Distributed Annotation System (DAS)
Introduction
Distributed Annotation System (DAS) is simple data accessing protocol for annotations on biological sequences. DAS is based on the robust server-client concept, of which the user determines the preferred client-side software while still able to utilize server-side data provided by multiple providers. More information on DAS can be found on the DAS homepage
We are providing a list of DAS compatible data on the G-Quadruplexes predicted using the Quadparser. The data is presented in the standard BED format, providing the location details for all the G-Quadruplex predicted. A simple example/tutorial on how to use these DAS data, is provided at the bottom of this page
Data
Below is a list of currently available DAS data. The left hand column provides the description and a direct link to the individual data, which you may use to retrive the data URL (e.g. right-click and choose 'Copy link location'), and then paste it to your preferred DAS client. Alternatively, the full URL for the data is also presented as plain text, which you may copy and paste it into the DAS client.
Human (Homo sapiens) Build 36
| Chromosome All | - http://www.quadruplex.org/das/homo_sapiens/36/All_b36_PQS.bed |
| Chromosome 1 | - http://www.quadruplex.org/das/homo_sapiens/36/1_b36_PQS.bed |
| Chromosome 2 | - http://www.quadruplex.org/das/homo_sapiens/36/2_b36_PQS.bed |
| Chromosome 3 | - http://www.quadruplex.org/das/homo_sapiens/36/3_b36_PQS.bed |
| Chromosome 4 | - http://www.quadruplex.org/das/homo_sapiens/36/4_b36_PQS.bed |
| Chromosome 5 | - http://www.quadruplex.org/das/homo_sapiens/36/5_b36_PQS.bed |
| Chromosome 6 | - http://www.quadruplex.org/das/homo_sapiens/36/6_b36_PQS.bed |
| Chromosome 7 | - http://www.quadruplex.org/das/homo_sapiens/36/7_b36_PQS.bed |
| Chromosome 8 | - http://www.quadruplex.org/das/homo_sapiens/36/8_b36_PQS.bed |
| Chromosome 9 | - http://www.quadruplex.org/das/homo_sapiens/36/9_b36_PQS.bed |
| Chromosome 10 | - http://www.quadruplex.org/das/homo_sapiens/36/10_b36_PQS.bed |
| Chromosome 11 | - http://www.quadruplex.org/das/homo_sapiens/36/11_b36_PQS.bed |
| Chromosome 12 | - http://www.quadruplex.org/das/homo_sapiens/36/12_b36_PQS.bed |
| Chromosome 13 | - http://www.quadruplex.org/das/homo_sapiens/36/13_b36_PQS.bed |
| Chromosome 14 | - http://www.quadruplex.org/das/homo_sapiens/36/14_b36_PQS.bed |
| Chromosome 15 | - http://www.quadruplex.org/das/homo_sapiens/36/15_b36_PQS.bed |
| Chromosome 16 | - http://www.quadruplex.org/das/homo_sapiens/36/16_b36_PQS.bed |
| Chromosome 17 | - http://www.quadruplex.org/das/homo_sapiens/36/17_b36_PQS.bed |
| Chromosome 18 | - http://www.quadruplex.org/das/homo_sapiens/36/18_b36_PQS.bed |
| Chromosome 19 | - http://www.quadruplex.org/das/homo_sapiens/36/19_b36_PQS.bed |
| Chromosome 20 | - http://www.quadruplex.org/das/homo_sapiens/36/20_b36_PQS.bed |
| Chromosome 21 | - http://www.quadruplex.org/das/homo_sapiens/36/21_b36_PQS.bed |
| Chromosome 22 | - http://www.quadruplex.org/das/homo_sapiens/36/22_b36_PQS.bed |
| Chromosome X | - http://www.quadruplex.org/das/homo_sapiens/36/X_b36_PQS.bed |
| Chromosome Y | - http://www.quadruplex.org/das/homo_sapiens/36/Y_b36_PQS.bed |
Chimpanzee (Pan troglodytes) Build 2.1
| Chromosome All | - http://www.quadruplex.org/das/pan_troglodytes/2.1/All_b2.1_PQS.bed |
| Chromosome 1 | - http://www.quadruplex.org/das/pan_troglodytes/2.1/1_b2.1_PQS.bed |
| Chromosome 2a | - http://www.quadruplex.org/das/pan_troglodytes/2.1/2a_b2.1_PQS.bed |
