QSB: an integrative computational tool for genetical genomics |
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.
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.
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
In your "QSB" directory, run the executable file QSB.bat, the following window will be shown:
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.
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
Click on any item in the table on the right, its network structure will be displayed in a seperate window.
Click on Bayesian Network, the result will be shown in a seperate window. (The process may take a few minutes.)
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.
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.
You can run Bayesian Network again here.
cm step
for interval mapping is the size
of each step increment in interval between the two flanking markers when
calculating the LOD score.
QSB is developed by Yan Cui's lab at University of Tennessee Health Science Center