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Analysis of genomic poly(A) sites
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  Interface for querying APA sites of a gene
 

"APAS search” feature is designed to search the interesting datasets in APASdb, and present APA information of a user’s genes of interest according to the searching tips. Keywords such as Gene ID, Gene name, Symbol and fuzzy description can be used for direct query. Clicking the button labeled “Example” yields an example keyword suited for searching the selected dataset.


Search using a ID (currently Ensembl or UCSC ID only), gene name, symbols or description variable in publications and databases. Examples: cxcl12a, cxcl, chemokine, also ENSDARG00000037116 (Ensembl id only for Danio.rerio), uc009dsc.2, uc003qht.2 (UCSC id only for Mus musculus and Homo sapiens).

http://mosas.sysu.edu.cn/utr/search_APAsdb.php.

 

More detailed description on the selected dataset can be unfolded and shown by clicking "+" icon in the "description" column of datasets list. Please refer the tips in the figure below.

 

 



  APA sites-contained genes in a dynamic table, resulting form a fuzzy query
 

Fuzzy keyword search may lead to a media page to list all the matched genes in a table, and facilitate the selective view of their corresponding APA information in a linked detail page, but searching using precise keywords, such as gene id and transcript id can give users quick access to the detail page to view more various types of information on APA sites and the related graphics.

 

Screen shot of the list of APA sites-contained genes matching the fuzzy keyword of “chemokine”. Each icon displayed in “APA sites” column of the result table links a detail page to show more corresponding APA sites information, and texts with URL links in other columns enable redirecting to other extensive resources, especially the texts in “locus” column guide user to the specified URLs to browse APA sites associated with genes in the popular genome browser (Gbrowse) in APASdb website. For interpretation of the example mentioned in this figure, the reader is asked to refer the URL address http://mosas.sysu.edu.cn/utr/search_APASdb.php?seqkeywords=chemokine.

 

Clicking "+" icon in the "APA sites" column of results list can quickly load the figure on APA sites location relative to their corresponding genome.

 


  The detailed results of APA sites from a precise keyword query
 

Searching using precise keywords, such as gene id, transcript id, and gene_name, can give users quick access to the detail page to view more various types of information on APA sites and the related graphics. The detailed page consists of a result panel with three tabs labeled “poly(A)-site map” ,“poly(A)-site used”and "heterogeneous cleavage-site selection" respectively.



 

Under "poly(A)-site map" tab

Under the “poly(A)-site map” tab, a summary of the queried gene and corresponding APA sites, the poly(A) signals, the positions of APA sites relative to the genome are listed. The alternatively polyadenylated poly(A) sites defined as mode poly(A) sites in SAPAS method were highlighted in dark red, also the heterogeneous cleavage sites around them were specially highlighted and underlined in light red, and the predicted poly(A) signal upstream each poly(A) site were highlighted in light green in 3’-UTR sequence if exist to facilitate manual checking. In particular, the APA sites, UTR region and exon-intron structure of transcript variants of the queried gene are graphically presented in a proper scale, which enables tracking them together with the corresponding genome.


Example is taken here, screen shot of the detail page with unfold “poly(A)-site map” tab to detail APA sites for cxcl12a, the chemokine (c-x-c motif) ligand 12a, from zebrafish. For interpretation of cxcl12a mentioned, the reader is asked to refer the URL address http://mosas.sysu.edu.cn/utr/search_APASdb.php?seqkeywords=cxcl12a.


Figure. Screen shot of the detail page with the unfolded “poly(A)-site map” tab to detail the APA sites for the chemokine (c-x-c motif) ligand 12a (cxcl12a) from zebrafish. The APA sites associated with genome, gene, transcript, and annotations are graphically presented. Also, a summary of the queried cxcl12a and corresponding APA sites, the poly(A) signals, the positions of APA sites were listed. Especially, all the detected alternatively polyadenylated bases clustered to a poly(A) site, and their upstream poly(A) signals if exist, are all highlighted in 3’-UTR sequence, containing the most-frequently used polyadenylated bases marked in dark red. For interpretation of cxcl12a mentioned here, the reader is asked to refer to the URL address http://mosas.sysu.edu.cn/utr/search_APASdb.php?method=quick&id=7202&seqkeywords=ENSDARG00000037116.



