add clique page with go information

bzhanglab · Feb 15, 2024 · b8fdaae · b8fdaae
1 parent d28f67c
commit b8fdaae
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diff --git a/clique/index.html b/clique/index.html
@@ -1,91 +1,106 @@
 <!doctype html>
 <html>
-    <head>
-        <meta charset="utf-8" />
-        <title>FunMap Clique Viewer</title>
-        <script src="../assets/js/echarts.min.js"></script>
-        <script src="../assets/js/min/dag.min.js"></script>
-        <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-        <link
-            rel="stylesheet"
-            type="text/css"
-            href="../assets/css/funmap.css"
-        />
-        <link rel="stylesheet" type="text/css" href="../docs/gd.min.css" />
-        <style>
-            body {
-                overflow-x: hidden;
-                font-family: "Segoe UI", Roboto, Oxygen-Sans, Ubuntu, Cantarell,
-                    "Helvetica Neue", sans-serif;
-            }
 
-            h1 {
-                text-align: center;
-            }
+<head>
+    <meta charset="utf-8" />
+    <title>FunMap Clique Viewer</title>
+    <script src="../assets/js/echarts.min.js"></script>
+    <script src="../assets/js/min/dag.min.js"></script>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <link rel="stylesheet" type="text/css" href="../assets/css/funmap.css" />
+    <link rel="stylesheet" type="text/css" href="../docs/gd.min.css" />
+    <style>
+        html {
+            background: none;
+        }
 
-            .container {
-                width: 100%;
-                display: flex;
-                flex-direction: row;
-                flex-wrap: wrap;
-                justify-content: center;
-                -webkit-box-sizing: border-box;
-                -moz-box-sizing: border-box;
-                box-sizing: border-box;
-            }
+        body {
+            overflow-x: hidden;
+        }
 
-            button {
-                display: inline-block;
-                font-size: 1.1875rem;
-                line-height: var(--leading);
-                font-family: var(--font);
-                -webkit-font-smoothing: antialiased;
-                -moz-osx-font-smoothing: grayscale;
-                font-weight: 400;
-                box-sizing: border-box;
-                width: fit-content;
-                height: 2.5rem;
-                margin-top: 0;
-                padding: 5px;
-                border: 2px solid var(--color-body);
-                border-radius: 0;
-                appearance: none;
-                box-shadow: none;
-                height: 2.5em;
-            }
+        h1 {
+            text-align: center;
+        }
 
-            .text {
-                height: 2.5em;
-                width: 50%;
-            }
+        .container {
+            width: 100%;
+            display: flex;
+            flex-direction: row;
+            flex-wrap: wrap;
+            justify-content: center;
+            -webkit-box-sizing: border-box;
+            -moz-box-sizing: border-box;
+            box-sizing: border-box;
+        }
 
-            #filler {
-                display: flex;
-                flex-direction: column;
-                /* justify-content: center; */
-                align-items: center;
-            }
-        </style>
-    </head>
+        button {
+            display: inline-block;
+            font-size: 1.1875rem;
+            line-height: var(--leading);
+            font-family: var(--font);
+            -webkit-font-smoothing: antialiased;
+            -moz-osx-font-smoothing: grayscale;
+            font-weight: 400;
+            box-sizing: border-box;
+            width: fit-content;
+            height: 2.5rem;
+            margin-top: 0;
+            padding: 5px;
+            border: 2px solid var(--color-body);
+            border-radius: 0;
+            appearance: none;
+            box-shadow: none;
+            height: 2.5em;
+        }
+
+        .text {
+            height: 2.5em;
+            width: 50%;
+        }
 
-    <body>
-        <div id="filler" style="height: 100%">
-            <h1>FunMap Clique Search</h1>
-            <div class="centering">
-                <h3 style="text-align: center">Clique ID</h3>
-                <div class="container">
-                    <input
-                        type="text"
