Create ovlp_gene.ref1.pl 

# variant of ltt4ic.pl modified for gene list input
# modification of ltt4gic to score position info relative to gene ts and gene expression pattern

$argc = scalar(@ARGV);
$chrCl = $ARGV[0];
$intervalList = $ARGV[1];
chomp $intervalList;

$local = 0;
$prtSwitch = 0;
$prtLim = 120;

$expParam = "expL"; #set to expL for expression level or expC for expression change
$expMinL = -27.5; # note - based on inspection of de.com.table.txt in JMP
$expMedL = -18.376; # note - based on inspection of de.com.table.txt in JM