From 513449e803f07cd5485375386cbb60786c33c5c5 Mon Sep 17 00:00:00 2001 From: Sudipto Bhattacharjee Date: Wed, 7 Feb 2024 13:33:14 +0530 Subject: [PATCH] Display MitoCarta3.0 pathwaysq --- protein.php | 158 +++++++++++++++++++++++++++++++++++++++++----------- 1 file changed, 126 insertions(+), 32 deletions(-) diff --git a/protein.php b/protein.php index bedc116..4946880 100644 --- a/protein.php +++ b/protein.php @@ -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."
"; - $pathwayStmt = $conn->prepare($pathwayQuery); - $pathwayStmt->bind_param("s", $uniprot); - $pathwayStmt->execute(); - $pathwayRows = execute_and_fetch_assoc($pathwayStmt); - $pathwayStmt->close(); -// echo count($pathwayRows)."
"; -// foreach($pathwayRows as $row) { + $keggPathwayQuery = "select ".implode(",", array_keys($keggPathwayAttributes))." from kegg_pathway where UniProtAccession=?;"; +// echo $keggPathwayQuery."
"; + $keggPathwayStmt = $conn->prepare($keggPathwayQuery); + $keggPathwayStmt->bind_param("s", $uniprot); + $keggPathwayStmt->execute(); + $keggPathwayRows = execute_and_fetch_assoc($keggPathwayStmt); + $keggPathwayStmt->close(); +// echo count($keggPathwayRows)."
"; +// foreach($keggPathwayRows as $row) { +// echo implode(",", array_keys($row))."
"; +// echo implode(",", $row)."
"; +// } + + $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."
"; + $mcPathwayStmt = $conn->prepare($mcPathwayQuery); + $mcPathwayStmt->bind_param("s", $uniprot); + $mcPathwayStmt->execute(); + $mcPathwayRows = execute_and_fetch_assoc($mcPathwayStmt); + $mcPathwayStmt->close(); +// echo count($mcPathwayRows)."
"; +// foreach($mcPathwayRows as $row) { // echo implode(",", array_keys($row))."
"; // echo implode(",", $row)."
"; // } @@ -167,6 +185,38 @@ function get_SourceID_links($text){ mitoPADdb - Mitochondrial Proteins Associated with Diseases database + @@ -198,7 +248,17 @@ function get_SourceID_links($text){ else echo "

Error !!! No protein exist in the database having Gene name: ".$key.".

"; } else { - echo "

UniProt accession ID: ".$uniprot."

"; + echo "

UniProt accession ID: ".$uniprot."

"; + echo + "

+ Users can access the four different data for this gene/protein either + by selecting a name here- + 1. Protein-disease associations, + 2. Protein-pathway associations, + 3. Disease-associated mutations, + 4. Disease-associated expression variation, + or by scrolling up/down the page. +

"; echo ""; // echo ""; @@ -220,11 +280,18 @@ function get_SourceID_links($text){ echo implode("; ", $diseases); echo ""; - echo ""; + + echo ""; echo ""; - echo ""; - echo ""; - echo ""; + $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 ""; + echo ""; + echo ""; + echo ""; + echo ""; + echo ""; echo "
AttributeValue
Pathways"; - $pathways = array(); - foreach($pathwayRows as $row) - array_push($pathways, "".$row["PathwayProteinInteractionID"].""); - echo implode("; ", $pathways); + echo "
KEGG pathways"; + $keggPathways = array(); + foreach($keggPathwayRows as $row) + array_push($keggPathways, "".$row["PathwayID"].""); + echo implode("; ", $keggPathways); + echo "
MitoCatra3.0 pathways"; + $mcPathways = array(); + foreach($mcPathwayRows as $row) + array_push($mcPathways, "".$row["PathwayProteinInteractionID"].""); + echo implode("; ", $mcPathways); echo "
Mutations"; @@ -245,15 +312,29 @@ function get_SourceID_links($text){ echo implode("; ", $expressions); echo "
Gene Ontology Cellular Component".$proteinRows[0]["GOCC"]."
Gene Ontology Molecular Function".$proteinRows[0]["GOMF"]."
Gene Ontology Biological Process".$proteinRows[0]["GOBP"]."
Gene Ontology Cellular Component".$proteinRows[0]["GOCC"]."
Gene Ontology Molecular Function".$proteinRows[0]["GOMF"]."
Gene Ontology Biological Process".$proteinRows[0]["GOBP"]."
"; ?> +
-

Protein-disease associations

+

Protein-disease associations


-

Protein-pathway associations

+

Protein-pathway associations

No pathway associations found in the database for UniProt accession ID: ".$uniprot." !!

"; else @@ -295,20 +376,33 @@ function get_SourceID_links($text){ ?>
- ".$attr.""; ?> + + "; - foreach(array_keys($pathwayAttributes) as $attr) { - if ($attr === "PathwayProteinInteractionID") - echo ""; - elseif ($attr === "PathwayID") - echo ""; + foreach($keggPathwayAttributes as $attr) echo ""; + ?> + + "; + foreach(array_keys($keggPathwayAttributes) as $attr) { + if ($attr === "PathwayID") + echo ""; else echo ""; } echo ""; } + foreach($mcPathwayRows as $row) { + echo ""; + echo ""; + echo ""; + echo ""; + echo ""; + echo ""; + echo ""; + echo ""; + } ?>
Pathway type ".$row[$attr]."".$row[$attr]."".$attr."
KEGG".$row[$attr]." ".$row[$attr]."
MitoCarta3.0".$row["PathwayProteinInteractionID"]."".$row["UniProtAccession"]."".$row["Pathway"]."
@@ -317,7 +411,7 @@ function get_SourceID_links($text){ ?>
-

Disease associated mutations

+

Disease-associated mutations


-

Expression

+

Disease-associated expression variation