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protein.php
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<?php
include('db.php');
function get_PubMed_links($text){
$img_tag = "<img src=\"resource/redirect-icon.png\" height=\"12px\" width=\"auto\" />";
$ids = explode("|", explode(":", $text)[1]);
$links = array();
foreach($ids as $id)
array_push($links, "<a class=\"link\" target=\"_blank\" href=\"https://pubmed.ncbi.nlm.nih.gov/".$id."\">".$id."</a>");
return implode("; ", $links)." ".$img_tag;
}
function get_SourceID_links($text){
$img_tag = "<img src=\"resource/redirect-icon.png\" height=\"12px\" width=\"auto\" />";
list($source, $id_text) = explode(":", $text);
$ids = explode("|", $id_text);
$links = array();
foreach($ids as $id){
if ($source === "PubMed")
array_push($links, "<a class=\"link\" target=\"_blank\" href=\"https://pubmed.ncbi.nlm.nih.gov/".$id."\">".$id."</a>");
elseif ($source === "ClinVar")
array_push($links, "<a class=\"link\" target=\"_blank\" href=\"https://www.ncbi.nlm.nih.gov/clinvar/".$id."\">".$id."</a>");
else
array_push($links, $id);
}
return $source.": ".implode("; ", $links)." ".$img_tag;
}
function refValues($arr){
$refs = array();
for($i=0; $i<count($arr); ++$i)
$refs[$i] = &$arr[$i];
return $refs;
}
$keytype = $_GET["keytype"];
$key = $_GET["key"];
// echo $keytype." ".$key."<br/>";
$conn = connect();
$uniprot = "";
if($keytype === 'ID') {
$uniprot = $key;
} elseif($keytype === "Any"){
$query = "select UniProtAccession from protein where GeneName=? or UniProtAccession=?;";
$stmt = $conn->prepare($query);
$values = array($key, $key);
array_unshift($values, "ss");
call_user_func_array(
array($stmt, "bind_param"),
refValues($values)
);
$stmt->execute();
// $stmt->bind_param("s", $key);
$stmt->execute();
$rows = execute_and_fetch_assoc($stmt);
if(count($rows) > 0)
$uniprot = $rows[0]["UniProtAccession"];
$stmt->close();
}else {
$query = "select UniProtAccession from protein where GeneName=?;";
$stmt = $conn->prepare($query);
$stmt->bind_param("s", $key);
$stmt->execute();
$rows = execute_and_fetch_assoc($stmt);
if(count($rows) > 0)
$uniprot = $rows[0]["UniProtAccession"];
$stmt->close();
}
if ($uniprot !== "") {
$proteinAttributes = array(
"UniProtAccession"=>"UniProt accession ID",
"GeneName"=>"Gene name",
"GOCC"=>"GO CC",
"GOMF"=>"GO MF",
"GOBP"=>"GO BP",
);
$proteinQuery = "select ".implode(",", array_keys($proteinAttributes))." from protein where UniProtAccession=?;";
// echo $proteinQuery."<br/>";
$proteinStmt = $conn->prepare($proteinQuery);
$proteinStmt->bind_param("s", $uniprot);
$proteinStmt->execute();
$proteinRows = execute_and_fetch_assoc($proteinStmt);
$proteinStmt->close();
// echo implode(",", $proteinRows[0])."<br/>";
$diseaseAttributes = array(
"MADID"=>"Disease ID",
"DiseaseName"=>"Disease name",
"DiseaseCategory"=>"Disease category",
"ProteinDiseaseAssociationID"=>"Association ID"
);
$diseaseQuery = "select disease.MADID,DiseaseName,DiseaseCategory,ProteinDiseaseAssociationID from disease inner join protein_disease_association on disease.MADID=protein_disease_association.MADID where UniProtAccession=?;";
// echo $diseaseQuery."<br/>";
$diseaseStmt = $conn->prepare($diseaseQuery);
$diseaseStmt->bind_param("s", $uniprot);
$diseaseStmt->execute();
$diseaseRows = execute_and_fetch_assoc($diseaseStmt);
$diseaseStmt->close();
// echo count($diseaseRows)."<br/>";
// foreach($diseaseRows as $row) {
// echo implode(",", array_keys($row))."<br/>";
// echo implode(",", $row)."<br/>";
// }
$keggPathwayAttributes = array(
"PathwayProteinInteractionID" => "Pathway Protein Interaction ID",
"UniProtAccession"=>"UniProt accession ID",
"Pathway" => "Pathway",
"PathwayID" => "Pathway ID",
"AdjustedPvalue" => "Adjusted p-value",
);
$keggPathwayQuery = "select ".implode(",", array_keys($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/>";
// }
$snpAttributes = array(
