Search Results, Section 3.2
- Analyze Search Results for GO terms, Section 3.3
- Add property columns to Search Results, Section 3.4
- Querying Curated Pathways and Interaction Networks, Section 3.5
- Querying Microarray Data, Section 3.6
- Querying Database to Build Pathways and explore Interaction Networks and gene relationships, Section 3.7
- Genomic Sequence analysis environment with Annotations of biomedical data, Section 6.0
1.1 Downloading and Install BiologicalNetworks
Downloading BiologicalNetwork will begin by clicking “Free download” for Windows or “Mac OS X” for MacOS. BiologicalNetworks (download size: ~60 MB; download time: depending on your internet connection ~2 minutes). After downloading install BiologicalNetworks on your own computer and start application. If BiologicalNetworks does not start, send a request to HELP.
1.2 Hardware Requirements
2GHz Intel CPU
Microsoft Windows XP/Vista/Windows 7
300MB Free Disk Space
1.8MHz PowerPC G4 or IntelMac
Mac OS X 10.4 and above
300MB Free Disk Space
2.0 Welcome Page
BiologicalNetworks appears first on the screen with the Welcome Page See Figure 1 and Project Panel. Welcome page of BiologicalNetworks contains a list of Driving Projects created by our users. Driving Projects are selected for their scientific merit in answering important biological questions and represent a broad range of research endeavors. At the same time Driving Projects stimulate the BiologicalNetworks project to improve its technologies and provide feedback on our work. Open these projects by clicking on the respective thumbnail.
Project Panel shows the database and your project contents See Figure 2
2.1 Exploring Opened Project/ Pathway
To explore opened Project/Pathway:
If you click on the Node Properties Paneit it will show you details of the chosen bioentity. See Figure 3
There are default, editable, expandable and reference fields on the Node Properties Pane.
Default fields: non editable fields for example GeneOntology annotation which are loaded with the data;
Editable fields: fields that could be edited or additional annotation could be added and saved either to local file or to database;
Expandable fields: fields that themselves have internal structure. See Figure 4
If you double click on the top of Node Properties Panel it will show you all information available for this bioentity. Figure 5
Reference fields: fields that refer to Internet resource that have information about this bioentity. See Figure 6
2.2 Interaction/Process/Reaction properties
Click on the Process/Reaction node. The Process/Reaction properties Panel will appear. See Figure 6
3.0 Querying Data in BiologicalNetworks
3.1 Quick Search
The General Search box is located at the top of the Properties Pane. See Figure 7
There is also Choose Organism Option in the Search. See Figure 8
You can also Load you gene list (tab delimeted or Comma separated) form a file to Search in the Database.
Type your favorite gene name or keywords to search for all available information about it presented in our database.
Your search results will be listed in the Search Results Pane. See Figure 9
You can copy/paste rows from the List Pane to your active pathway, or save the search results as an individual group in the Groups/Clusters folder.
3.2 Save Search results
You can Save Your Search Results to Excel File and Build a Pathway from selected group of bioentities. See Figure 10
3.3 Analyze Search Results for GO terms
GO analysis, generates a table that functionally characterize your set of genes. See Figure 11
3.4 Add property columns to Search Results
Add Column – You can add any attribute for the list of attributes collected from many external public databases.See Figure 12
3.5 Querying Curated Pathways and Interaction Networks.
Search in Curated Pathways and Interaction Networks. See Figure 13
3.6 Querying Microarray data.
To search in Microarray data, use Search Box at the top of the Microarray DataSource Pane.
Microarray Data Pane contains results found for your search from the compendium of the microarray expression data collected from several data sources (i.e. Gene Expression Omnibus). See Figure 14
3.7 Querying Database to Build Pathways and explore Interaction Networks and gene relationships
Choosing Build Pathway from Search Results list, from opened network or pathway, from microarray experiment and practically from any list of genes opens BuildPathwayWizard Panel. See Figure 10
Build Pathway Wizard
BuildPathwayWizard allows you to create pathways, using molecular interaction data from the database.
It starts by suggesting several ways to determine starting entities, and then opens the Build Pathway dialog box.
Check entities for your pathway, See Figure 15
Choose an algorithm for pathway building, See Figure 16
Check the Filter option and set up the filter, if needed, See Figure 17
Press the Finish button to start data mining. The new pathway diagram appears in the Pathway Pane.
Refer to the Tutorials to learn more about the BuildPathway Wizard.
4.0 Exploring Curated Project/ Pathway
To explore a repository of our Curated Pathways:
Click Pathways DataSource tap in the left panel of application window to bring up Curated Pathways. See Figure 18
The Curated Pathways tab pane has database tree panel.
Click the KEGG node to show available organisms in KEGG database.
After retrieving the data, 213 most popular organism nodes are appeared. (Number of nodes may vary from this value.) See Figure 18
Double click one of the organism nodes to show the accompanying pathways. See Figure 19
Double click one of the pathways shows list of reaction nodes. See Figure 19
To load the pathways into the Pathway Panel simply click Open Network. See Figure 20
The loaded pathways containing reactions, compounds and their interactions are drawn in model workspace window.
To get nice positioning force-directed layout is used.
4.1 Viewing Pathways
Open the Public Pathways, or Curated Pathways folder in the Curated Pathways Pane;
The pathway diagram appears in the Pathway Pane;
Use the Zoom by Rectangle, or Magnifier option to zoom in on parts of the pathway; See Figure 22
Use Force-Directed or Hierarchical Layout option to layout the pathway by cell localization. Refer to the Tutorials to learn more about pathway editing.
5.0 Working with Microarray Data
Use search on the top of Microarray DataSource Windows to find Microarray Data. See Figure 23
Loaded Microarray data opening in new tab. See Figure 24
Apply different clustering algorithms available from Analysis> Clustering>K-Means/Medians Clustering. See Figure 25
Clustering analysis results appear in the Project Panel.
Functionalities available from Microarray submenu and Microarray Experiment Manager Menu bar, allows the user to:
– sort the experiment by a particular sample.
– Create new> pathways as well as new groups from an expression experiment.
– Select a number of genes and create a group or a pathway from them.
– Expression data can be visually displayed on an existing pathway diagram by showing different shades of green/red depending on the fold change of expression.
5.1 Color network by expression values.
To overlay Expression Experiment results onto an existing pathway diagram:
- Open an expression experiment;
- Open a pathway of interest;
- Press the Coloring by Expression Values Toolbar button to color the active pathway by expression values;
- From drop down menu choose the sample time point you would like to visualize on the active Pathway Pane
6.0 Sequence viewer.
To open Sequence:
- Just select and open an existing sequence file from any desired file location by using standard File Open dialog.
- Currently supported sequence file format is GBK and such file should have the same extension. Please expect upcoming support for a number of other file formats.
- Now supported both one-sequence and multi-sequence (with locus list) gbk file formats.
- Viewer supports Zooming feature, Scrollbar navigation, Color change for annotations and Disable/Enable feature for any type of annotations.