Template: Test area: Difference between revisions

Revision as of 15:22, 1 November 2024

Basic information about the TSS

TSS ID:	{{{tss_id}}}
Species:
Chr:

Start:
End:
Strand:

Source datasets

Protocol

TSS cluster detected^*

* The number of TSS cluster called data-sets (maximum 5)

cCREs annotation

Description:
Category:

* cCREs are candidates for cis regulatory elements generated from the subset of representative DNase hypersensitivity sites supported by either histone modifications or CTCF-binding data. Find more details here.

Gene and protein annotation

Transcript_name:
Distance:
GeneID:
HGNC/MGI_ID:
UniProt_ID:

Gene_name:
Gene_symbol:
Gene_synonyms:
Gene_source:

TATA-Box annotation

Distance to TSS:
Nearest PromoterID:
Entrez ID:
Nearest Unigene:
Nearest Refseq:
Nearest Ensembl:
Gene Name:
Gene Alias:
Gene Description:
Gene Type:
CpG%:
GC%:
TATA-Box(TBP)/Promoter/Homer Distance From Peak(sequence,strand,conservation):

@@ Line 1: / Line 1: @@
-{{Loading|loadingimage=sprites.gif}}<noinclude>[[Category:Sample pages]]</noinclude>
+{{DISPLAYTITLE:{{{tss_id}}}}}
 <html><style>
 	table {
@@ Line 17: / Line 17: @@
      text-align:left;
      width:60px;
+}
+.item_label_middle {
+    text-align:left;
+    width:120px;
 }
 .item_label_long {
      text-align:left;
-     width:200px;
+     width:270px;
+    word-wrap:break-word;
+}
+.item_label_long2 {
+    text-align:left;
+    width:350px;
      word-wrap:break-word;
 }
@@ Line 27: / Line 36: @@
      word-wrap:break-word;
 }
-</style></html>
+.rotate90 {
+  -webkit-transform: rotate(-90deg);
+  -moz-transform: rotate(-90deg);
+  -webkit-transform-origin: 6px 18px;
+  -moz-transform-origin: 6px 18px;
+  width:1px;
+  word-wrap: initial;
+  overflow-wrap: initial;
+  font-size: 0.9em;
+}
+.highlight { background-color: yellow }
+.captop caption {
+	caption-side: top;
+}
+.hm {
+	z-index: 110;
+	align: center;
+	position:relative;
+}
+.egf {
+	display:none;
+	height:100%;
+	position:absolute;
+	background-color:gray;
+	top:0;
+	left: 0;
+	z-index: 50;
+}
+.edt {
+	position:absolute;
+	align: left;
+	top:0;
+	left: 0;
+	display:block;
+	z-index: 100;
+}
+</style>
+</html>
 <span class="section_head">Basic information about the TSS</span>
-<hr width="370px" size="2" style="text-align:left;margin-left:0" noshade>
+<hr width="300px" size="2" style="text-align:left;margin-left:0" noshade>
-<table width="370px"><tr><td>
+<table style="table-layout:fixed;width:100%"><tr><td style="width:28%;">
-<div style="width:42%; float:left;">
+<table class="inner" >
+<tr><th scope="row" class="item_label_long">TSS ID:</th><td>{{{tss_id}}}</td></tr>
+{{#if:{{{tss_id_v3|}}}|<tr><th scope="row" class="item_label_long">TSS ID(Version3):</th><td>{{#arraymap:{{{tss_id_v3}}}|;|x|[[TSS:x|x]]|<br />}} }}
+<tr><th scope="row" class="item_label_long">Species:</th><td>{{{species|}}}</td></tr>
+<tr><th scope="row" class="item_label_long">Chr:</th><td>{{{chr|}}}</td></tr>
+</table></td><td style="width:4%;"></td><td style="width:68%;">
 <table class="inner" >
-<tr><th scope="row" class="item_label">TSS ID:</th><td>[[Tss id::{{{tss_id}}}]]</td></tr>
+<tr><th scope="row" class="item_label_middle">Start:</th><td>{{{start|}}}</td></tr>
-<tr><th scope="row" class="item_label">Species:</th><td>{{{species}}}</td></tr>
+<tr><th scope="row" class="item_label_middle">End:</th><td>{{{end|}}}</td></tr>
-<tr><th scope="row" class="item_label">Chr:</th><td>{{{chr}}}</td></tr>
+<tr><th scope="row" class="item_label_middle">Strand:</th><td>{{{strand|}}}</td></tr>
-<tr><th scope="row" class="item_label">TSS Classification:</th><td>{{{tss_classification}}}</td></tr>
 </table>
-</div>
+</td></tr>
-<div style="width:42%; float:right;margin-left:40px">
+<tr style='border-bottom-style: dotted;border-bottom-width: thin;vertical-align:top'><th >Source datasets</th><td colspan='2'>{{#wrapAtPipes: {{{source_datasets|}}} }}</td></tr>
-<table class="inner" >
+<tr style='border-bottom-style: dotted;border-bottom-width: thin;vertical-align:top'><th>Protocol</th><td colspan='2'>{{#wrapAtPipes: {{{methods|}}} }}</td></tr>
-<tr><th scope="row" class="item_label">Start:</th><td>{{{start}}}</td></tr>
+<tr style='border-bottom-style: dotted;border-bottom-width: thin;vertical-align:top'><th>TSS cluster detected<sup>*</sup></th><td colspan='2'>{{{tss_cluster_detected|}}}</td></tr>
-<tr><th scope="row" class="item_label">End:</th><td>{{{end}}}</td></tr>
+</table>
-<tr><th scope="row" class="item_label">Strand:</th><td>{{{strand}}}</td></tr>
+<p style='word-wrap: break-word;overflow-wrap: break-word;'><span style='font-size:0.7em;'>&nbsp;&nbsp;* The number of TSS cluster called data-sets (maximum {{#ifeq:{{{species|}}}|human|17|5}}) </span></p>
-<tr><th scope="row" class="item_label">TSS Score:</th><td>{{{strand}}}</td></tr>
+<!--
+<table class="inner" width="420px">
+<tr><th scope="row" class="item_label_long2">Start of the center position in the TSS region:</th><td>{{{start_of_center_position|}}}</td></tr>
+<tr><th scope="row" class="item_label_long2">End of the center position in the TSS region:</th><td>{{{end_of_center_position|}}}</td></tr>
 </table>
-</div></td></tr>
+-->
+<br/>
+<span class="section_head">cCREs annotation</span>
+<hr width="270px" size="2" style="text-align:left;margin-left:0" noshade>
+<table class="inner" style="width:560px">
+<tr><th scope="row" align="left">Description:</th><td>{{#ifeq:{{{ccre_description|}}}|N|-|{{#ccre_link:{{{ccre_description|}}}}}}}</td></tr>
+<tr><th scope="row" align="left">Category:</th><td>{{#ifeq:{{{ccre_category|}}}|N|-|{{{ccre_category|}}}}}</td></tr>
 </table>
+<p style='word-wrap: break-word;overflow-wrap: break-word;'><span style='font-size:0.7em;'>&nbsp;&nbsp;* cCREs are candidates for cis regulatory elements generated from the subset of representative DNase hypersensitivity sites supported by either histone modifications or CTCF-binding data. Find more details [https://screen.encodeproject.org/ here].</span></p>
 <br/>
 <br/>
 <span class="section_head">Gene and protein annotation</span>
 <hr width="270px" size="2" style="text-align:left;margin-left:0" noshade>
-<table border="0" ><tr><td>
+<table border="0" style="width:560px"><tr><td style="width:36%;">
-<div style="width:42%; float:left;">
 <table class="inner" >
-<tr><th scope="row" align="left">Transcript_name:</th><td>{{{transcript_name}}}</td></tr>
+<tr><th scope="row" align="left">Transcript_name:</th><td>{{{transcript_name|}}}</td></tr>
-<tr><th scope="row" align="left">Distance:</th><td>{{{distance}}}</td></tr>
+<tr><th scope="row" align="left">Distance:</th><td>{{{distance|}}}</td></tr>
-<tr><th scope="row" align="left">GeneID:</th><td>{{{gene_id}}}</td></tr>
+<tr><th scope="row" align="left">GeneID:</th><td>{{#if:{{{gene_id|}}}|[[EntrezGene:{{{gene_id|}}}|{{{gene_id}}}]]|}}</td></tr>
-<tr><th scope="row" align="left">HGNC/MGI_ID:</th><td>{{{hgnc_mgi_id}}}</td></tr>
+<tr><th scope="row" align="left">HGNC/MGI_ID:</th><td>{{{hgnc_mgi_id|}}}</td></tr>
-<tr><th scope="row" align="left">UniProt_ID:</th><td>{{{uniprot_id}}}</td></tr>
+<tr><th scope="row" align="left">UniProt_ID:</th><td>{{{uniprot_id|}}}</td></tr>
-</table></div>
+</table></td><td style="width:4%;"></td><td style="width:60%;">
-<div style="width:42%; float:right;">
 <table class="inner" >
-<tr><th scope="row" align="left">Gene_name:</th><td>{{{gene_name}}}</td></tr>
+<tr><th scope="row" align="left">Gene_name:</th><td>{{{gene_name|}}}</td></tr>
-<tr><th scope="row" align="left">Gene_symbol:</th><td>{{{gene_symbol}}}</td></tr>
+<tr><th scope="row" align="left">Gene_symbol:</th><td>{{{gene_symbol|}}}</td></tr>
-<tr><th scope="row" align="left">Gene_synonyms:</th><td>{{{gene_synonyms}}}</td></tr>
+<tr><th scope="row" align="left">Gene_synonyms:</th><td>{{{gene_synonyms|}}}</td></tr>
-<tr><th scope="row" align="left">Gene_source:</th><td>{{{gene_source}}}</td></tr>
+<tr><th scope="row" align="left">Gene_source:</th><td>{{{gene_source|}}}</td></tr>
