Manual for Program

This program is designed to calculate the expression relationships between genes using our local clustering algorithm. Because one advantage of our algorithm is to find out the “time-delayed” relationship between gene pairs, the expression information of each gene should be from time course experiments, i.e. examining the genes’ expression levels at different time points. And a uniform interval between time points is suggested. For details about the algorithm, please refer to our paper (Qian et al, 2001). 



Input Format:

The input data file should be a text file. .txt file is suggested. All of the expression data should be already normalized to a "Z-socres" fasion. The content of the file should be in the format as below:

   Gene1 Expression1 Expression2 …  ExpressionN 
   Gene2 Expression1 Expression2 …  ExpressionN
   .
   .
   .
The data is spaced by a space or tab.



Output Format:

   gene1, gene2, max_score, startx, starty, len, pos_or_neg
   .
   .
   .
Note:
gene1, gene2: gene names of a pair of genes
max_score: maximum of the match score
startx, starty: starting time point from which two genes’ expression levels begin to match
len: number of gene pairs through which two genes’ expression levels match with each other
pos_or_neg: defines the type of the relationships between genes: 1 means two genes’ expression levels are positive related; 0 means negative