 

Under "poly(A)-site usage" tab

When the tab labelled “poly(A)-site usage” is clicked, another two matched graphics will be dynamically drawn. One is a bar chart indicating the usage quantification of different APA sites in various biological conditions defined in the searching dataset, and the other is a curve diagram created to show the expression pattern of queried gene represented by the sum of supporting reads of corresponding APA sites.


Example is used, screen shot of the detail page with unfold “poly(A)-site usage” tab to reveal dynamic usage of APA sites of cxcl12a during zebrafish embryonic development, and help analyzing the APA-site swithcing. The bar chart indicates the usage quantification of different APA sites of cxcl12a from 0 hours post fertilization (hpf) to 5 days post fertilization (dpf). Also, the curve diagram describes the expression-pattern of cxcl12a, represented by the sum of supporting reads of corresponding APA sites, from 0hpf to 5dpf.Y-axis, numbers of normalized reads. Reads, read number normalized to per million mapped read; pA, poly (A) sites. For interpretation of the example mentioned, the reader is asked to refer the URL address http://mosas.sysu.edu.cn/utr/search_APASdb.php?seqkeywords=cxcl12.


Figure. Screen shot of the detail page with the unfolded “polyA-site usage” tab to reveal the dynamic usage of APA sites and gene expression pattern of cxcl12a during zebrafish development. The bar chart indicates the usage quantification of different APA sites of cxcl12a from 0 hours post fertilization (hpf) to 5 days post fertilization (dpf), helping analyze the APA-site switching of cxcl12a involved in embryogenesis. Also the curve diagram describes the expression-pattern of cxcl12a in embryogenesis, represented by the supporting reads sum of corresponding APA sites. Y-axis, numbers of normalized reads. Reads, read number normalized to per million mapped read; pAsite, poly (A) sites. For direct viewing, the reader is referred to http://mosas.sysu.edu.cn/utr/search_APASdb.php?method=quick&id=7202&seqkeywords=ENSDARG00000037116.



 

Under "heterogeneous cleavage-site selection" tab

Clicking on the tab labeled “heterogeneous cleavage-site selection”, details the positions and usage of all the heterogeneous cleavage sites clustered to a poly(A) site downstream each poly(A) signal. Zebrafish cxcl12a is taken for example, for interpretation of the example mentioned, the reader is asked to refer the URL address http://mosas.sysu.edu.cn/utr/search_APASdb.php?seqkeywords=cxcl12a.

 

A series of figures were created to detail the location and usage quanification of the heterogeneous cleavage sites downstream each poly(A) signal. As shown below (Figure-group 1), the first of them describes the mapping overview of the heterogeneous cleavage sites clusters (Figure-group 1A), and clicking on the first figure will open a new page to show the dynamic change of clusters in different biological situations or diseases (Figure-group 2). Following the first, several figures are drawn to zoom in these corresponding clusters respectively(Figure-group 1B, I-VIII), and clicking on these figures can respectively load the new page to detail the selection of heterogeneous cleavage sites downstream their correponding poly(A) signal in various biological conditions or diseases (Figure-group 3). The heterogeneous cleavage sites were underlined in a cluster, that clearly presents the polyadenylated bases downstream a poly(A) signal. The most-frequently used cleavage site underlined in bold, that has the max reads in a cluster and is defined as a poly(A) site in 3’-UTR, and the reads sum for all the heterogeneous cleavage sites in the cluster was considered as the usage of this poly(A) site.Y-axis, numbers of normalized reads. hpf, hours post fertilization.

 

Figure-group 1. Mapping and usage of all the cleavage sites in zebrafish cxcl12a locus. (A) Mapping overview of all the cleavage sites in zebrafish cxcl12a locus. Eight read-clusters of heterogeneous cleavage sites are obvious and indicated in the dashed frames (I to VIII). They corresponds the poly(A) sites in the annotated 3’-UTR or the downstream 1kb region of cxcl12a. (B) Detailing the locations and reads of heterogeneous cleavage sites clustered to each poly(A) site. A series of cartons are created and numbered to detail the heterogeneous cleavage sites (underlined). Also, the 6-bases poly(A) signals upstream of cleavage sites are underlined if exist. Y-axis, numbers of normalized reads. cxcl12a, the chemokine (c-x-c motif) ligand 12a. For direct browsing the example mentioned here, users are asked to refer to the website [>> view online]

 

 

 

Figure-group 2. Mapping and usage change of the cleavage sites of cxcl12a during zebrafish embryonic development from 0 hpf to 120 hpf. Y-axis, numbers of normalized reads. hpf, hours post fertilization. For the example mentioned, the reader is asked to refer the URL address [>> view online].