| Chromosome 2b | - http://www.quadruplex.org/das/pan_troglodytes/2.1/2b_b2.1_PQS.bed |
| Chromosome 3 | - http://www.quadruplex.org/das/pan_troglodytes/2.1/3_b2.1_PQS.bed |
| Chromosome 4 | - http://www.quadruplex.org/das/pan_troglodytes/2.1/4_b2.1_PQS.bed |
| Chromosome 5 | - http://www.quadruplex.org/das/pan_troglodytes/2.1/5_b2.1_PQS.bed |
| Chromosome 6 | - http://www.quadruplex.org/das/pan_troglodytes/2.1/6_b2.1_PQS.bed |
| Chromosome 7 | - http://www.quadruplex.org/das/pan_troglodytes/2.1/7_b2.1_PQS.bed |
| Chromosome 8 | - http://www.quadruplex.org/das/pan_troglodytes/2.1/8_b2.1_PQS.bed |
| Chromosome 9 | - http://www.quadruplex.org/das/pan_troglodytes/2.1/9_b2.1_PQS.bed |
| Chromosome 10 | - http://www.quadruplex.org/das/pan_troglodytes/2.1/10_b2.1_PQS.bed |
| Chromosome 11 | - http://www.quadruplex.org/das/pan_troglodytes/2.1/11_b2.1_PQS.bed |
| Chromosome 12 | - http://www.quadruplex.org/das/pan_troglodytes/2.1/12_b2.1_PQS.bed |
| Chromosome 13 | - http://www.quadruplex.org/das/pan_troglodytes/2.1/13_b2.1_PQS.bed |
| Chromosome 14 | - http://www.quadruplex.org/das/pan_troglodytes/2.1/14_b2.1_PQS.bed |
| Chromosome 15 | - http://www.quadruplex.org/das/pan_troglodytes/2.1/15_b2.1_PQS.bed |
| Chromosome 16 | - http://www.quadruplex.org/das/pan_troglodytes/2.1/16_b2.1_PQS.bed |
| Chromosome 17 | - http://www.quadruplex.org/das/pan_troglodytes/2.1/17_b2.1_PQS.bed |
| Chromosome 18 | - http://www.quadruplex.org/das/pan_troglodytes/2.1/18_b2.1_PQS.bed |
| Chromosome 19 | - http://www.quadruplex.org/das/pan_troglodytes/2.1/19_b2.1_PQS.bed |
| Chromosome 20 | - http://www.quadruplex.org/das/pan_troglodytes/2.1/20_b2.1_PQS.bed |
| Chromosome 21 | - http://www.quadruplex.org/das/pan_troglodytes/2.1/21_b2.1_PQS.bed |
| Chromosome 22 | - http://www.quadruplex.org/das/pan_troglodytes/2.1/22_b2.1_PQS.bed |
| Chromosome X | - http://www.quadruplex.org/das/pan_troglodytes/2.1/X_b2.1_PQS.bed |
| Chromosome Y | - http://www.quadruplex.org/das/pan_troglodytes/2.1/Y_b2.1_PQS.bed |
Mouse (Mus musculus) Build 37
| Chromosome All | - http://www.quadruplex.org/das/mus_musculus/37/All_b37_PQS.bed |
| Chromosome 1 | - http://www.quadruplex.org/das/mus_musculus/37/1_b37_PQS.bed |
| Chromosome 2 | - http://www.quadruplex.org/das/mus_musculus/37/2_b37_PQS.bed |
| Chromosome 3 | - http://www.quadruplex.org/das/mus_musculus/37/3_b37_PQS.bed |
| Chromosome 4 | - http://www.quadruplex.org/das/mus_musculus/37/4_b37_PQS.bed |
| Chromosome 5 | - http://www.quadruplex.org/das/mus_musculus/37/5_b37_PQS.bed |
| Chromosome 6 | - http://www.quadruplex.org/das/mus_musculus/37/6_b37_PQS.bed |
| Chromosome 7 | - http://www.quadruplex.org/das/mus_musculus/37/7_b37_PQS.bed |
| Chromosome 8 | - http://www.quadruplex.org/das/mus_musculus/37/8_b37_PQS.bed |
| Chromosome 9 | - http://www.quadruplex.org/das/mus_musculus/37/9_b37_PQS.bed |
| Chromosome 10 | - http://www.quadruplex.org/das/mus_musculus/37/10_b37_PQS.bed |
| Chromosome 11 | - http://www.quadruplex.org/das/mus_musculus/37/11_b37_PQS.bed |
| Chromosome 12 | - http://www.quadruplex.org/das/mus_musculus/37/12_b37_PQS.bed |
| Chromosome 13 | - http://www.quadruplex.org/das/mus_musculus/37/13_b37_PQS.bed |
| Chromosome 14 | - http://www.quadruplex.org/das/mus_musculus/37/14_b37_PQS.bed |
| Chromosome 15 | - http://www.quadruplex.org/das/mus_musculus/37/15_b37_PQS.bed |
| Chromosome 16 | - http://www.quadruplex.org/das/mus_musculus/37/16_b37_PQS.bed |
| Chromosome 17 | - http://www.quadruplex.org/das/mus_musculus/37/17_b37_PQS.bed |