-                        class="text"
-                        id="clique_id"
-                        name="clique_id"
-                        value="Clique ID: 160"
-                    />
-                    <button id="search_button">Search</button>
+        #filler {
+            display: flex;
+            flex-direction: column;
+            /* justify-content: center; */
+            align-items: center;
+        }
+    </style>
+</head>
+
+<body>
+    <div id="filler" style="height: 100%">
+        <h1>FunMap Clique Search</h1>
+        <div class="centering">
+            <small style="color: var(--color-body-light)">Fully connected subnetworks with limited overlap to other cliques identified with the clique enumeration (ICE) algorithm</small>
+            <h3 style="text-align: center">Clique ID</h3>
+            <div class="container">
+                <input type="text" class="text" id="clique_id" name="clique_id" value="Clique ID: 160" />
+                <button id="search_button">Search</button>
+            </div>
+        </div>
+        <h4 id="clique_title">Clique: </h4>
+        <div style="display: flex; align-content: center; vertical-align: center; width: 70%; height: 50%;">
+            <div style="width:60%; padding-right: 5%;">
+                <h5 style="margin-bottom: 0pt">GO Enrichment</h5>
+                <small style="color: var(--color-body-light)">Highest enriched GO terms for clique using
+                    over-representation analysis</small>
+                <table style="margin-top: 1em;">
+                    <thead>
+                        <tr>
+                            <th>GO Category</th>
+                            <th>Go ID</th>
+                            <th>Go Term</th>
+                            <th>FDR</th>
+                        </tr>
+                    </thead>
+                    <tbody id="table_body"></tbody>
+                </table>
+                <h5 style="margin-bottom: 0pt">Clique Members</h5>
+                <div id="members">
                 </div>
+                <button id="download_button">Download Clique</button>
             </div>
-
-            <div style="display: flexbox; align-content: center; vertical-align: center; width: 30%; height: 50%;">
+            <div style="flex-grow:1;">
                 <div id="dag" style="width: 100%; height: 100%; border: 1px solid black"></div>
                 <p style="color: var(--color-body-light); font-size: var(--unit); text-align: center">
                     Scroll to zoom, click and drag to move nodes.
@@ -103,6 +118,56 @@ <h3 style="text-align: center">Clique ID</h3>
                     (ignore_size = true),
                     (host = "../"),
                 );
+                dag_chart.then((chart) => {
+                    let member_data = chart.getOption().series[0].nodes;
+                    let member_list = document.getElementById("members");
+                    let member_text = "<p>";
+                    for (let i = 0; i < member_data.length; i++) {
+                        let member = member_data[i];
+                        member_text += member.name;
+                        if (i != member_data.length - 1) {
+                            member_text += ", ";
+                        }
+                    }
+                    member_text += "</p>";
+                    member_list.innerHTML = member_text;
+                });
+                fetch(`../data/go/clique/${clique_id}.json`)
+                    .then((res) => res.json())
+                    .then((data) => {
+                        let table_body = document.getElementById("table_body");
+                        document.getElementById("clique_title").innerHTML = `Clique ID: ${clique_id}`;
+                        table_body.innerHTML = "";
+                        let categories = ["gobp", "gomf", "gocc"];
+                        let category_name = {
+                            gobp: "Biological Process",
+                            gomf: "Molecular Function",
+                            gocc: "Cellular Component",
+                        };
+                        for (let i = 0; i < categories.length; i++) {
+                            let go_cat = categories[i];
+                            let row = document.createElement("tr");
+                            let go_category = document.createElement("td");
