The CONFAC software finds the conserved Transcription Factor Binding Sites (TFBS) in the 
promoter regions of the genes of given Human genes and the corresponding Mouse homolog. 

    The process involves four steps. 

 
Step 1: 

    Input the file containing the Gene Names and GB or mRNA Accessions/RefSeq 
IDs of genes of Human genes. The program uses the Gene Names as Identifiers for 
the output and uses the Accessions/RefSeq IDs to get the Mouse orthologs from 
ENSEMBL Mart databases and the Genomic sequences from the UCSC Genome database. 
Gene Names should NOT have any spaces in them. Also, repetitions in Gene Names 
will be over-written ie.,only the last occurance will be taken. Please see the 
input format file for the exact format of the input file. When you press the 
button, the program reads from you input file / input in the text area and 
displays the information on the screen.    
    

 
Step 2:    

    The next step brings the  Orthologous Mouse genes for the Human Genes in the 
input and displays the same along with the Genomic co-ordinates, of both the 
Human and Mouse genes in a table. Those genes for which no known ortholog could 
be found are displayed as Not Found    
    

 
Step 3:    

    Step 3 involves doing a pairwise BLAST on the Human - Mouse orthologous 
genes to  get the  conserved  parts which  are  submitted to the MATCH program. 
The output  from MATCH is  consolidated  into a  set  of  reports  which show 
the various Conserved Transcription Factor Binding Sites in the  promoter 
regions of the genes, in output files listed below.    
Raw MATCH output for Human (yourfilename-Hs.tf) and Mouse 
(yourfilename-Mm.tf)    genes.    
Consolidated MATCH output for Human (yourfilename-Hs.tf-cons.unique) 
Genes.    
All the Conserved Transcription Factor Binding Sites in the Human and 
Mouse (yourfilename-all.confac) Genes.    
Consolidated the Conserved Transcription Factor Binding Sites in the Human 
and  Mouse (yourfilename-cons.confac) Genes. 
    
    

 
Step 4:    

    The next step is for the comparison of two sets of genes to find if they are 
regulated differently. In this step, the user has to go to the Mann-Whitney test 
page. Click here to use the Mann-Whitney test. 
Select a sample file to load or select one from your files on the server. 
Select a file to be used as a control data, to upload or select one from 
the default control files or from your other files on the server.