$module's detailed annotation
"; ######functional module $query=mysql_query("SELECT * FROM module_member WHERE module = '$module'"); $node = array(); $sort_node_p = array(); $sort_node_n = array(); $cyto_node = array(); $edge = array(); $tmp_edge=array(); while($result=mysql_fetch_row($query)) { $query_anno=mysql_query("SELECT * FROM functional_annotation WHERE gene = '$result[1]'"); $result_anno=mysql_fetch_row($query_anno); $element = "\t\t{ data: { id: '$result[1]', name: '$result[1]', weight: 15, faveColor: '#86B342', faveShape: 'octagon', annotation: '$result_anno[1]' } },\n"; array_push($node,$result[1]); array_push($cyto_node,$element); } sort($node); #### relationship $query=mysql_query("SELECT * FROM module_edge WHERE module = '$module'"); while($result=mysql_fetch_row($query)) { if($result[2] > 0){ $element = "\t\t{ data: { source: '$result[0]', target: '$result[1]', faveColor: '#EDA1ED', strength: 5 } },\n"; $tmp_value=$result[0]."\t".$result[1]."\t".$result[2]."\t".$result[3]."\t"."positive\n"; array_push($edge,$element); array_push($tmp_edge,$tmp_value); } if($result[2] < 0){ $element = "\t\t{ data: { source: '$result[0]', target: '$result[1]', faveColor: '#6FB1FC', strength: 5 } },\n"; array_push($edge,$element); $tmp_value=$result[0]."\t".$result[1]."\t".$result[2]."\t".$result[3]."\t"."negative\n"; array_push($tmp_edge,$tmp_value); } } if(count($node)<1){ echo "
Protein:
Yellow color--query protein
Green color--interaction proteins.
Interaction line:
Pink--proteins own interaction and positive co-expression relationship with target protein
Blue--proteins own interaction and negative co-expression relationship with target protein
Orange--proteins own interaction and protein-protein relationship with target protein
This network produced by cytoscapeweb
"; } #####GSEA enrichment annotation echo "

Module annotation (GSEA enrichment result)

"; echo ""; $query=mysql_query("SELECT * FROM module_annotation WHERE module = '$module'"); while($result=mysql_fetch_row($query)) { if($result[0]==""){echo "";} else{ echo "";} } echo "
Function AnnotationP valueFDR
---
$result[1]$result[2]$result[3]

"; #####members echo "

Module member annotation

"; echo ""; foreach($node as $gene) { $query=mysql_query("SELECT gene,ortholog,annotation FROM annotation WHERE gene = '$gene'"); if($result=mysql_fetch_row($query)) { if($result[1] == "-"){ echo "";} else { echo ""; } } else{ echo ""; } } echo "
Gene IDOrtholog in Arabidopsis Annotation in Arabidopsis
$gene-$result[3]
$gene$result[1] $result[2]
$gene--

"; #####connection modules /* echo "

Direct connection functional modules

"; echo ""; $query=mysql_query("SELECT * FROM module_connection WHERE moduleA = '$module' or moduleB = '$module'"); while($result=mysql_fetch_row($query)) { if($result[0] == $module) { echo ""; } else { echo ""; } } echo "
Module IDFunction AnnotationOverlap condition
$result[1]"; $query1=mysql_query("SELECT * FROM module_annotation WHERE module = '$result[1]'"); while($result2=mysql_fetch_row($query1)) { echo "$result2[1]
"; } echo "
details
$result[0]"; $query1=mysql_query("SELECT * FROM module_annotation WHERE module = '$result[0]'"); while($result1=mysql_fetch_row($query1)) { echo "$result1[1]
"; } echo "
details
"; */ /*$nodelist=base64_encode(serialize($node)); echo "
more details
"; */ ?>