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Display MitoCarta3.0 pathwaysq
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@ttsudipto
ttsudipto committed Feb 7, 2024
1 parent ef067a9 commit 513449e
Showing 1 changed file with 126 additions and 32 deletions.
158 changes: 126 additions & 32 deletions protein.php
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Original file line number Diff line number Diff line change
Expand Up @@ -84,22 +84,40 @@ function get_SourceID_links($text){
// }


$pathwayAttributes = array(
$keggPathwayAttributes = array(
"PathwayProteinInteractionID" => "Pathway Protein Interaction ID",
"UniProtAccession"=>"UniProt accession ID",
"Pathway" => "Pathway",
"PathwayID" => "Pathway ID",
"AdjustedPvalue" => "Adjusted p-value",
);
$pathwayQuery = "select ".implode(",", array_keys($pathwayAttributes))." from kegg_pathway where UniProtAccession=?;";
// echo $pathwayQuery."<br/>";
$pathwayStmt = $conn->prepare($pathwayQuery);
$pathwayStmt->bind_param("s", $uniprot);
$pathwayStmt->execute();
$pathwayRows = execute_and_fetch_assoc($pathwayStmt);
$pathwayStmt->close();
// echo count($pathwayRows)."<br/>";
// foreach($pathwayRows as $row) {
$keggPathwayQuery = "select ".implode(",", array_keys($keggPathwayAttributes))." from kegg_pathway where UniProtAccession=?;";
// echo $keggPathwayQuery."<br/>";
$keggPathwayStmt = $conn->prepare($keggPathwayQuery);
$keggPathwayStmt->bind_param("s", $uniprot);
$keggPathwayStmt->execute();
$keggPathwayRows = execute_and_fetch_assoc($keggPathwayStmt);
$keggPathwayStmt->close();
// echo count($keggPathwayRows)."<br/>";
// foreach($keggPathwayRows as $row) {
// echo implode(",", array_keys($row))."<br/>";
// echo implode(",", $row)."<br/>";
// }

$mcPathwayAttributes = array(
"PathwayProteinInteractionID" => "Pathway Protein Interaction ID",
"UniProtAccession"=>"UniProt accession ID",
"Pathway" => "Pathway",
);
$mcPathwayQuery = "select ".implode(",", array_keys($mcPathwayAttributes))." from mitocarta_pathway where UniProtAccession=?;";
// echo mcPathwayQuery."<br/>";
$mcPathwayStmt = $conn->prepare($mcPathwayQuery);
$mcPathwayStmt->bind_param("s", $uniprot);
$mcPathwayStmt->execute();
$mcPathwayRows = execute_and_fetch_assoc($mcPathwayStmt);
$mcPathwayStmt->close();
// echo count($mcPathwayRows)."<br/>";
// foreach($mcPathwayRows as $row) {
// echo implode(",", array_keys($row))."<br/>";
// echo implode(",", $row)."<br/>";
// }
Expand Down Expand Up @@ -167,6 +185,38 @@ function get_SourceID_links($text){
<meta charset="UTF-8">
<title>mitoPADdb - Mitochondrial Proteins Associated with Diseases database</title>
<link rel = "stylesheet" type = "text/css" href = "css/main.css" />
<script>
go_cc = null;
go_mf = null;
go_bp = null;
function truncate(type, container_id) {
if (type == 'cc')
var whole_data = go_cc;
else if (type == 'mf')
var whole_data = go_mf;
else if (type == 'bp')
var whole_data = go_bp;
if (whole_data.length > 5) {
var truncated_data = whole_data.slice(1, 6);
truncated_data = truncated_data.join('; ') + '<a class="link" style="cursor:pointer;" onclick="expand(\'' + type + '\', \'' + container_id + '\')"> ... [More]</a>';
} else
var truncated_data = whole_data.join('; ');
document.getElementById(container_id).innerHTML = truncated_data;
}
function expand(type, container_id) {
if (type == 'cc')
var whole_data = go_cc;
else if (type == 'mf')
var whole_data = go_mf;
else if (type == 'bp')
var whole_data = go_bp;
if (whole_data.length > 5)
whole_data = whole_data.join('; ') + '<a class="link" style="cursor:pointer;" onclick="truncate(\'' + type + '\', \'' + container_id + '\')"> [Less]</a>';
else
whole_data = whole_data.join('; ');
document.getElementById(container_id).innerHTML = whole_data;
}
</script>
<!-- <script type = "text/javascript" src = "js/advance_search_input.js"></script> -->
</head>
<body>
Expand Down Expand Up @@ -198,7 +248,17 @@ function get_SourceID_links($text){
else
echo "<center><p>Error !!! No protein exist in the database having Gene name: ".$key.".</p></center>";
} else {
echo "<center><h2>UniProt accession ID: ".$uniprot." <a target=\"_blank\" href=\"https://www.uniprot.org/uniprotkb/".$uniprot."\"><img src=\"resource/redirect-icon.png\" height=\"18px\" width=\"auto\" /></a></h2></center>";
echo "<center><h2 id=\"sec-1\">UniProt accession ID: ".$uniprot." <a target=\"_blank\" href=\"https://www.uniprot.org/uniprotkb/".$uniprot."\"><img src=\"resource/redirect-icon.png\" height=\"18px\" width=\"auto\" /></a></h2></center>";
echo
"<p style=\"width:80%; margin:10px 10% 5px 10%;\">
<b>Users can access the four different data for this gene/protein</b> either
by selecting a name here-
<a class=\"link\" href=\"#protein-disease-associations\">1. Protein-disease associations</a>,
<a class=\"link\" href=\"#protein-pathway-associations\">2. Protein-pathway associations</a>,
<a class=\"link\" href=\"#disease-associated-mutations\">3. Disease-associated mutations</a>,
<a class=\"link\" href=\"#disease-associated-expression-variation\">4. Disease-associated expression variation</a>,
or by scrolling up/down the page.
</p>";
echo "<table class=\"details\" border=\"1\">";

