Supporting Page of "Efficiently Finding Genome-wide Three-way Gene Interactions from Transcript- and Genotype-Data"
by Mitsunori Kayano, Ichigaku Takigawa, Motoki Shiga, Koji Tsuda and Hiroshi Mamitsuka,


Binary files of FTGI (Fast finding Three-way Gene Interactions) are available.
This supporting page shows a brief summary for running the binary file.
An online readme file is available here.

Download

Each of the following compressed files includes a binary file ("ftgi"), sample files (geno.txt, exp.txt, allele.txt, out_sample.txt) and a readme file.

Platform File
Linux (x86_64) ftgi_linux.tar.gz (test version)
Apple Mac (i386, PPC) ftgi_mac.dmg (test version)
Microsoft Windows (Win32) ftgi_win.zip (test version)

The result of the sample input (geno.txt, exp.txt, allele.txt) was outputted in "out_sample.txt".
These input files include synthetic data of two SNPs and expression values of seven genes for 30 individuals.

How to run

A tutorial is found here.

Example
Please type the following command at a terminal window of Linux and Mac.
     >> ./ftgi -g geno.txt -e exp.txt -a allele.txt -o out.txt 
     >> threshold of MC test's pvalue?: (enter a threshold value, for example 0.001)

The command for windows is given by replacing "./ftgi" by "ftgi" in the above.

Options
'-g' specifies a data file for genotypes "geno.txt".
'-e' specifies a data file for expression values of genes "exp.txt".
'-a' specifies a data file for alleles "allele.txt".
'-o' specifies an output file "out.txt".

Data format

Each of input files contains numerical or characteristic data which are written as a matrix formulation:

data type
genotype:
expression:
allele:
 size (rows × columns)
n × 2 #SNPs
#genes × n
#SNPs × 2
delimiters
white space / tab
white space / tab
white space / tab
 sample
"geno.txt"
"exp.txt"
"allele.txt"

Where n is the number of the individuals.

Both white space and tab are available as delimiters of data.
However, continuing spaces and continuing tabs are NOT ALLOWED.

Results

The result will be printed in "out.txt":
--------------------------------------------------------------------
Results of FTGI:
threshold = 0.001
SNP Gene1 Gene2 flag p-value(MC) likelihood(LDA) p-value(IT)
0 0 1 0 -0.246028 1.0 1.0
0 0 2 0 -0.824060 1.0 1.0
...
1 5 6 1 -4.747279 -32.584872 -6.618216
-------------------------------------------------------------------- 

1st column: SNP number (0, 1, ..., #SNPs-1)
2nd column: Gene1 number (0, 1, ..., #Genes-2)
3rd column: Gene2 number (1, 2, ..., #Genes-1)
4th column: flag for the prunings* (0, 1, 2)
5th column: log10(p-value) of MC test 
6th column: log-likelihood value by LDA
7th column: log10(p-value) of the IT (Interaction Test)

* : flag = 0 (pruned by MC test), =1 (not pruned), =2(pruned by LDA).