miRTargetLink Human
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=0){
mysqli_data_seek($res,$row);
$resrow = (is_numeric($col)) ? mysqli_fetch_row($res) : mysqli_fetch_assoc($res);
if (isset($resrow[$col])){
return $resrow[$col];
}
}
return false;
}
function getDistinct($x, $y){
$z = [];
foreach($x as $a){
if(!in_array($a, $y)){
array_push($z, $a);
}
}
return $z;
}
function getConsensus($arrays){
$check = [];
$consensus = [];
$interactionCount = [];
// foreach($arrays as $key){
foreach($arrays as $val){
$name = explode("##", $val)[1];
if(!in_array($name, $check)){
array_push($check, $name);
$interactionCount[$name] = 1;
}else{
$interactionCount[$name]++;
array_push($consensus, $name);
}
}
// }
return array(array_unique($consensus), $interactionCount);
}
$con = mysqli_connect($server, $username, $password, $database);
// @mysql_select_db($database) or die( "Unable to select database");
$result = NULL;
$strongMap = [];
$weakMap = [];
// $predMap = [];
if($type == 'miRNA'){
foreach($queries as $qval){
$allMap[$qval] = mysqli_query($con, "SELECT DISTINCT Target_Gene, miRTarBase_ID FROM miRTarBase WHERE miRNA = \"$qval\";");//" AND Support_Type LIKE '%Weak%';");
$weakMap[$qval] = mysqli_query($con, "SELECT DISTINCT Target_Gene, miRTarBase_ID FROM miRTarBase WHERE miRNA = \"$qval\" AND Support_Type LIKE '%Weak%';");
$strongMap[$qval] = mysqli_query($con, "SELECT DISTINCT Target_Gene, miRTarBase_ID FROM miRTarBase WHERE miRNA = \"$qval\" AND Support_Type NOT LIKE '%Weak%';");
}
// $predMap[$qval] = mysqli_query($con, "SELECT DISTINCT Target_Gene FROM miRanda WHERE miRNA = \"$qval\"");
}else{
foreach($queries as $qval){
$allMap[$qval] = mysqli_query($con, "SELECT DISTINCT miRNA, miRTarBase_ID FROM miRTarBase WHERE Target_Gene = \"$qval\";");// AND Support_Type LIKE '%Weak%';");
$weakMap[$qval] = mysqli_query($con, "SELECT DISTINCT miRNA, miRTarBase_ID FROM miRTarBase WHERE Target_Gene = \"$qval\" AND Support_Type LIKE '%Weak%';");
$strongMap[$qval] = mysqli_query($con, "SELECT DISTINCT miRNA, miRTarBase_ID FROM miRTarBase WHERE Target_Gene = \"$qval\" AND Support_Type NOT LIKE '%Weak%';");
// $predMap[$qval] = mysqli_query($con, "SELECT DISTINCT miRNA FROM miRanda WHERE Target_Gene = \"$qval\"");
}
}
// making array of results
if($evidence == 'strong'){
$map = $strongMap;
}
elseif($evidence == 'weak'){
$map = $weakMap;
}
else{
$map = $allMap;
}
$allResults = [];
$mti = [];
foreach ($queries as $key) {
$res = $map[$key];
$i = 0;
$j = mysqli_num_rows($res);
while($i < $j){
$result = mysqli_result($res, $i, $qtype);
$mti[$key."##".$result] = mysqli_result($res, $i, "miRTarBase_ID");
array_push($allResults, $key."##".$result);
$i++;
}
}
$allResults = array_unique($allResults);
$overlap = getConsensus($allResults);
$consensus = $overlap[0];
$interactionCount = $overlap[1];
$resultStrongArray = [];
foreach ($queries as $key) {
$res = $strongMap[$key];
$i = 0;
$j = mysqli_num_rows($res);
while($i < $j){
$result = mysqli_result($res, $i, $qtype);
$mti[$result] = mysqli_result($res, $i, "miRTarBase_ID");
array_push($resultStrongArray, $key."##".$result);
$i++;
}
}
$resultStrongArray = array_unique($resultStrongArray);
$rEdges = [];
$tarId = [];
$resultSize = sizeOf($consensus);
$clickInfo = "
- Hover over the edges to see the interaction
- Double click to generate interaction landscape
(opens in new tab) ";
$weak = " - Weaker experimental evidence "; function getCount($arr, $b){ $count = []; foreach($arr as $a){ $info = explode("##", $a); if(in_array($info[1], $b)){ if(!array_key_exists($info[0], $count)){ $count[$info[0]] = 1; }else{ $count[$info[0]]++; } } } return $count; } function getOccur($array, $val){ $count = 0; foreach ($array as $item) { if ($item == $val) { $count++; } } // echo $item." ".$count."