| Chromosome 18 | - http://www.quadruplex.org/das/mus_musculus/37/18_b37_PQS.bed |
| Chromosome 19 | - http://www.quadruplex.org/das/mus_musculus/37/19_b37_PQS.bed |
| Chromosome X | - http://www.quadruplex.org/das/mus_musculus/37/X_b37_PQS.bed |
| Chromosome Y | - http://www.quadruplex.org/das/mus_musculus/37/Y_b37_PQS.bed |
Example of usage (Tutorial)
The DAS data provided here can be used in various analyses. In this example/tutorial, we will demonstrate how the data can be used to visualize the G-Quadruplexes in the region of interest. In this example, we will use the Ensembl DAS enabled webpages as the DAS client. More information on the DAS in Ensembl is available here.
In this example/tutorial, we are interested in the proto-oncogene c-Kit and the G-Quadruplexes in the promoter. We start by locating the c-Kit gene in the Ensembl webpage. To do this, we go to Ensembl and type in 'c-kit' as our search term under the box 'Search Ensembl', and limit the search to human genes only by selecting 'Homo sapiens' in the drag down box, as shown in the figure below.
After clicking on the 'Go' button, a list of results is presented. We then go into the detail page of the c-Kit gene by clicking on the c-Kit link, presented in the result page as 'Ensembl protein_coding Gene: ENSG00000157404 (HGNC Symbol: KIT)'. From the c-Kit page, we want to then go to the contig-view/graphical-view page, which is capable of accepting DAS data. To do so, we click on the 'Graphical view' link found on the left navigational column, under the option 'View of Chromosome 4' (highlighted in the figure below). It may be noted that you are able to go to the same contig-view/graphic-view page by clicking on the Contig view option available next to the c-Kit link at the previous result page.
At the contig-view page, click on the 'DAS Sources' on top of the figure under the 'Detailed view' section.
This will reveal a drop down list of DAS sources available. In order to include the G-Quadruplex data provided here, select the option 'URL based data...' at the bottom of the drop down list. A pop-up window will then appear, allowing you to type in the URL of the DAS data. As the c-Kit is in Chromosome 4, we will copy and paste the URL below, for the G-Quadruplex Chromosome 4 DAS data.
http://www.quadruplex.org/das/homo_sapiens/36/4_b36_PQS.bed
After clicking on 'Add source' button, you should now see an extra line appears in the figure (under the 'Detailed view' section), with the description of 'Quadruplex' on the right, similar to the figure below.
The highlighted areas (vertical red lines) represent the regions, which the predicted G-quadruplexes are located. In this case, you can see that in the figure, there are 7 G-Quadruplexes predicted in the intron regions. However, we are interested in the G-Quadruplexes in the promoter region, which is not shown in the default contig-view window, for KIT. Hence, we click on the '< Window' button to shift the contig-view window towards the 5' direction to reveal the promoter region.
Now, we can see that there are two G-Quadruplexes predicted near the transcriptional start site. These two G-Quadruplexes are the two G-Quadruplexes reported in [ref1] and [ref2]. Note: Details (e.g. the sequence) on each of the G-Quadruplexes may be obtained by click it in the figure.
See it live on the Ensembl webpage here.
Website provided as a service to the quadruplex community by Han-Min Wong, Simon Rodgers and Julian Huppert, University of Cambridge.
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