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{{Loading|loadingimage=sprites.gif}}{{#vardefine:geneids_content|{{#ask:[[Category:EntrezGene]][[tax_id::9606]][[tf?::true]]
|?GeneID
|?Symbol
|?Associated motif id
|?Description
|format=array
|headers=hide
|sort=Symbol
|order=DESC
|mainlabel=-
|sep=?
|propsep=/
|manysep=!
|recordsep=<RCRD>
|limit=10
}}
}}
{{#vardefine:db_content}}


{{#arraydefine:geneids_array|{{#var:geneids_content}}|?}}
Data sources used in FANTOM5 SSTAR


{{
  #loop: j
  | 0         
  | {{#arraysize:geneids_array}}
  | <nowiki/>
{{#vardefine:ID|{{#explode:{{#arrayindex:geneids_array|{{#var:j}}}}|/|0}}}}
{{#vardefine:Symbol|{{#explode:{{#arrayindex:geneids_array|{{#var:j}}}}|/|1}}}}
{{#vardefine:MotifId|{{#explode:{{#arrayindex:geneids_array|{{#var:j}}}}|/|2}}}}
{{#vardefine:Description|{{#explode:{{#arrayindex:geneids_array|{{#var:j}}}}|/|3}}}}
{{#vardefine:PeakCount|{{#ask: [[Category:FFCP]][[EntrezGene::{{#var:ID}}]]|format=count}}}}


{{#arraydefine: defined_array{{#var:j}} |{{#var:ID}}/{{#var:Symbol}}/{{#var:MotifId}}/{{#var:Description}}/{{#var:PeakCount}}}}
=== CAGE peaks ===
{{#vardefine:db_content|{{#arrayprint:defined_array{{#var:j}}}}?{{#var:db_content}}  }}
* CAGE peak location (with the robust threshold) , annotation, and expression
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/CAGE_peaks/hg19.cage_peak_phase1and2combined_tpm_ann.osc.txt.gz Human]</span>
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/CAGE_peaks/mm9.cage_peak_phase1and2combined_tpm_ann.osc.txt.gz Mouse]</span>
* Ontology-based sample term enrichment analysis
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/ Human]</span>
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/ Mouse]</span>


}}
=== Genes ===
==Human transcription factors==
* Transcription factors (curated list)
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/TF2CLUSTER_human_official.xls Human]</span>
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/TF2CLUSTER_mouse_official.xls Mouse]</span>


<html>
* Gene details (obtained from EntrezGene)
<script type="text/javascript" src="/5/sstar/rb_js/jquery-1.7.1.min.js"></script>
** <span class="plainlinks">[ftp://ftp.ncbi.nih.gov/gene/DATA/ Human and Mouse]</span>
<script type="text/javascript" src="/5/sstar/rb_js/html5button/datatables.min.js"></script>
<style type="text/css" title="currentStyle">
@import "/5/sstar/rb_js/html5button/datatables.css";


.ImageBorder
=== Coexpression module ===
{
* FFCP member list
    border:1px solid lightgrey;
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/SYNC015_combined_clustertables.txt Human]</span>
    width      : 90px;
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mouse_filtered2_p75_m22_T.clusters.txt Mouse]</span>
    height      : 20px;
* Sample ontology enrichment analysis
}
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/ human]</span>
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/ mouse]</span>
* GOStat results on Coexpression module
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19_co-expression_GOstats.tar.gz human]</span>
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9_co-expression_GOstats.tar.gz mouse]</span>
* Pathway enrichment analysis
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19_co-expression_modules.tar.gz human]</span>
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9_co-expression_modules.tar.gz mouse]</span>
* TFBS overrepresentation
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19.novel_motif.coexpression_clusters_overrepresentation.txt.gz human_novel_motif]</span>
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19.KNOWN_JASPAR_130.coexpression_clusters_overrepresentation.txt.gz human_jaspar_motif]</span>
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9.novel_motif.coexpression_clusters_overrepresentation.txt.gz mouse_novel_motif]</span>
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9.KNOWN_JASPAR_130.coexpression_clusters_overrepresentation.txt.gz  mouse_jaspar_motif]</span>
* <span class="plainlinks">[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/ENCODE_TF_ChIP-seq_peak_enrichment_coexprclusterencode.filtered.csv.gz ENCODE_TF_ChIP-seq_peak enrichment analysis]</span>
* Relative expression of the co-expression module
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/coexpression_DPI_cluster_scores_median_human_Aug3_2012.txt.gz human]</span>
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/coexpression_DPI_cluster_scores_median_mouse_Oct9_2012.txt.gz mouse]</span>


</style>
=== Motifs ===
<script type="text/javascript">
* Novel motifs GREAT analysis results
            var content = "";
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_GREAT_analysis_results/hg19.table.txt Human]</span>
            var m_data = {};
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_GREAT_analysis_results/mm9.table.txt Mouse]</span>
            m_data.content = [];
* Novel motifs Significance of the correlation with CAGE expression
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_Significance_of_the_correlation_with_CAGE_expression/hg19.pvalues.txt Human]</span>
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_Significance_of_the_correlation_with_CAGE_expression/mm9.pvalues.txt Mouse]</span>
* Jaspar motifs Significance of the correlation with CAGE expression
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/jaspar_Significance_of_the_correlation_with_CAGE_expression/hg19.pvalues.txt Human]</span>
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/jaspar_Significance_of_the_correlation_with_CAGE_expression/mm9.pvalues.txt Mouse]</span>


