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<!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1"> <title> GOnet </title> <link rel="icon" href="/gonet/static/figs/favicon-64.png" sizes="64x64"> <link rel="stylesheet" href="/gonet/static/css/main.css"> <link rel="stylesheet" href="/gonet/static/css/bootstrap.min.css"> <link rel="stylesheet" href="/gonet/static/css/dice_tools_header.css"> <link rel="stylesheet" href="/gonet/static/css/submit.css"> <script type="text/html" id="bg-popover-content"> <p class="my-0">BHLHE40</p> <p class="my-0">CCDC75</p> <p class="my-0">ABCB1</p> <p class="my-0">CCL20</p> <a id="bg-popover-dismiss" class="my-1 float-right">dismiss</a> </script> <script type="text/html" id="bg-popover-title"> <p class="my-1">Plain text with one gene per line, e.g.</p> </script> </head> <body> <!-- <div class="container-fluid header"> --> <nav class="navbar header navbar-expand-sm"> <a class="navbar-brand" id="navbar-logo" href="https://tools.dice-database.org/"> <img src="/gonet/static/figs/tools_shrunk.svg" class="d-inline-block align-top" alt="" height="30"> Tools </a> <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarNavAltMarkup" aria-controls="navbarNavAltMarkup" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div class="collapse navbar-collapse" id="navbarNavAltMarkup"> <div class="navbar-nav navbar-right"> <a href="/GOnet/"> <img class="float-right mx-4" src="/gonet/static/figs/GOnet_logo.png" alt="GOnet-logo" height="50px" /> </a> <a href="https://dice-database.org" class="nav-item nav-link">DICEDB</a> <a href="/GOnet/doc/index" class="nav-item nav-link">Help</a> <a href="/GOnet/doc/contact" class="nav-item nav-link">Contact/Citation</a> </div> </div> </nav> <!-- </div> --> <div class="content"> <div class="container submitform"> <form id="input-form" name="formular" action="/GOnet/" method="post" enctype="multipart/form-data"> <input type="hidden" name="csrfmiddlewaretoken" value="uXXSudV2F8aI28TLjsqemnsMxw738fAUzTgJGMauf30ESo85ydIBJiXn5NrcWYSY"> <table class="table table-sm table-condensed table-bordered my-4"> <tr class="table-primary"> <th class="par_grp_sep"><div class="d-inline"><h2>Input parameters</h2></div></th> <td> <button type="button" id="samp_data_button">Insert example</button> <button type="button" id="reset-btn" >Reset</button> </td> </tr> <tr> <td>Species</td> <td id="organism"> <label for="id_organism_0"> Human <span class="radio"><input type="radio" name="organism" value="human" id="id_organism_0" required checked></span> </label> <label for="id_organism_1"> Mouse <span class="radio"><input type="radio" name="organism" value="mouse" id="id_organism_1" required></span> </label> </td> </tr> <tr> <td>Upload a CSV file</td> <td><input type="file" name="uploaded_file" id="id_uploaded_file"></td> </tr> <tr> <td> <p>Or paste data here</p> <p><a href="/GOnet/doc/input">Input format</a></p> </td> <td><textarea name="paste_data" cols="40" rows="10" id="id_paste_data"> </textarea></td></tr> <tr> <td>Job name (optional)</td> <td><input type="text" name="job_name" maxlength="40" id="id_job_name"></td> </tr> <tr> <td> <p class="my-1">Contrast value separator</p> <p class="my-1">(matters only if contrast value is supplied)</p> </td> <td><select name="csv_separator" id="id_csv_separator"> <option value=" ">{tab}</option> <option value=",">{,}</option> <option value="\s+">Any whitespace</option> </select></td> </tr> <tr class="table-primary"><th colspan="2" class="par_grp_sep">Job parameters</th></tr> <tr> <td>GO namespace</td><td><select name="namespace" id="id_namespace"> <option value="biological_process" selected>biological_process</option> <option value="molecular_function">molecular_function</option> <option value="cellular_component">cellular_component</option> </select></td> </tr> <tr> <td>Select analysis type </td><td> <div id="analysis_type" class="form-check form-check-inline"> <label class="form-check-label mx-1" for="id_analysis_type_0"> <span class="radio"><input type="radio" name="analysis_type" value="enrich" id="id_analysis_type_0" required checked></span> GO term enrichment </label> <label class="form-check-label mx-1" for="id_analysis_type_1"> <span class="radio"><input type="radio" name="analysis_type" value="annot" id="id_analysis_type_1" required></span> GO term annotation </label> </div> <a class="mx-3" href="/GOnet/doc/analysis_types">?</a> </td> </tr> </table> <div class="container-fluid"> <div class="row"> <div class="col" id="enrich_param"> <div class="text-primary">Enrichment analysis options</div> <table class="table table-sm table-condensed table-bordered"> <tr><td>q-value threshold</td><td><select name="qvalue" id="id_qvalue"> <option value="0.05">* (≤ 0.05)</option> <option value="0.01">** (≤ 0.01)</option> <option value="0.001">*** (≤ 0.001)</option> <option value="0.0001">**** (≤ 0.0001)</option> </select></td></tr> <tr><td>Background<a class="mx-3" href="/GOnet/doc/enrich_bg">?</a></td><td><select name="bg_type" id="id_bg_type"> <option value="all">all annotated genes</option> <option value="custom">custom gene list</option> <option value="predef">predefined backgrounds</option> </select></td></tr> <tr id="predef_bg_row"><td>All genes expressed in</td><td><select name="bg_cell" id="id_bg_cell"> <option value="DICE-any">Any DICE-DB celltype</option> <option value="DICE-Tcells">T-cells (any DICE-DB T-cells)</option> <option value="HPA-any">Any HPA celltype</option> <option value="DICE-Monocyte (classical)">(DICE-DB) Monocyte (classical)</option> <option value="DICE-Monocyte (non-classical)">(DICE-DB) Monocyte (non-classical)</option> <option value="DICE-B cell (naive)">(DICE-DB) B cell (naive)</option> <option value="DICE-NK">(DICE-DB) NK</option> <option value="DICE-Th1">(DICE-DB) Th1</option> <option value="DICE-Th2">(DICE-DB) Th2</option> <option value="DICE-Th17">(DICE-DB) Th17</option> <option value="DICE-Th1Th17">(DICE-DB) Th1Th17</option> <option value="DICE-Tfh">(DICE-DB) Tfh</option> <option value="DICE-Treg (naive)">(DICE-DB) Treg (naive)</option> <option value="DICE-Treg (memory)">(DICE-DB) Treg (memory)</option> <option value="DICE-CD4 T cell (naive)">(DICE-DB) CD4 T cell (naive)</option> <option value="DICE-CD4 T cell (stim)">(DICE-DB) CD4 T cell (stim)</option> <option value="DICE-CD8 T cell (naive)">(DICE-DB) CD8 T cell (naive)</option> <option value="DICE-CD8 T cell (stim)">(DICE-DB) CD8 T cell (stim)</option> <option value="HPA-adipose tissue">(HPA) adipose tissue</option> <option value="HPA-adrenal gland">(HPA) adrenal gland</option> <option value="HPA-bone marrow">(HPA) bone marrow</option> <option value="HPA-cerebral cortex">(HPA) cerebral cortex</option> <option value="HPA-colon">(HPA) colon</option> <option value="HPA-duodenum">(HPA) duodenum</option> <option value="HPA-endometrium">(HPA) endometrium</option> <option value="HPA-esophagus">(HPA) esophagus</option> <option value="HPA-fallopian tube">(HPA) fallopian tube</option> <option value="HPA-gall bladder">(HPA) gall bladder</option> <option value="HPA-heart">(HPA) heart</option> <option value="HPA-kidney">(HPA) kidney</option> <option value="HPA-liver">(HPA) liver</option> <option value="HPA-lung">(HPA) lung</option> <option value="HPA-lymph node">(HPA) lymph node</option> <option value="HPA-ovary">(HPA) ovary</option> <option value="HPA-pancreas">(HPA) pancreas</option> <option value="HPA-placenta">(HPA) placenta</option> <option value="HPA-prostate gland">(HPA) prostate gland</option> <option