- Hover over any node or edge to see more info about the interaction.
- Double click on a gene or microRNA to open its interaction landscape in a new tab.
- Move nodes around by clicking and dragging, select multiple nodes to move a group.
- Right click -> 'save image as...' to download network as png image.
- Click on microRNAs or genes in the table below to open a genecards or miRBase link in a new tab.
"; return $count; } $edgeCount = getCount($allResults, $consensus); $rNodes = []; $qNodes = []; $qId = []; for($i = 0; $i < sizeof($queries); $i++){ $qId[$queries[$i]] = $i; } $noEdges = []; $mass = 150; $fac = 3.1; if($resultSize<50){$fac = 2.5;} $mass = $fac*$resultSize; $fix = false; $qNodeIds = []; foreach($queries as $qval){ $edges = $edgeCount[$qval]; if($edges == 0){ array_push($noEdges, $qId[$qval]); } array_push($qNodeIds, $qId[$qval]); array_push($rNodes, ["id" => $qId[$qval], "selectable" => false, "label" => $qval, "color" => "#6E3E0B", "font" => "16px arial white", "shape" => "box", "title" => "".$qval."
".$edges." shared interactions".$clickInfo, "fixed" => $fix, "mass" => $mass]); } $qNodeIds = getDistinct($qNodeIds, $noEdges); $n = sizeof($rNodes); $m = sizeof($rNodes); foreach($consensus as $tar){ $tarId[$tar] = $n; $n++; } $done = []; $download = []; $weakEdges = []; $strongTargets = []; $weakTargets = []; $strongNames = []; for ($i = 0; $i < sizeOf($allResults); $i++) { $kv = explode('##', $allResults[$i]); $base = $kv[0]; $target = $kv[1]; if(in_array($target, $consensus)){ $o = $tarId[$target]; $l = 10*$fac; $s = 0.5; $edges = $interactionCount[$target]; if($edges > 2){ // $l = $l*3; $s = 10; $nColour = "#FF8000"; $tColour = "black"; $eColour = "#FF4000"; }else{ $nColour = "#0431B4"; $tColour = "white"; $eColour = "#0431B4"; } if(!in_array($o, $done)){ array_push($rNodes, ["id" => $o, "label" => $target, "color" => $nColour, "mass" => 1, "font" => "16px arial ".$tColour, "shape" => "box", "title" => "".$target."
validated interaction with ".$edges." ".$rtype."
".$clickInfo]); array_push($done, $o); array_push($allNodeIds,$o); } $eTitle = $target." - ".$base; if(!in_array($base."##".$target, $resultStrongArray)){ $eTitle = $eTitle."
Backed up solely by weak evidence"; $edge = ["id" => $base.$target,"title" => $eTitle, "from" => $o, "to" => $qId[$base], "color" => $eColour, "width" => 1.1]; array_push($weakTargets, $o); array_push($weakEdges, $base.$target); array_push($download, $base.",".$target.","."weak"); } else{ if($evidence == 'weak'){$eTitle = $eTitle."
Backed up by weak and strong evidence";} else{$eTitle = $eTitle."
Backed up by strong evidence";} $edge = ["title" => $eTitle, "from" => $o, "to" => $qId[$base], "color" => "green", "width" => 1.3]; array_push($strongTargets, $o); array_push($download, $base.",".$target.","."strong"); array_push($strongNames, $target); } array_push($rEdges, $edge); } } function array_count_values_of($value, $array) { $counts = array_count_values($array); return $counts[$value]; } $lonelyStrong = []; foreach($strongTargets as $st){ if(array_count_values_of($st, $strongTargets) < 2){ array_push($lonelyStrong, $st); } } $weakTargets = array_unique($weakTargets); $lonelyStrong = array_unique($lonelyStrong); $weakTargets = getDistinct($weakTargets, $lonelyStrong); // $lonelyStrong = getDistinct($lonelyStrong, $weakTargets); function sortNodes($nodes){ $ret = []; for($i=0; $i
miRTargetLink found two or more of the selected in the '' category
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Edit network:
Generate subnetwork for selection:
>
| Evidence category | miRTarBase ID | ||
|---|---|---|---|
| title= target="_blank"> | title= target="_blank"> |
Table filter:
No shared interactions found in the evidence category.
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Perform Over-representation analysis with GeneTrail2, a tool for statistical analysis of molecular signatures that was developed in the Chair for Bioinformatics at the University of Saarland.
Perform Over-representation analysis for:
The colour of the indicates the amount of interactions they are involved in. Orange three or more , that two are coloured Blue. If there are that any in the overlapping interaction set they are excluded from the graph. Note that interactions shown here are all experimentally validated. Interactions with strong experimental evidence are depicted by green edges, interactions with weaker evidence are depicted by blue or orange edges.