Interpret Large Networks through Filtering

User Guide

The guide for the interactive interface of VISIONET is shown in the below figure.


Input format guidelines

Two input files are required: (1) the tuples that describe the transcription factor network, and (2) the tuples for the microarray intensity.

  • (1) Single network file: each line contains the tuples that describe the transcription factor network. The file can be tab- or comma-separated.
  • (1) Multiple ChIP-Seq files: each file (COD) format must contain 6 columns, where one of the column must be names annotation.
  • (2) Single expression fold-change file (TXT): the fold-change values are pre-calculated before uploading. Note that the values must be expressed in the standard log-scale format.
  • (2) Multiple raw expression file (SOFT): the tab-separated text file must contain three columns: Identifier, Gene symbol and each DATA_# column containing the microarray data in log-scale format.

Input files (1,2) are provided in tab- or comma-separated format, and (1) also accepts GraphML format (Brandes, et al., 2002). Alternatively, the user can supply the raw ChIP-Seq peak list for (1) in the standard COD format, and the raw microarray file for (2) in the in tab- or comma-separated format.

For sample inputs, please refer to VISIONET main page.

VISIONET Desktop Companion software instructions

A companion desktop version of VISIONET is available here as a Microsoft Excel add-in. As this requires proprietary software, the desktop version is provided solely as additional convenience to users. The GraphML format enables users to work interchangeably between the web-based and desktop versions of VISIONET, and is convertible to the standard SBML format via the Cytoscape GraphMLReader plug-in.

Installation steps:

  • Install Microsoft Excel 2007 or 2010 on a Windows machine.
  • Extract and run "Setup.exe"the prerequisite NodeXL library ""(redistributed under Microsoft Public License)
  • Open the VISIONET template "VISTIONET-Desktop-Template.xlsx" in Microsoft Excel

Whenever ready, please proceed to VISIONET


Monash University         SBI Australia