// echo "<tr><th>Attribute</th><th>Value</th></tr>";
Expand All @@ -220,11 +280,18 @@ function get_SourceID_links($text){
echo implode("; ", $diseases);
echo "</td></tr>";

echo "<tr><td style=\"width:25%\"><b>Pathways</b></td><td style=\"width:75%\">";
$pathways = array();
foreach($pathwayRows as $row)
array_push($pathways, "<a class=\"link\" href=\"#".$row["PathwayProteinInteractionID"]."\">".$row["PathwayProteinInteractionID"]."</a>");
echo implode("; ", $pathways);
echo "<tr><td style=\"width:25%\"><b>KEGG pathways</b></td><td style=\"width:75%\">";
$keggPathways = array();
foreach($keggPathwayRows as $row)
array_push($keggPathways, "<a class=\"link\" href=\"#".$row["PathwayID"]."\" title=\"".$row["Pathway"]."\">".$row["PathwayID"]."</a>");
echo implode("; ", $keggPathways);
echo "</td></tr>";

echo "<tr><td style=\"width:25%\"><b>MitoCatra3.0 pathways</b></td><td style=\"width:75%\">";
$mcPathways = array();
foreach($mcPathwayRows as $row)
array_push($mcPathways, "<a class=\"link\" href=\"#".$row["PathwayProteinInteractionID"]."\" title=\"".$row["Pathway"]."\">".$row["PathwayProteinInteractionID"]."</a>");
echo implode("; ", $mcPathways);
echo "</td></tr>";

echo "<tr><td style=\"width:25%\"><b>Mutations</b></td><td style=\"width:75%\">";
Expand All @@ -245,15 +312,29 @@ function get_SourceID_links($text){
echo implode("; ", $expressions);
echo "</td></tr>";

echo "<tr><td style=\"width:25%\"><b>Gene Ontology Cellular Component</b></td><td style=\"width:75%\">".$proteinRows[0]["GOCC"]."</td>";
echo "<tr><td style=\"width:25%\"><b>Gene Ontology Molecular Function</b></td><td style=\"width:75%\">".$proteinRows[0]["GOMF"]."</td>";
echo "<tr><td style=\"width:25%\"><b>Gene Ontology Biological Process</b></td><td style=\"width:75%\">".$proteinRows[0]["GOBP"]."</td>";
$cc_array = explode('; ', $proteinRows[0]["GOCC"]);
$mf_array = explode('; ', $proteinRows[0]["GOMF"]);
$bp_array = explode('; ', $proteinRows[0]["GOBP"]);
array_walk($cc_array, function(&$x) {$x = "'$x'";});
array_walk($mf_array, function(&$x) {$x = "'$x'";});
array_walk($bp_array, function(&$x) {$x = "'$x'";});
echo "<script>go_cc = [".implode(',', $cc_array)."]</script>";
echo "<script>go_mf = [".implode(',', $mf_array)."]</script>";
echo "<script>go_bp = [".implode(',', $bp_array)."]</script>";
echo "<tr><td style=\"width:25%\"><b>Gene Ontology Cellular Component</b></td><td id=\"cc_container\" style=\"width:75%\">".$proteinRows[0]["GOCC"]."</td>";
echo "<tr><td style=\"width:25%\"><b>Gene Ontology Molecular Function</b></td><td id=\"mf_container\" style=\"width:75%\">".$proteinRows[0]["GOMF"]."</td>";
echo "<tr><td style=\"width:25%\"><b>Gene Ontology Biological Process</b></td><td id=\"bp_container\" style=\"width:75%\">".$proteinRows[0]["GOBP"]."</td>";