-</table>
+</table></td></tr>
-</div></td></tr>
-</table>
-<br/>
-<br/>
-<span class="section_head">Transcript annotation</span>
-<hr width="200px" size="2" style="text-align:left;margin-left:0" noshade>
-<table class="inner" border="0" >
-<tr><th scope="row" align="left">Transcript_name:</th><td>{{{transcript_name}}}</td></tr>
-<tr><th scope="row" align="left">Distance:</th><td>{{{distance}}}</td></tr>
-<tr><th scope="row" align="left">Num_trans:</th><td>{{{num_trans}}}</td></tr>
-<tr><th scope="row" align="left">All_trans:</th><td>:{{{all_trans}}}</td></tr>
 </table>
 <br/>
@@ Line 85: / Line 132: @@
 <hr width="200px" size="2" style="text-align:left;margin-left:0" noshade>
 <table class="inner" style="width: 600px;table-layout:fixed;">
-<tr><th scope="row" class="item_label_long">Distance to TSS:</th><td class="ttb">{{{distance_to_tss}}}</td></tr>
+<tr><th scope="row" class="item_label_long">Distance to TSS:</th><td class="ttb">{{{distance_to_tss|}}}</td></tr>
-<tr><th scope="row" class="item_label_long">Nearest PromoterID:</th><td class="ttb">{{{nearest_promoter_id}}}</td></tr>
+<tr><th scope="row" class="item_label_long">Nearest PromoterID:</th><td class="ttb">{{{nearest_promoter_id|}}}</td></tr>
-<tr><th scope="row" class="item_label_long">Entrez ID:</th><td class="ttb">{{{entrez_id}}}</td></tr>
+<tr><th scope="row" class="item_label_long">Entrez ID:</th><td class="ttb">{{{entrez_id|}}}</td></tr>
-<tr><th scope="row" class="item_label_long">Nearest Unigene:</th><td class="ttb">{{{nearest_unigene}}}</td></tr>
+<tr><th scope="row" class="item_label_long">Nearest Unigene:</th><td class="ttb">{{{nearest_unigene|}}}</td></tr>
-<tr><th scope="row" class="item_label_long">Nearest Refseq:</th><td class="ttb">{{{nearest_refseq}}}</td></tr>
+<tr><th scope="row" class="item_label_long">Nearest Refseq:</th><td class="ttb">{{{nearest_refseq|}}}</td></tr>
-<tr><th scope="row" class="item_label_long">Nearest Ensembl:</th><td class="ttb">{{{nearest_ensembl}}}</td></tr>
+<tr><th scope="row" class="item_label_long">Nearest Ensembl:</th><td class="ttb">{{{nearest_ensembl|}}}</td></tr>
-<tr><th scope="row" class="item_label_long">Gene Name:</th><td class="ttb">{{{gene_name}}}</td></tr>
+<tr><th scope="row" class="item_label_long">Gene Name:</th><td class="ttb">{{{gene_name|}}}</td></tr>
-<tr><th scope="row" class="item_label_long">Gene Alias:</th><td class="ttb">{{{gene_alias}}}</td></tr>
+<tr><th scope="row" class="item_label_long">Gene Alias:</th><td class="ttb">{{{gene_alias|}}}</td></tr>
-<tr><th scope="row" class="item_label_long">Gene Description:</th><td class="ttb">{{{gene_description}}}</td></tr>
+<tr><th scope="row" class="item_label_long">Gene Description:</th><td class="ttb">{{{gene_description|}}}</td></tr>
-<tr><th scope="row" class="item_label_long">Gene Type:</th><td class="ttb">{{{gene_type}}}</td></tr>
+<tr><th scope="row" class="item_label_long">Gene Type:</th><td class="ttb">{{{gene_type|}}}</td></tr>
-<tr><th scope="row" class="item_label_long">CpG%:</th><td class="ttb">{{{cpg_percent}}}</td></tr>
+<tr><th scope="row" class="item_label_long">CpG%:</th><td class="ttb">{{{cpg_percent|}}}</td></tr>
-<tr><th scope="row" class="item_label_long">GC%:</th><td class="ttb">{{{gc_percent}}}</td></tr>
+<tr><th scope="row" class="item_label_long">GC%:</th><td class="ttb">{{{gc_percent|}}}</td></tr>
-<tr><th scope="row" class="item_label_long">TATA-Box(TBP)/Promoter/Homer Distance From TSS(sequence,strand,conservation):</th><td class="ttb">{{{tata_box}}}</td></tr>
+<tr><th scope="row" class="item_label_long">TATA-Box(TBP)/Promoter/Homer Distance From Peak(sequence,strand,conservation):</th><td class="ttb">{{{tata_box|}}}</td></tr>
 </table>
-[[Test area::{{{param1}}}e{{{param2}}} m²|{{{param1}}} × 10<sup>{{{param2}}}</sup> m²]]
+<br>
+<br>
+{{#if:{{{gene_symbol|}}}|<span class="section_head">TSS expression</span><includeonly>{{#gene_exptable:{{{species|}}}|{{{gene_symbol}}} }}</includeonly>| }}