#!/usr/bin/perl use CGI qw(param); use GD; $id = param("id"); $id =~ tr/a-z/A-Z/; open(RAW_DATA, "./MIPS_level2.txt"); while($buffer = ){ chomp($buffer); ($in1, $others) = split(/\t/, $buffer); $func{$in1} = $others; } close(RAW_DATA); open(RAW_DATA, "./Uetz_orf.txt"); while($buffer = ){ ($in1, $in2, $others) = split(/\t/, $buffer); $pair = $in1 . ":" . $in2; $inte{$pair} = 1; } close(RAW_DATA); open(RAW_DATA, "./ORF-gene.txt"); while($buffer = ){ chomp($buffer); ($orf, $genes) = split(/\t/, $buffer); ($g1, @others) = split(/ +/, $genes); $gene_ORF{$orf} = $g1; } close(RAW_DATA); print "Content-type:text/html\n\n"; print "\n"; print "

The correlated genes with $id

\n"; for($num_method = 0; $num_method < 3; $num_method++){ $im = new GD::Image(300, 300); $white = $im->colorAllocate(255,255,255); $black = $im->colorAllocate(0,0,0); $grey = $im->colorAllocate(200,200,200); $red = $im->colorAllocate(250,0,0); $green = $im->colorAllocate(0,255,0); $blue = $im->colorAllocate(0,0,255); $greenblue = $im->colorAllocate(0,255,255); if($num_method == 0){ print "Using method of local pattern
"; open(RAW_DATA, "pseu_dp_all_g16.out"); } elsif($num_method == 2){ print "

Using method of spectral analysis
"; open(RAW_DATA, "fft_compare_g0.98.out"); } else{ print "

Using method of simultaneous correlation
"; open(RAW_DATA, "ttt_compare_g0.95.out"); } $ii = 0; while($buffer= ){ chomp($buffer); if($num_method == 0){ ($num1, $num2, $gene1, $gene2, $score, $x, $y, $len) = split(/ +/, $buffer); } elsif($num_method == 2){ ($num1, $num2, $gene1, $dum1, $gene2, $dum2, $score) = split(/ +/, $buffer); } else{ ($num1, $num2, $gene1, $dum1, $gene2, $dum2, $score) = split(/ +/, $buffer); } if($gene1 eq $id){ $level1{$ii} = $gene2; $fun1 = $func{$gene1}; $fun2 = $func{$gene2}; $found = 0; $found_inter = 0; if(length($fun1) !=0 && length($fun2) !=0 && $fun1 ne "99." && $fun2 ne "99."){ (@funs1) = split(/:/, $fun1); (@funs2) = split(/:/, $fun2); $l1 = @funs1; $l2 = @funs2; for($i=0; $i<$l1; $i++){ for($j=0; $j<$l2; $j++){ if($funs1[$i] eq $funs2[$j]){ $found = 1; break; } } } } if($found == 1){ $func{$ii} = 1; } else{ $func{$ii} = 0; } #######interaction test $pair = $gene1 . ":" . $gene2; if($inte{$pair} == 1){ $found_inter =1; } else{ $pair = $gene2 . ":" . $gene1; if($inte{$pair} == 1){ $found_inter =1; } } if($found_inter == 1){ $interaction{$ii} =1; } else{ $interaction{$ii} =0; } $ii++; } if($gene2 eq $id){ $level1{$ii} = $gene1; $fun1 = $func{$gene1}; $fun2 = $func{$gene2}; $found = 0; $found_inter = 0; if(length($fun1) !=0 && length($fun2) !=0 && $fun1 ne "99." && $fun2 ne "99."){ (@funs1) = split(/:/, $fun1); (@funs2) = split(/:/, $fun2); $l1 = @funs1; $l2 = @funs2; for($i=0; $i<$l1; $i++){ for($j=0; $j<$l2; $j++){ if($funs1[$i] eq $funs2[$j]){ $found = 1; break; } } } } if($found == 1){ $func{$ii} = 1; } else{ $func{$ii} = 0; } $pair = $gene1 . ":" . $gene2; if($inte{$pair} == 1){ $found_inter =1; } else{ $pair = $gene2 . ":" . $gene1; if($inte{$pair} == 1){ $found_inter =1; } } if($found_inter == 1){ $interaction{$ii} =1; } else{ $interaction{$ii} =0; } $ii++; } } close(RAW_DATA); $num_level1 = $ii; if($num_level1 == 0){ print "No strong correlated genes found
"; } if($num_level1 == 1){ $centerx = 120; $centery = 150; $im->arc($centerx,$centery,12,12,0,360,$red); $im->fill($centerx, $centery, $red); # $gn = $gene_ORF{$id}; $gn = $id; if(length($gn) == 0){ $gn = $id; } $im->string(gdMediumBoldFont,$centerx-16,$centery+8,$gn, $red); } else{ $centerx = 150; $centery = 150; $im->arc($centerx,$centery,12,12,0,360,$red); $im->fill($centerx, $centery, $red); # $gn = $gene_ORF{$id}; $gn = $id; if(length($gn) == 0){ $gn = $id; } $im->string(gdMediumBoldFont,$centerx-16,$centery+8,$gn, $red); } $dis = 80; if($num_method == 0 && $num_level1 > 0){ print "\n"; } elsif($num_method == 2 && $num_level1 > 0){ print "\n"; } elsif($num_method == 1 && $num_level1 > 0){ print "\n"; } if($num_level1 > 0){ for($i = 0; $i < $num_level1; $i++){ $angle = $i * 2*3.1415926/$num_level1; $posx = $centerx + $dis * cos($angle); $posy = $centery + $dis * sin($angle); $name = $level1{$i}; # $gn = $gene_ORF{$name}; $gn = $name; if(length($gn) == 0){ $gn = $name; } if($interaction{$i} == 1 && $interaction{$i} == 1){ draw_node($posx, $posy, $name, $gn, $greenblue); } if($func{$i} == 1){ draw_node($posx, $posy, $name, $gn, $blue); } elsif($func{$i} == 1){ draw_node($posx, $posy, $name, $gn, $green); } else{ draw_node($posx, $posy, $name, $gn, $black); } draw_edge($posx, $posy, $centerx, $centery); } print ""; $imgname = $id . $num_method . ".png"; open(DISPLAY,">./tmp/$imgname"); flock(DISPLAY, LOCK_EX); binmode DISPLAY; print DISPLAY $im->png; close(DISPLAY); if($num_method == 0){ print "

"; } elsif($num_method == 2){ print "

"; } else{ print "

"; } } #print "
"; } print "

green dots: interact with the central gene
"; print "blue dots: have the same function as the central gene
"; print "black dots: none of the above
"; print ""; sub draw_node { my($xx, $yy, $nn, $gn, $cc) = @_; $im->arc($xx,$yy,12,12,0,360,$cc); $im->fill($xx, $yy, $cc); $im->string(gdMediumBoldFont,$xx-16,$yy+8,$gn, $black); $x1 = $xx-4; $y1 = $yy-4; $x2 = $xx+4; $y2 = $yy+4; print < imgarea } sub draw_edge { my($x1, $y1, $x2, $y2) = @_; $im->line($x1, $y1, $x2, $y2, $black); }