$(document).ready(function() {
=== Sample ===
                    content= "</html>{{#var:db_content}}<html>";
* sample name and attributes
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.6/basic/HumanSamples2.0.sdrf.xlsx Human]</span>
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.6/basic/MouseSamples2.3.sdrf.xlsx Mouse]</span>
* <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/ Transcription factors, relative expression]</span>
* <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/ HOMER motifs]</span>
* Repeat family, relative expression
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Repeat_expression/DPI_cluster_scores_human_median_by_repFamilies_Aug06_2012.txt.gz human]</span>
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Repeat_expression/DPI_cluster_scores_mouse_median_by_repFamilies_Aug06_2012.txt.gz mouse]</span>


                    var content_array = content.split("?");
=== Ontology ===
                    for(i=0;i<content_array.length-1;i++){
* <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Ontology/ Sample ontology(FF), Cell ontology(CL), Human disease ontology(DOID) and Uber anatomy ontology (UBERON)]</span>
                    var temp = content_array[i];
* <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Ontology/ Ontology mapping: FF sample <--> CL, DOID, UBERON, FF term]</span>
                    var temp_array =temp.split("/");
                    var mot_id="";
                        if(temp_array[2].length> 0){ mot_id=temp_array[2];}else{mot_id="NA";}
                   
                    m_data.content.push({EntrezGene:'<a href=/5/sstar/EntrezGene:'+temp_array[0]+'>'+temp_array[0]+'</a>',            Symbol:temp_array[1],MotifId:mot_id,Description:temp_array[3],PeakCount:temp_array[4]});
               
                }
$('#tf_table').DataTable( {
        dom: 'Blfrtip',
                processing: true,
                pageLength: 25,
        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
        lengthMenu: [[10, 25, 50, -1], [10, 25, 50, "All"]],
                scrollCollapse: true,
                autoWidth: false,
                jQueryUI: false,
                order: [[ 2, "asc" ]],
                data: m_data.content,
        columns: [
{ data: "EntrezGene", title: "EntrezGene"},
            { data: "Symbol", title: "Symbol"},
            { data: "MotifId", title: "Associated Motif",
              render: function ( data, type, row, meta ) {
var motid = data;
if (motid == "NA") {
    return_val = "NA";
} else {
    var splitted = motid.split("!");
    if (splitted != null) {
        if (splitted.length > 1) {
            var return_val = "";
            for (i = 0; i < splitted.length; i++) {
                if (splitted[i].toString().indexOf("JASPAR motif") >= 0) {
                    return_val = '<a href=\"/5/sstar/' + splitted[i] + '\"><img src=\"/5/sstar/seqlogo/jaspar/' + splitted[i].split(":")[1] + '.png"  class="ImageBorder"  alt="' + splitted[i] + '">' + '</a>' + return_val;
                } else if (splitted[i].toString().indexOf("Swissregulon") >= 0) {
                    /*return_val = '<a href=\"/5/sstar/'+ splitted[i] + '\"><img src=\"/5/sstar/seqlogo/' + replaceAll(splitted[i].split(":")[1]," ","_") + '.png"  class="ImageBorder"  alt="' + splitted[i] + '">' + '</a>' + return_val;*/
return_val = "";
                }
                else{
                    return_val = "";
                }
            }
        } else {
            if (splitted[0].toString().indexOf("JASPAR motif") >= 0) {
                return_val = '<a href=\"/5/sstar/' + splitted[0] + '\"><img src=\"/5/sstar/seqlogo/jaspar/' + splitted[0].split(":")[1] + '.png"  class="ImageBorder"  alt="' + splitted[0] + '">' + '</a>' ;
            } else if (splitted[0].toString().indexOf("Swissregulon") >= 0) {


              /* return_val = '<a href=\"/5/sstar/' + splitted[0] + '\"><img src=\"/5/sstar/seqlogo/' + replaceAll(splitted[0].split(":")[1]," ","_") + '.png"  class="ImageBorder"  alt="' + splitted[0] + '">' + '</a>' ;*/
=== CAGEd-oPOSSUM ===
return_val = "";
* <span class="plainlinks">[https://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM/results/precomputed/human/index.html Human]</span>
            }
* <span class="plainlinks">[https://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM/results/precomputed/mouse/index.html Mouse]</span>
            else{
                    return_val = "";
                }
        }
    } else {
        return_val = "NA";
    }
}
 
return return_val;
}
                                },
                                {data: "Description",title: "Description"},
                                {data: "PeakCount",title: "#of peaks"}
                                ]
} );
 
 
} );
 
function replaceAll(str, token, newtoken) {
    if(token!=newtoken)
    while(str.indexOf(token) > -1) {
        str = str.replace(token, newtoken);
    }
    return str;
}
</script>
<span id="export_tool"></span>
</html>
 
<table cellpadding="0" cellspacing="0" border="0" class="stripe cell-border order-column compact" id="tf_table"> 
</table>

Latest revision as of 20:55, 16 February 2022

Data sources used in FANTOM5 SSTAR


CAGE peaks

  • CAGE peak location (with the robust threshold) , annotation, and expression
  • Ontology-based sample term enrichment analysis

Genes

Coexpression module

Motifs

  • Novel motifs GREAT analysis results
  • Novel motifs Significance of the correlation with CAGE expression
  • Jaspar motifs Significance of the correlation with CAGE expression

Sample

Ontology

CAGEd-oPOSSUM

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