Regulation of OCT4 in mammalian ES cells

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Gene regulatory networks provide insight into the mechanisms of differential gene expression at a system level. However, the methods for inference, functional analysis and visualization of regulatory modules and networks require the user to collect heterogeneous data from many sources using numerous bioinformatics tools. This makes the analysis expensive and time-consuming. In this work, the BiologicalNetworks application -the data integration and network visualization environment – was extended with tools for inference and analysis of gene regulatory modules and networks. The backend database of the application integrates public data on gene expression, pathways, transcription factor binding sites, gene and protein sequences, and functional annotations. Thus, all data essential for the analysis can be mined publicly. In addition, the user’s data can either be integrated in the database and become public, or kept private within the application. The capabilities to analyze multiple gene expression experiments are also provided. The generated network, regulatory modules and binding sites can be visualized and further analyzed within this same application.

The developed tools were applied to the OCT4 regulatory network in embryonic stem cells.

Biological Articles:


  1. What is BiologicalNetworks?
  2. What is PathSys?
  3. Why do we need BiologicalNetworks?
  4. What is GeneOntology?
  5. Where can I view or download the complete sets of GO annotations?
  6. How can I update my GeneOntology annotations?
  1. BiologicalNetworks is a general-purpose software environment for retrieval, construction, and visualization of complex biological networks. BiologicalNetworks provides querying services (querying languages and a querying engine) and an information management framework over PathSys system.
  2. PathSys is a data integration platform that provides dynamic integration over diverse set of databases.
  3. Due to difficulties in integrating heterogeneous data types coping with continuous updating of existing databases or with disparate confidence levels associated with different data sets, most biological databases are focused on a specific subset of biological knowledge. To facilitate this process, we constructed PathSys system and BiologicalNetworks framework over it.
  4. Ontologies are ‘specifications of a relational vocabulary’. In other words they are sets of defined terms like the sort that you would find in a dictionary, but the terms are networked. The terms in a given vocabulary are likely to be restricted to those used in a particular field, and in the case of GO, the terms are all biological.
  5. You do not need update your GO annotations. Every time you run BiologicalNetworks Java Web Start version, programs checks the last version of GO you have, and automatically updates it if needed.
  6. As with the vocabularies, the gene product/GO association sets from contributing groups are available at the GO web site. Tab-delimited files of the associations between gene products and GO terms that are made by the member organizations are available from their individual FTP sites or from a link on the Current Annotations table.

Biological Articles:

Tutorials – 2. Getting Started

2. Getting Started
This Chapter covers the following:

  • What types of files are required to run BiologicalNetworks
  • How to modify computer’s configurations to run BiologicalNetworks
  • Java WEB START intsructions
  • How to download and install BiologicalNetworks
  • How to download additional Data files

2.1 System Requirements

In order to run BiologicalNetworks successfully, your computer must meet the following minimum system requirements.

1GHz Intel Pentium CPU
Microsoft Windows 95, 98, 2000 and XP
25MB Free Disk Space

Linux 2.2.* Kernel on i686 processors
25MB Free Disk Space

800MHz PowerPC G3 or G4
Mac OS X 10.1 and above
25MB Free Disk Space

2.2 Java WEB START Instructions

Begin by clicking WEB START version of the BiologicalNetworks (download size: ~20 MB; download time: depending on your internet connection ~ 2 minutes first download and ~10 seconds all subsequent runs). This starts BiologicalNetworks on your own computer, after downloading the program and annotation from our website. (On subsequent runs, the program or annotation will not be downloaded again unless we have new versions or new annotation for you to use.) If BiologicalNetworks does not start, you may need to install last version of JAVA with Java Web Start inside. It is highly recommended to read the Tutorials section, before starting to use the program.

2.3 Download Additional Data Files.

  1. For making Microarray, 3D protein structure, Functional Data analysis you can download example data files.
    Download the ExampleData.ZIP file containing Stanford (tab delimited), Affymetrix, TIGR, GenePix microarray data, GeneOnology data files and PDB 3D structures of proteins from the BiologicalNetworks website ( Before you download a file, notice that its byte size is provided on the download page. Once the download has completed, check that you have downloaded the full, uncorrupted data file.
  2. Zip file also contains GO annotation files, to make GeneOntology annotation analysis.
  3. Unzip the file anywhere into your hard drive. Now you can load these data files into BiologicalNetworks analysis environment.

2.4 Troubleshooting.

If you have problems running BiologicalNetworks try to disable you firewall program and launch BiologicalNetworks again. If it helps you need to change firewall settings to allow Sun Java to connect to Internet.

For example to enable Sun Java access to Internet in Norton Internet Security you may follow these steps:

  1. Open NIS.
  2. Click on Status & Setting menu item on the left.
  3. Click on Personal Firewall.
  4. Press Configure button.
  5. Select Programs tab.
  6. Find java item in list.
  7. Select Permit All option in Internet Access column.
  8. Click OK.

For other firewall program please refer to it’s manual for more details.

If it doesn’t help try to restart your computer.

Biological Articles: