Interpret Large Networks through Filtering

User Guide

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

VISIONET User Guide

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 "Prerequisite-NodeXL-Installer.zip"(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