+                            let go_id = document.createElement("td");
+                            let go_term = document.createElement("td");
+                            let fdr = document.createElement("td");
+                            go_category.innerHTML = category_name[go_cat];
+                            let go_id_text = data[go_cat].set;
+                            go_id.innerHTML = `<a href="https://amigo.geneontology.org/amigo/term/${go_id_text}" target="_blank">${go_id_text}</a>`;
+                            go_term.innerHTML = data[go_cat].set_name;
+                            let fdr_val = parseFloat(data[go_cat].fdr);
+                            fdr.innerHTML = fdr_val != 0.0 ? fdr_val.toExponential(5) : "< 2.2e-16";
+                            row.appendChild(go_category);
+                            row.appendChild(go_id);
+                            row.appendChild(go_term);
+                            row.appendChild(fdr);
+                            table_body.appendChild(row);
+                        }
+                    });
+                let download_button = document.getElementById("download_button");
+                download_button.onclick = function () {
+                    window.open(`../data/dag/dense_modules/${clique_id}.json`, "_blank");
+                };
             }
             let button = document.getElementById("search_button");
             button.addEventListener("click", function () {
@@ -128,5 +193,6 @@ <h3 style="text-align: center">Clique ID</h3>
             };
             document.getElementById("clique_id").focus();
         </script>
-    </body>
-</html>
+</body>
+
+</html>
diff --git a/data/go/clique/C1.json b/data/go/clique/C1.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0003735", "set_name": "structural constituent of ribosome", "fdr": "0"}, "gobp": {"set": "GO:0022411", "set_name": "cellular component disassembly", "fdr": "0"}, "gocc": {"set": "GO:0005759", "set_name": "mitochondrial matrix", "fdr": "0"}}
diff --git a/data/go/clique/C10.json b/data/go/clique/C10.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0005201", "set_name": "extracellular matrix structural constituent", "fdr": "0"}, "gobp": {"set": "GO:0030198", "set_name": "extracellular matrix organization", "fdr": "0"}, "gocc": {"set": "GO:0031012", "set_name": "extracellular matrix", "fdr": "0"}}
diff --git a/data/go/clique/C100.json b/data/go/clique/C100.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0017160", "set_name": "Ral GTPase binding", "fdr": "2.72E-08"}, "gobp": {"set": "GO:0006893", "set_name": "Golgi to plasma membrane transport", "fdr": "1.11E-06"}, "gocc": {"set": "GO:0099023", "set_name": "tethering complex", "fdr": "0"}}
diff --git a/data/go/clique/C101.json b/data/go/clique/C101.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0019784", "set_name": "NEDD8-specific protease activity", "fdr": "0.003801071"}, "gobp": {"set": "GO:0000715", "set_name": "nucleotide-excision repair, DNA damage recognition", "fdr": "0"}, "gocc": {"set": "GO:0008180", "set_name": "COP9 signalosome", "fdr": "0"}}
diff --git a/data/go/clique/C102.json b/data/go/clique/C102.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0015399", "set_name": "primary active transmembrane transporter activity", "fdr": "0"}, "gobp": {"set": "GO:1902600", "set_name": "proton transmembrane transport", "fdr": "0"}, "gocc": {"set": "GO:0016469", "set_name": "proton-transporting two-sector ATPase complex", "fdr": "0"}}
diff --git a/data/go/clique/C103.json b/data/go/clique/C103.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0008353", "set_name": "RNA polymerase II CTD heptapeptide repeat kinase activity", "fdr": "0"}, "gobp": {"set": "GO:0006294", "set_name": "nucleotide-excision repair, preincision complex assembly", "fdr": "0"}, "gocc": {"set": "GO:0000428", "set_name": "DNA-directed RNA polymerase complex", "fdr": "0"}}
diff --git a/data/go/clique/C104.json b/data/go/clique/C104.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0003774", "set_name": "motor activity", "fdr": "0.674182183"}, "gobp": {"set": "GO:0002495", "set_name": "antigen processing and presentation of peptide antigen via MHC class II", "fdr": "0"}, "gocc": {"set": "GO:0005869", "set_name": "dynactin complex", "fdr": "0"}}
diff --git a/data/go/clique/C105.json b/data/go/clique/C105.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0003730", "set_name": "mRNA 3'-UTR binding", "fdr": "0.927504586"}, "gobp": {"set": "GO:0043488", "set_name": "regulation of mRNA stability", "fdr": "0.176967924"}, "gocc": {"set": "GO:0036464", "set_name": "cytoplasmic ribonucleoprotein granule", "fdr": "0.054725193"}}
diff --git a/data/go/clique/C106.json b/data/go/clique/C106.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0038023", "set_name": "signaling receptor activity", "fdr": "0.016993639"}, "gobp": {"set": "GO:0050852", "set_name": "T cell receptor signaling pathway", "fdr": "1.60E-05"}, "gocc": {"set": "GO:0009897", "set_name": "external side of plasma membrane", "fdr": "3.76E-06"}}
diff --git a/data/go/clique/C107.json b/data/go/clique/C107.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0005201", "set_name": "extracellular matrix structural constituent", "fdr": "0"}, "gobp": {"set": "GO:0030199", "set_name": "collagen fibril organization", "fdr": "7.74E-11"}, "gocc": {"set": "GO:0031012", "set_name": "extracellular matrix", "fdr": "0"}}
diff --git a/data/go/clique/C108.json b/data/go/clique/C108.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0015078", "set_name": "proton transmembrane transporter activity", "fdr": "9.05E-07"}, "gobp": {"set": "GO:0007007", "set_name": "inner mitochondrial membrane organization", "fdr": "0"}, "gocc": {"set": "GO:0044455", "set_name": "mitochondrial membrane part", "fdr": "0"}}
diff --git a/data/go/clique/C109.json b/data/go/clique/C109.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0005201", "set_name": "extracellular matrix structural constituent", "fdr": "1.66E-10"}, "gobp": {"set": "GO:0030198", "set_name": "extracellular matrix organization", "fdr": "0.468506698"}, "gocc": {"set": "GO:0062023", "set_name": "collagen-containing extracellular matrix", "fdr": "3.07E-07"}}
diff --git a/data/go/clique/C11.json b/data/go/clique/C11.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0038023", "set_name": "signaling receptor activity", "fdr": "0.044336303"}, "gobp": {"set": "GO:0006909", "set_name": "phagocytosis", "fdr": "1.34E-10"}, "gocc": {"set": "GO:0070821", "set_name": "tertiary granule membrane", "fdr": "2.97E-07"}}
diff --git a/data/go/clique/C110.json b/data/go/clique/C110.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0004866", "set_name": "endopeptidase inhibitor activity", "fdr": "0.005835945"}, "gobp": {"set": "GO:0002526", "set_name": "acute inflammatory response", "fdr": "1.43E-08"}, "gocc": {"set": "GO:0072562", "set_name": "blood microparticle", "fdr": "1.68E-12"}}
diff --git a/data/go/clique/C111.json b/data/go/clique/C111.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0003779", "set_name": "actin binding", "fdr": "3.47E-04"}, "gobp": {"set": "GO:0007229", "set_name": "integrin-mediated signaling pathway", "fdr": "0.039889029"}, "gocc": {"set": "GO:0005925", "set_name": "focal adhesion", "fdr": "1.07E-10"}}
diff --git a/data/go/clique/C112.json b/data/go/clique/C112.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0042800", "set_name": "histone methyltransferase activity (H3-K4 specific)", "fdr": "0.107134787"}, "gobp": {"set": "GO:0051568", "set_name": "histone H3-K4 methylation", "fdr": "0.040252949"}, "gocc": {"set": "GO:0035097", "set_name": "histone methyltransferase complex", "fdr": "1.19E-04"}}
diff --git a/data/go/clique/C113.json b/data/go/clique/C113.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0038023", "set_name": "signaling receptor activity", "fdr": "0.058076613"}, "gobp": {"set": "GO:0006954", "set_name": "inflammatory response", "fdr": "0.285539239"}, "gocc": {"set": "GO:0043196", "set_name": "varicosity", "fdr": "1"}}
diff --git a/data/go/clique/C114.json b/data/go/clique/C114.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0042809", "set_name": "vitamin D receptor binding", "fdr": "6.79E-09"}, "gobp": {"set": "GO:0006367", "set_name": "transcription initiation from RNA polymerase II promoter", "fdr": "1.36E-06"}, "gocc": {"set": "GO:0016592", "set_name": "mediator complex", "fdr": "2.43E-07"}}
diff --git a/data/go/clique/C115.json b/data/go/clique/C115.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0035614", "set_name": "snRNA stem-loop binding", "fdr": "1"}, "gobp": {"set": "GO:0043967", "set_name": "histone H4 acetylation", "fdr": "0.002368776"}, "gocc": {"set": "GO:1902562", "set_name": "H4 histone acetyltransferase complex", "fdr": "4.86E-05"}}