"MPMutationID"=>"Mutation ID",
"dbSNPID"=>"dbSNP ID",
"NucleotideVariation"=>"Nucleotide change",
"AminoAcidChange"=>"Amino acid change",
"UniProtAccession"=>"UniProt accession ID",
"length(MPMutationID)"=>"Gene Name",
"disease.MADID"=>"Disease ID",
"DiseaseName"=>"Disease name",
"SourceID"=>"Source ID",
// "PMID"=>"PMID",
);
$snpQuery = "select ".implode(",", array_keys($snpAttributes))." from nucleotide_variation inner join disease on nucleotide_variation.MADID=disease.MADID where UniProtAccession=?;";
// echo $snpQuery."<br/>";
$snpStmt = $conn->prepare($snpQuery);
$snpStmt->bind_param("s", $uniprot);
$snpStmt->execute();
$snpRows = execute_and_fetch_assoc($snpStmt);
$snpStmt->close();
// echo count($snpRows)."<br/>";
// foreach($snpRows as $row) {
// echo implode(",", array_keys($row))."<br/>";
// echo implode(",", $row)."<br/>";
// }
$expAttributes = array(
"DiseaseProteinExpressionID"=>"Expression ID",
"ExpressionVariation"=>"Expression variation",
"ExpressionMolecule"=>"Expression molecule",
"Sample"=>"Sample",
"Method"=>"Method",
"UniProtAccession"=>"UniProt accession ID",
"length(DiseaseProteinExpressionID)"=>"Gene Name",
"disease.MADID"=>"Disease ID",
"DiseaseName"=>"Disease name",
"Remarks"=>"Remarks",
"PMID"=>"PubMed ID",
);
$expQuery = "select ".implode(",", array_keys($expAttributes))." from expression inner join disease on expression.MADID=disease.MADID where UniProtAccession=?;";
// echo $expQuery."<br/>";
$expStmt = $conn->prepare($expQuery);
$expStmt->bind_param("s", $uniprot);
$expStmt->execute();
$expRows = execute_and_fetch_assoc($expStmt);
$expStmt->close();
// echo count($expRows)."<br/>";
// foreach($expRows as $row) {
// echo implode(",", array_keys($row))."<br/>";
// echo implode(",", $row)."<br/>";
// }
} else {
$proteinRows = array();
}
closeConnection($conn);
?>
<!DOCTYPE html>
<html>
<head>
<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>
<div class = "section_header">
<center><p class="title">mitoPADdb - Mitochondrial Proteins Associated with Diseases database</p></center>
</div>
<div class = "section_menu">
<center>
<table cellpadding="3px">
<tr class="nav">
<td class="nav"><a href="index.html" class="side_nav">Home</a></td>
<td class="nav"><a href="browse.html" class="side_nav">Browse</a></td>
<td class="nav"><a href="statistics.html" class="side_nav">Statistics</a></td>
<td class="nav"><a href="help.html" class="side_nav">Help</a></td>
<td class="nav"><a href="team.html" class="side_nav">Team</a></td>
</tr>
</table>
</center>
</div>
<!--<div class = "section_left"></div>-->
<div class = "section_middle">
<?php
if(count($proteinRows) < 1) {
if ($keytype === "ID")
echo "<center><p>Error !!! No protein exist in the database having UniProt accession ID: ".$uniprot.".</p></center>";
elseif ($keytype === "Any")
echo "<center><p>Error !!! No protein exist in the database having UniProt accession ID: ".$key." or Gene name: ".$key."</p></center>";
else
echo "<center><p>Error !!! No protein exist in the database having Gene name: ".$key.".</p></center>";
} else {
echo "<center><h2 id=\"sec-1\">UniProt accession ID: ".$uniprot." <a target=\"_blank\" href=\"https://www.uniprot.org/uniprotkb/".$uniprot."\"><img src=\"resource/redirect-icon.png\" height=\"18px\" width=\"auto\" /></a></h2></center>";
echo
"<p style=\"width:80%; margin:10px 10% 5px 10%;\">
<b>Users can access the four different data for this gene/protein</b> either
by selecting a name here-
<a class=\"link\" href=\"#protein-disease-associations\">1. Protein-disease associations</a>,
<a class=\"link\" href=\"#protein-pathway-associations\">2. Protein-pathway associations</a>,
<a class=\"link\" href=\"#disease-associated-mutations\">3. Disease-associated mutations</a>,
<a class=\"link\" href=\"#disease-associated-expression-variation\">4. Disease-associated expression variation</a>,
or by scrolling up/down the page.
