Welcome to the SIRENE program %%%%%%%%%%%%%%%%%%%%%%%%%%%%% This document aims at providing a potential user some help concerning in particular the type of input which is allowed by SIRENE. You should read this while having a look at M-file run.m which allows you to choose the parameters and then run your experiments. %%%%%%%%%%%% DATA INPUT % %%%%%%%%%%%% - the expression file (file 'expression.txt' in ecoli data) must be a tabulated file containing an expression matrix where the number of lines is the number of genes N and the number of columns P is the number of experiments in the compendium of profiles. - the regulation data (file 'regulation.txt' in ecoli data) which you should provide is required to be a tabulated file containing the known regulations under the shape of a list of pair indexes, one by line, such as 10 23 22 56 etc... meaning that gene with index 10 in [1:N] is a transcription factor, regulating gene with index 23 in [1:N] - The gene names file is optional. If provided, it should contain the name of the genes whose expression is measured in' expression.txt' in the same order. Then, in the result file giving the predicted interactions, the genes will be given their names, otherwise they will be called by their number in the expression matrix. It should look like a list : aas aat abc abrB accA etc... - an optional file describing the operons can be provided, such as the one used in our experiments in E coli, which must constitute of a list with the operon numbers in the same order as the genes in the expression matrix. When a gene is not known to belong to an operon, it should be considered to belong to an operon with a unique gene in it. It should look like this : 900 901 467 900 1 etc... This means that gene 1 (named 'aas') belongs to operon 900 together with gene 4 (named 'abrB'). This is a fictitious example. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% REQUIRED ARGUMENTS AND DEFAULT BEHAVIORS % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Each M-file contains some help concerning the arguments which should imperatively be passed to the function and those which are optional and for which the function has some default behavior. It can be obtained by typing 'help myfunction' at the matlab prompt from the src directory of SIRENE. For instance, try to type 'help sirene_cv'...