diff --git a/data/go/clique/C116.json b/data/go/clique/C116.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0005200", "set_name": "structural constituent of cytoskeleton", "fdr": "0.052032702"}, "gobp": {"set": "GO:0042168", "set_name": "heme metabolic process", "fdr": "1"}, "gocc": {"set": "GO:0014731", "set_name": "spectrin-associated cytoskeleton", "fdr": "2.31E-05"}}
diff --git a/data/go/clique/C117.json b/data/go/clique/C117.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0016853", "set_name": "isomerase activity", "fdr": "1"}, "gobp": {"set": "GO:0006465", "set_name": "signal peptide processing", "fdr": "0.325931797"}, "gocc": {"set": "GO:0005787", "set_name": "signal peptidase complex", "fdr": "0.009309232"}}
diff --git a/data/go/clique/C118.json b/data/go/clique/C118.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0017069", "set_name": "snRNA binding", "fdr": "0.942672884"}, "gobp": {"set": "GO:0008380", "set_name": "RNA splicing", "fdr": "0.07317738"}, "gocc": {"set": "GO:0044454", "set_name": "nuclear chromosome part", "fdr": "0.058582579"}}
diff --git a/data/go/clique/C119.json b/data/go/clique/C119.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0008320", "set_name": "protein transmembrane transporter activity", "fdr": "2.17E-04"}, "gobp": {"set": "GO:0006839", "set_name": "mitochondrial transport", "fdr": "5.14E-06"}, "gocc": {"set": "GO:0098798", "set_name": "mitochondrial protein complex", "fdr": "5.22E-06"}}
diff --git a/data/go/clique/C12.json b/data/go/clique/C12.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0017069", "set_name": "snRNA binding", "fdr": "0.00226308"}, "gobp": {"set": "GO:0006397", "set_name": "mRNA processing", "fdr": "0"}, "gocc": {"set": "GO:0016607", "set_name": "nuclear speck", "fdr": "0"}}
diff --git a/data/go/clique/C120.json b/data/go/clique/C120.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0031996", "set_name": "thioesterase binding", "fdr": "1"}, "gobp": {"set": "GO:0051225", "set_name": "spindle assembly", "fdr": "0"}, "gocc": {"set": "GO:0070652", "set_name": "HAUS complex", "fdr": "0"}}
diff --git a/data/go/clique/C121.json b/data/go/clique/C121.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0048037", "set_name": "cofactor binding", "fdr": "0.093579333"}, "gobp": {"set": "GO:0016054", "set_name": "organic acid catabolic process", "fdr": "0.023436906"}, "gocc": {"set": "GO:0005759", "set_name": "mitochondrial matrix", "fdr": "3.53E-05"}}
diff --git a/data/go/clique/C122.json b/data/go/clique/C122.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0022857", "set_name": "transmembrane transporter activity", "fdr": "0.155826849"}, "gobp": {"set": "GO:0007005", "set_name": "mitochondrion organization", "fdr": "0.0325369"}, "gocc": {"set": "GO:0005743", "set_name": "mitochondrial inner membrane", "fdr": "1.02E-07"}}
diff --git a/data/go/clique/C123.json b/data/go/clique/C123.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0003684", "set_name": "damaged DNA binding", "fdr": "0.011290735"}, "gobp": {"set": "GO:0042276", "set_name": "error-prone translesion synthesis", "fdr": "5.37E-04"}, "gocc": {"set": "GO:0005662", "set_name": "DNA replication factor A complex", "fdr": "1.60E-04"}}
diff --git a/data/go/clique/C124.json b/data/go/clique/C124.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0000149", "set_name": "SNARE binding", "fdr": "0.445166081"}, "gobp": {"set": "GO:0099518", "set_name": "vesicle cytoskeletal trafficking", "fdr": "0"}, "gocc": {"set": "GO:1904115", "set_name": "axon cytoplasm", "fdr": "0"}}
diff --git a/data/go/clique/C125.json b/data/go/clique/C125.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0017112", "set_name": "Rab guanyl-nucleotide exchange factor activity", "fdr": "0"}, "gobp": {"set": "GO:0006888", "set_name": "ER to Golgi vesicle-mediated transport", "fdr": "2.90E-07"}, "gocc": {"set": "GO:0030008", "set_name": "TRAPP complex", "fdr": "0"}}
diff --git a/data/go/clique/C126.json b/data/go/clique/C126.json
@@ -0,0 +1 @@
+{"gomf": {"set": "GO:0031491", "set_name": "nucleosome binding", "fdr": "1"}, "gobp": {"set": "GO:0070828", "set_name": "heterochromatin organization", "fdr": "1"}, "gocc": {"set": "GO:0000786", "set_name": "nucleosome", "fdr": "1"}}