</p>";
echo "<table class=\"details\" border=\"1\">";
// echo "<tr><th>Attribute</th><th>Value</th></tr>";
// foreach ($proteinAttributes as $name=>$fname) {
// if ($name !== "UniProtAccession") {
// echo "<tr>";
// echo "<td style=\"width:25%\"><b>".$fname."</b></td>";
// echo "<td style=\"width:75%\">".$proteinRows[0][$name]."</td>";
// echo "</tr>";
// }
// }
echo "<tr><td style=\"width:25%\"><b>Gene name</b></td><td style=\"width:75%\">".$proteinRows[0]["GeneName"]."</td>";
echo "<tr><td style=\"width:25%\"><b>Disease associations</b></td><td style=\"width:75%\">";
$diseases = array();
foreach($diseaseRows as $row)
array_push($diseases, "<a class=\"link\" href=\"#".$row["MADID"]."\">".$row["DiseaseName"]."</a>");
echo implode("; ", $diseases);
echo "</td></tr>";
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%\">";
$snps = array();
foreach($snpRows as $row)
array_push($snps, "<a class=\"link\" href=\"#".$row["MPMutationID"]."\">".$row["MPMutationID"]."</a>");
echo implode("; ", $snps);
echo "</td></tr>";
echo "<tr><td style=\"width:25%\"><b>Expression</b></td><td style=\"width:75%\">";
$expressions = array();
foreach($expRows as $row) {
if($row["ExpressionVariation"] === "Down regulation")
array_push($expressions, "<a class=\"link\" href=\"#".$row["DiseaseProteinExpressionID"]."\">".$row["DiseaseProteinExpressionID"]."</a><font color=\"red\" title=\"Down regulation\">↓</font>");
else
array_push($expressions, "<a class=\"link\" href=\"#".$row["DiseaseProteinExpressionID"]."\">".$row["DiseaseProteinExpressionID"]."</a><font color=\"green\" title=\"Up regulation\">↑</font>");
}
echo implode("; ", $expressions);
echo "</td></tr>";
$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 id="protein-disease-associations">Protein-disease associations</h3></center>
<?php
if(count($diseaseRows) < 1) {
if ($keytype === "ID")
echo "<center><p>No disease associations found in the database for UniProt accession ID: ".$uniprot." !!</p></center>";
elseif ($keytype === "Any")
echo "<center><p>No disease associations found in the database having UniProt accession ID: ".$key." or Gene name: ".$key."</p></center>";
else
echo "<center><p>No disease associations found in the database for Gene name: ".$key." (UniProt accession ID: ".$uniprot.") !!</p></center>";
} else {
?>
<div style="overflow:auto;">
<table class="summary">
<tr><?php foreach($diseaseAttributes as $attr) echo "<th>".$attr."</th>"; ?></tr>
<?php
foreach($diseaseRows as $row) {
echo "<tr>";
foreach(array_keys($diseaseAttributes) as $attr) {
if ($attr === "MADID")
echo "<td id=\"".$row[$attr]."\"><a class=\"link\" href=\"disease.php?key=".$row[$attr]."\">".$row[$attr]."</a></td>";
else
echo "<td>".$row[$attr]."</td>";
}
echo "</tr>";
}
?>
</table>
</div>
<?php
}
?>
<br/>
<center><h3 id="protein-pathway-associations">Protein-pathway associations</h3></center>
<?php
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>";
elseif ($keytype === "Any")
echo "<center><p>No pathway associations found in the database having UniProt accession ID: ".$key." or Gene name: ".$key."</p></center>";
else
echo "<center><p>No pathway associations found in the database for Gene name: ".$key." (UniProt accession ID: ".$uniprot.") !!</p></center>";
} else {
?>
<div style="overflow:auto;">
<table class="summary">
<tr>
<th>Pathway type</th>
<?php
foreach($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>".$row["Pathway"]."</td>";
echo "<td></td>";
echo "<td></td>";
echo "</tr>";
}
?>
</table>