 

 

Figure-group 3. Dynamic selection of the heterogeneous cleavage sites clustered to poly(A) site of 31040950 (cxcl12a) during zebrafish embryonic development from 0 hpf to 120 hpf. The selected cleavage sites were underlined, and the 6-bases poly(A) signals upstream poly(A) site are underlined if exist. Y-axis, numbers of normalized reads. hpf, hours post fertilization. For the example mentioned, the reader is asked to refer the URL address [>> view online].


 

Dynamic and graphical browsing of APA sites via a popular genome browser(Gbrowse)

APASdb provides the interactive and dynamic browsing of APA sites associated with genomes, genes, transcripts, and transcript annotations on a genome-wide scale online (“APAS Browse” feature). The selective view in three layers such as overview, region and details, are supplied for browsing APA sites in several reference genomes, including human (Homo sapiens_hg19), mouse (Mus musculus_mm9) and zebrafish (Danio rerio_Zv9). One or more APA datasets from these species can be quickly loaded and graphically browsed by clicking the “Update image” button after selecting the corresponding checkboxes of datasets labeled in "Tracks" panel, enabling a direct and visual way to compare the general and specific APA sites used in different biological conditions or diseases .

 

 


Figrue . Screen shots of several display of APA sites-related information for human GPR126, using the provided “APA browse” feature in APASdb site. Here, we give an example for APA sites of G protein-coupled receptor 126 (GPR126) in human breast cancer cell lines MCF7 and MB231, normal breast tissue and rectal cancer tissue. As tracked and indicated in detailed layers, the poly(A) sites (pA:142767384, pA:142767390 and pA:142767391) are located within 24nt from each other in the same strand, so they are usually taken for a same poly(A) site, seeming to be the general poly(A) sites for human breast cancer and rectum cancer. The poly(A) sites (pA:142765090 and pA:142767294) may be specific in human breast tissue, especially, the poly(A) site (pA:142767294) appeared only in human breast cancer cell lines MCF7 and MB231[>> view onlne].


 
V1.0 (2014-09-16)
Revising scripts

Revise: revising scripts to show poly(A) sites in a full transcrpit locus, containg the 5' and 3' flanking region of 1kb. Also adding selective view of multiple poly(A) sites in different samples integrated in a searching dataset.


V1.0 (2014-04-30)
Adding new datasets

Add: adding new APA-datasets involved in human normal twenty tissues, such as brain, lung, thyroid, spleen, stomach, kidney, cervix, heart, lymphNode, placenta, uterus, bladder, breast, prostate, liver, pancreas, small Intestine, thymus, adipose, skeletal Muscle, ovary and testicle.

 

V1.0 (2013-10-28)
Searching result page

Add: detailing the danymic selection of heterogeneous cleavage sites downstream of poly(A) signals in various biological conditions or diseases.

 

V0.9 (2013-09-16)
Searching result page

Add: Add "heterogeneous cleavage-site selection" tab in the result panel to specially and graphically detail the positions and usage frequence of the heterogeneous cleavage sites downstream each poly(A) signal in 3'-UTR.


V0.8 (2013-08-28)
Searching result page
Change: Highlight the most-frequently used cleavage site which was defined as a mode cleavage site (usually called poly(A) site) in SAPAS method in dark red, and highlight and underline the heterogeneous cleavage sites clustered a poly(A) site downstream of each poly(A) signal in light red.

 

V0.7 (2013-08-10)
APAS browsing page
Add: Integrate Gbrowse database and APA datasets generated with the SAPAS method, and provide dynamical and graphical browse of all the APA sites on a genome-wide scale by the popular open-source generic genome browser GBrowse.

V0.6 (2013-07-28)
Searching result page
Add: Graphical show for not only Quantification of APA sites but also expression pattern of a searched gene.

 

V0.5 (2013-01-28)
The first version online.

 

 
May 27, 2016. last modified
 
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