value="HPA-rectum">(HPA) rectum</option> <option value="HPA-saliva-secreting gland">(HPA) saliva-secreting gland</option> <option value="HPA-skeletal muscle tissue">(HPA) skeletal muscle tissue</option> <option value="HPA-small intestine">(HPA) small intestine</option> <option value="HPA-smooth muscle tissue">(HPA) smooth muscle tissue</option> <option value="HPA-spleen">(HPA) spleen</option> <option value="HPA-stomach">(HPA) stomach</option> <option value="HPA-testis">(HPA) testis</option> <option value="HPA-thyroid gland">(HPA) thyroid gland</option> <option value="HPA-tonsil">(HPA) tonsil</option> <option value="HPA-urinary bladder">(HPA) urinary bladder</option> <option value="HPA-vermiform appendix">(HPA) vermiform appendix</option> <option value="HPA-zone of skin">(HPA) zone of skin</option> <option value="Bgee-any">Any Bgee celltype</option> <option value="Bgee-adult mammalian kidney">(Bgee) adult mammalian kidney</option> <option value="Bgee-bone marrow">(Bgee) bone marrow</option> <option value="Bgee-bone marrow macrophage">(Bgee) bone marrow macrophage</option> <option value="Bgee-brown adipose tissue">(Bgee) brown adipose tissue</option> <option value="Bgee-cerebellum">(Bgee) cerebellum</option> <option value="Bgee-cerebral cortex">(Bgee) cerebral cortex</option> <option value="Bgee-embryonic stem cell">(Bgee) embryonic stem cell</option> <option value="Bgee-fibroblast">(Bgee) fibroblast</option> <option value="Bgee-heart">(Bgee) heart</option> <option value="Bgee-liver">(Bgee) liver</option> <option value="Bgee-lung">(Bgee) lung</option> <option value="Bgee-spleen">(Bgee) spleen</option> </select></td></tr> <tr id="custom_bg_row"> <td>List of background genes <a data-toggle="popover" id="popoverbutton"> (File format)</a></td> <td><input type="file" name="bg_file" id="id_bg_file"></td></tr> </table> </div> <div class="col" id="annot_param"> <div class="text-primary">Annotation analysis options</div> <table class="table table-sm table-condensed table-bordered"> <tr><td>GO subset</td><td><select name="slim" id="id_slim"> <option value="goslim_generic" selected>Generic GO slim</option> <option value="goslim_immunol">GO slim for immunology (experimental; process only)</option> <option value="custom">Custom GO terms</option> </select></td></tr> <tr id="custom_terms_row" style=""> <td> <div id="paste_left" class="my-0 custom-terms-expand"><p class="my-0">Paste custom GO terms</p> <p class="my-0">(one per line in the form GO:XXXXXX)</p></div> </td> <td><textarea name="custom_terms" cols="16" rows="10" id="id_custom_terms"> </textarea></td></tr> </table> </div> </div> </div> <table class="table table-sm table-condensed table-bordered my-4"> <tr class="table-primary"><th colspan="2" class="par_grp_sep">Output parameters</th></tr> <tr id="output_type"><td>Select output type</td><td><select name="output_type" id="id_output_type"> <option value="graph" selected>Interactive Graph</option> <option value="txt">Hierarchical TXT</option> <option value="csv">CSV</option> </select></td></tr> <tr> <td> <button class="btn btn-outline-primary" type="submit" name="submit">Submit</button> </td> <td> <span> <a class="mtop-3" href="/GOnet/doc/index">Help</a> </span> <span class="mx-4"> <a href="/GOnet/doc/contact">Contact/Citation</a> </span> </td> </tr> </table> </form> </div> <script src="/gonet/static/JavaScript/bundles/GOnet_submit_page.bundle.js" type="text/javascript"></script> </div> <div class="container"> <footer class="my-5 py-3 border-top"> <ul class="list-unstyled float-right"> <li class="text-muted">Ontology version: 2019-07-01</li> <li class="text-muted">Human annotation version: 2019-07-01</li> <li class="text-muted">Mouse annotation version: 2019-07-01</li> </ul> </footer> </div> </body> </html>