</div>
<?php
}
?>
<br/>
<center><h3 id="disease-associated-mutations">Disease-associated mutations</h3></center>
<?php
if(count($snpRows) < 1) {
if ($keytype === "ID")
echo "<center><p>No mutations found in the database for UniProt accession ID: ".$uniprot." !!</p></center>";
elseif ($keytype === "Any")
echo "<center><p>No mutations found in the database having UniProt accession ID: ".$key." or Gene name: ".$key."</p></center>";
else
echo "<center><p>No mutations found in the database for Gene name: ".$key." (UniProt accession ID: ".$uniprot.") !!</p></center>";
} else {
?>
<div style="overflow:auto;">
<table class="summary">
<tr><?php foreach($snpAttributes as $attr) echo "<th>".$attr."</th>"; ?></tr>
<?php
foreach($snpRows as $row) {
echo "<tr>";
foreach(array_keys($snpAttributes) as $attr) {
// if ($attr === "dbSNP")
// echo "<td><b><a target=\"_blank\" href=\"https://www.ncbi.nlm.nih.gov/snp/".$row[$attr]."\">".$row[$attr]." <img src=\"resource/redirect-icon.png\" height=\"12px\" width=\"auto\" /></a></b></td>";
if ($attr === "MPMutationID")
echo "<td id=\"$row[$attr]\">".$row[$attr]."</td>";
elseif ($attr === "disease.MADID")
echo "<td><a class=\"link\" href=\"disease.php?key=".$row["MADID"]."\">".$row["MADID"]."</a></td>";
elseif ($attr === "UniProtAccession")
echo "<td id=\"$row[$attr]\"><a class=\"link\" href=\"protein.php?keytype=ID&key=".$row[$attr]."\">".$row[$attr]."</a></td>";
elseif ($attr === "length(MPMutationID)")
echo "<td>".$proteinRows[0]["GeneName"]."</td>";
elseif($attr === "SourceID")
echo "<td>".get_SourceID_links($row[$attr])."</td>";
else
echo "<td>".$row[$attr]."</td>";
}
echo "</tr>";
}
?>
</table>
</div>
<?php
}
?>
<br/>
<center><h3 id="disease-associated-expression-variation">Disease-associated expression variation</h3></center>
<?php
if(count($expRows) < 1) {
if ($keytype === "ID")
echo "<center><p>No expression data found in the database for UniProt accession ID: ".$uniprot." !!</p></center>";
elseif ($keytype === "Any")
echo "<center><p>No expression data found in the database having UniProt accession ID: ".$key." or Gene name: ".$key."</p></center>";
else
echo "<center><p>No expression data found in the database for Gene name: ".$key." (UniProt accession ID: ".$uniprot.") !!</p></center>";
} else {
?>
<div style="overflow:auto;">
<table class="summary">
<tr><?php foreach($expAttributes as $attr) echo "<th>".$attr."</th>"; ?></tr>
<?php
foreach($expRows as $row) {
echo "<tr>";
foreach(array_keys($expAttributes) as $attr) {
if ($attr === "disease.MADID")
echo "<td><a class=\"link\" href=\"disease.php?key=".$row["MADID"]."\">".$row["MADID"]."</a></td>";
elseif ($attr === "DiseaseProteinExpressionID")
echo "<td id=\"$row[$attr]\">".$row[$attr]."</td>";
elseif ($attr === "UniProtAccession")
echo "<td id=\"$row[$attr]\"><a class=\"link\" href=\"protein.php?keytype=ID&key=".$row[$attr]."\">".$row[$attr]."</a></td>";
elseif ($attr === "length(DiseaseProteinExpressionID)")
echo "<td>".$proteinRows[0]["GeneName"]."</td>";
elseif ($attr === "PMID")
echo "<td>".get_PubMed_links($row[$attr])."</td>";
else
echo "<td>".$row[$attr]."</td>";
}
echo "</tr>";
}
?>
</table>
</div>
<?php
}
}
?>
<br/><hr/>
<p style="font-size:0.9em;text-align:center;">
© 2024 Bose Institute. All rights reserved. For queries, please contact Dr. Sudipto Saha
(<a class="link" href="mailto:[email protected]">[email protected]</a>,
<a class="link" href="mailto:[email protected]">[email protected]</a>).
</p>
</div>
</body>
</html>