echo "</table>";
?>

<script>
truncate('cc', 'cc_container');
truncate('mf', 'mf_container');
truncate('bp', 'bp_container');
</script>
<br/>
<center><h3>Protein-disease associations</h3></center>
<center><h3 id="protein-disease-associations">Protein-disease associations</h3></center>
<?php
if(count($diseaseRows) < 1) {
if ($keytype === "ID")
Expand Down Expand Up @@ -284,9 +365,9 @@ function get_SourceID_links($text){
?>

<br/>
<center><h3>Protein-pathway associations</h3></center>
<center><h3 id="protein-pathway-associations">Protein-pathway associations</h3></center>
<?php
if(count($pathwayRows) < 1) {
if(count($keggPathwayRows) + count($mcPathwayRows) < 1) {
if ($keytype === "ID")
echo "<center><p>No pathway associations found in the database for UniProt accession ID: ".$uniprot." !!</p></center>";
else
Expand All @@ -295,20 +376,33 @@ function get_SourceID_links($text){
?>
<div style="overflow:auto;">
<table class="summary">
<tr><?php foreach($pathwayAttributes as $attr) echo "<th>".$attr."</th>"; ?></tr>
<tr>
<th>Pathway type</th>
<?php
foreach($pathwayRows as $row) {
echo "<tr>";
foreach(array_keys($pathwayAttributes) as $attr) {
if ($attr === "PathwayProteinInteractionID")
echo "<td id=\"".$row[$attr]."\">".$row[$attr]."</td>";
elseif ($attr === "PathwayID")
echo "<td><a class=\"link\" href=\"https://www.kegg.jp/entry/".$row[$attr]."\">".$row[$attr]."</a></td>";
foreach($keggPathwayAttributes as $attr) echo "<th>".$attr."</th>";
?>
</tr>
<?php
foreach($keggPathwayRows as $row) {
echo "<tr><td>KEGG</td>";
foreach(array_keys($keggPathwayAttributes) as $attr) {
if ($attr === "PathwayID")
echo "<td><a class=\"link\" id=\"".$row[$attr]."\" href=\"https://www.kegg.jp/entry/".$row[$attr]."\">".$row[$attr]." <img src=\"resource/redirect-icon.png\" height=\"12px\" width=\"auto\" /></a></td>";
else
echo "<td>".$row[$attr]."</td>";
}
echo "</tr>";
}
foreach($mcPathwayRows as $row) {
echo "<tr>";
echo "<td>MitoCarta3.0</td>";
echo "<td id=\"".$row["PathwayProteinInteractionID"]."\">".$row["PathwayProteinInteractionID"]."</td>";
echo "<td>".$row["UniProtAccession"]."</td>";
echo "<td>".$row["Pathway"]."</td>";
echo "<td></td>";
echo "<td></td>";
echo "</tr>";
}
?>
</table>
</div>
Expand All @@ -317,7 +411,7 @@ function get_SourceID_links($text){
?>

<br/>
<center><h3>Disease associated mutations</h3></center>
<center><h3 id="disease-associated-mutations">Disease-associated mutations</h3></center>
<?php
if(count($snpRows) < 1) {
if ($keytype === "ID")
Expand Down Expand Up @@ -358,7 +452,7 @@ function get_SourceID_links($text){
?>

<br/>
<center><h3>Expression</h3></center>
<center><h3 id="disease-associated-expression-variation">Disease-associated expression variation</h3></center>
<?php
if(count($expRows) < 1) {
if ($keytype === "ID")
Expand Down

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