This question on previously asked on biostar may help you: How Can I Extract All Bidirectional Promoters In The Human Genome From Ucsc Genome Browser?

Or you could use a shell script to loop over each pair of genes:

while read L1
 do
    while read L2
      do
        echo $L1 $L2  #### DO SOME FILTERING HERE (same chromosome, etc..), e.g. USING `awk`
      done < mygenes.txt
 done  < mygenes.txt

Thanks for the reply.

I was earlier just extracting gene_name, chr_strand, start(bp), end(bp) and other details using.

   > mysql --user=anonymous 
    > --host=ensembldb.ensembl.org --database=ensembl_compara_59 --port=5306 
    > 
    > 
    > 
    > SELECT stable_id, family_id,
    > display_label, taxon_id, chr_name,
    > chr_strand, chr_start, chr_end FROM
    > member, family_member WHERE
    > member.member_id =
    > family_member.member_id AND
    > source_name = 'ENSEMBLGENE' AND
    > taxon_id = 9606 INTO OUTFILE
    > '/Datasets/family_ids.txt'

The link that you helped me with is bit difficult for me to understand as I new to MySql. I didn't follow how K1.name and K2.name can be extracted for genes.

I want to do something very similar to the example but just with genes and their orientation. thanks.