Test: Difference between revisions

Revision as of 15:00, 18 June 2021

Q1. Is there dataset of transcription start sites collected with only noncording RNA regions?

A1. Currently, there are no data that collects only the transcription start sites of non-coding RNAs. It is possible to extract noncording RNAs by concatenating the GENCODE annotation file and the following files:
http://reftss.clst.riken.jp/datafiles/3.0/human/refTSS_v3.0_human_annotation.txt.gz
http://reftss.clst.riken.jp/datafiles/3.0/mouse/refTSS_v3.0_mouse_annotation.txt.gz

Q2. Why the range of some TSSs are so much greater than others? For most TSSs the range is in the region of 8-24 bp, while for others the range is over 100 bp.

A2. The range of TSSs is in the region of 8-24 bp, while for others the range can be over 100 bp. We computationally identify TSS regions based on the mapping results with 5'-end sequences.

@@ Line 1: / Line 1: @@
-{{#vardefine:param_tssid | {{#urlget:id|}} }}
+<html>
-{{#ask:[[tss_id::{{#var:param_tssid}}]]
+<style>
-|?distance_to_tss
+/* メニュー全体 */
-|?nearest_promoter_id
+.menu {
-|?entrez_id
+  width: 100%;
-|?nearest_unigene
+}
-|?nearest_refseq
-|?nearest_ensembl
+/* チェックボックスは非表示にする（内部的な Off/On の機能だけ利用する） */
-|?gene_name
+.menu input {
-|?gene_alias
+    display: none;
-|?gene_description
+}
-|?gene_type
-|?cpg_percent
+/* 開いた状態のサブメニュー */
-|?gc_percent
+.menu input:checked + ul {
-|?tata_box
+    display: block;
-|format=template
+}
-|template=TATA-Box_annotation
-|template arguments=named
+/* 閉じた状態のサブメニュー */
-|named args=yes
+.menu ul {
-}}
+    display: none;
+    /* 下記は開閉によらず共通の設定 */
+    background: #fff;
+    list-style: none;
+    margin: 0;
+    padding: 1rem;
+}
+/* 親項目の装飾 */
+.menu label {
+    display: block;
+    margin: 0;
+    padding: 0.5rem;
+    background: #fff;
+    cursor: pointer;
+}
+.menu label:hover {
+    color: blue;
+}
+</style>
+<div class="menu">
+  <label for="item1">Q1. Is there dataset of transcription start sites collected with only noncording RNA regions?</label>
+  <input type="checkbox" id="item1">
+  <ul>
+    <li>A1. Currently, there are no data that collects only the transcription start sites of non-coding RNAs. It is possible to extract noncording RNAs by concatenating the GENCODE annotation file and the following files:<br>
+<a href="http://reftss.clst.riken.jp/datafiles/3.0/human/refTSS_v3.0_human_annotation.txt.gz">http://reftss.clst.riken.jp/datafiles/3.0/human/refTSS_v3.0_human_annotation.txt.gz</a><br>
+<a href="http://reftss.clst.riken.jp/datafiles/3.0/mouse/refTSS_v3.0_mouse_annotation.txt.gz">http://reftss.clst.riken.jp/datafiles/3.0/mouse/refTSS_v3.0_mouse_annotation.txt.gz</a>
+</li>
+  </ul>
+  <label for="item2">Q2. Why the range of some TSSs are so much greater than others? For most TSSs the range is in the region of 8-24 bp, while for others the range is over 100 bp.</label>
+  <input type="checkbox" id="item2">
+  <ul>
+    <li>A2. The range of TSSs is in the region of 8-24 bp, while for others the range can be over 100 bp. We computationally identify TSS regions based on the mapping results with 5'-end sequences.</li>
+  </ul>
+</div>
+</html>