QSB: an integrative computational tool for genetical genomics

Table of Contents

  1. Introduction
  2. Download and Installation
    1. System requirements
    2. Download QSB
  3. Running QSB
    1. Input data Format
    2. A walk-through using sample input data
      1. Start
      2. Create new project
      3. QTL Mapping
      4. Visualize QTL network structure
      5. Infer gene modulatory network using Bayesian network
      6. Single Nucleotide Polymorphism Analysis
      7. Visualize SNP network structure
      8. Infer SNP gene modulatory network using Bayesian network
    3. Threshold Setting
  4. Contact information

1. Introduction

QSB is a computational tool developed for genetical genomics, an emerging field that combines quantitative genetics and genomics. QSB takes marker genotype data and expression microarray data of a segregating population as input and identify the significant QTLs that module gene expression. DNA sequence polymorphism analysis and Bayesian Network (BN) is then used to further evaluate the candidate modulator genes in the QTL intervals. The modulatory relations that best explain the microarray data are used to construct gene modulatory networks. It has four modules: (1) transcriptome QTL (or eQTL) mapping, (2) DNA sequence polymorphism analysis, (3) inferring gene modulatory network using Bayesian network (BN) and (4) gene network visualization. QSB stands for QTL mapping, Sequence polymorphism analysis (or SNP analysis) and Bayesian network.

2.Download and Installation

2.1  System requirements

QSB is written in Java and has been tested on Windows 2000/XP, Redhat Linux 9.0 and MacOS 10.8.
It requires Java Runtime Environment (J2SE JRE) 1.4.2 or later version.
To get JRE, you can go to www.java.com, click on button Java Software Download.

2.2  Download and Installation

3. Running QSB

To run QSB:

3.1 Input data Format

QSB takes three types of input data files: Gene Express Trait File, Marker Genotype File, Single Nucleotide Polymorphism (SNP) File. The sample files have been bundled the distribution zip file

 

Unique ID

Gene Symbol

Anotation

Chromosome

Position (Mb)

Strain1

Strain2

...

4930442A21Rik

4930442A21Rik

RIKEN cDNA 4930442A21 gene

1

52.02804

5.551

6.097

...

Inpp1(93942_at)

Inpp1

inositol polyphosphate-1-phosphatase

1

53.35034

8.288

7.323

...

...

...

...

...

...

...

...

...

   

Marker Name

Chromosome

Position (Mb)

Position (CM)

Strain1

Strain2

...

Marker1

1

3.06

1

B

B

...

Marker2

1

4.69

2

B

D

...

...

...

...

...

...

...

...

 

It is a one column text file, this column is the gene's  unique IDs which have SNP

 

Notes:

1.The Gene Express Data File and Marker Genotype Data File should be tab-delimited text file.
2.The order of the strains in Gene Express Data File and Marker Genotype data File should meet.
3.The data of strains in Marker Genotype Data File can contains three types of characters: B, D, H

3.2 A walk-through using sample input data

3.2.1 Start

In your "QSB" directory, run the executable file QSB.bat, the following window will be shown:

3.2.2 Create new project

Click on Project, and select the sub-menu Create New Project, you will see a window popped up for you to enter the name and directory of a new project. If the entered project name already exists, you will be given an option to choose a new name or override the existing project.

3.2.3 QTL Mapping

After the creation the new project, you will be requested for input data:

Test Run the program with sample data:
Select sample "Gene Expression Trait File": TraitSample.txt;
Select sample "Marker Genotype File": MarkerSample.txt;
keep other parameters the default value and click on OK

For more information about threashold setting , please refer to 3.3 Threashold Setting

It will take a few minutes, depending on the speed of your CPU, then the  following window will be shown

3.2.4. Visualize QTL network structure, or skip to 3.2.5

Click on any item in the table on the right, its network structure will be displayed in a seperate window.

 

3.2.5 Infer gene modulatory network using Bayesian network

Click on Bayesian Network, the result will be shown in a seperate window. (The process may take a few minutes.)

 

3.2.6 Single Nucleotide Polymorphism Analysis

On the bottom left of the window, there is a button for you to input SNP data. Select the sample SNP data file: NPSample.txt. SNP analysis will be started by clicking OK.

 

3.2.7 Visualize SNP network structure

The results from SNP analysis are displayed in the table on the right. Clicking on any row in the table will show the network structure of the clicked item.

 

3.2.8 Infer SNP gene modulatory network using Bayesian network

You can run Bayesian Network again here.

 

3.3 Threshold setting


4. Contact information

QSB is developed by Yan Cui's lab at University of Tennessee Health Science Center