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APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals.

You L, Wu J, Feng Y, Fu Y, Guo Y, Long L, Zhang H, Luan Y, Tian P, Chen L, Huang G, Huang S, Li Y, Li J, Chen C, Zhang Y, Chen S, Xu A - Nucleic Acids Res. (2014)

Bottom Line: Furthermore, APASdb provides the quantification of a given APA variant among transcripts with different APA sites by computing their corresponding normalized-reads, making our database more useful.In addition, APASdb supports URL-based retrieval, browsing and display of exon-intron structure, poly(A) signals, poly(A) sites location and usage reads, and 3'-untranslated regions (3'-UTRs).Currently, APASdb involves APA in various biological processes and diseases in human, mouse and zebrafish.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou 510006, People's Republic of China School of Basic Medical Sciences, Beijing University of Chinese Medicine, Beijing 100029, People's Republic of China.

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Screen shot of the searching page and the media page resulting from a fuzzy query keyword of ‘chemokine’. (A) User retrieval interface designed to query datasets. (B) Descript list of datasets in retrieval interface. The List summarizes the released datasets and directs user's query. The ‘view’ button supports quick access to a example query of dataset and the ‘chr’ button links the browsing of dataset in a genome browser (Gbrowse). (C) List of APA sites-contained genes matching the fuzzy keyword of ‘chemokine’. Each icon displayed in ‘APAS’ column of the result table links a detail page to show more corresponding information of APA sites and the number highlighted in ‘APAS’ column indicates the number of APA-sites located in the transcript locus, and texts with hyperlinks 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 a genome browser. For direct viewing the example mentioned here, the reader is asked to refer to http://mosas.sysu.edu.cn/utr/search_APASdb.php?seqkeywords=chemokine.
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Figure 2: Screen shot of the searching page and the media page resulting from a fuzzy query keyword of ‘chemokine’. (A) User retrieval interface designed to query datasets. (B) Descript list of datasets in retrieval interface. The List summarizes the released datasets and directs user's query. The ‘view’ button supports quick access to a example query of dataset and the ‘chr’ button links the browsing of dataset in a genome browser (Gbrowse). (C) List of APA sites-contained genes matching the fuzzy keyword of ‘chemokine’. Each icon displayed in ‘APAS’ column of the result table links a detail page to show more corresponding information of APA sites and the number highlighted in ‘APAS’ column indicates the number of APA-sites located in the transcript locus, and texts with hyperlinks 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 a genome browser. For direct viewing the example mentioned here, the reader is asked to refer to http://mosas.sysu.edu.cn/utr/search_APASdb.php?seqkeywords=chemokine.

Mentions: Our ‘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. Currently, Ensembl id (for D. rerio) and UCSC id (for M. musculus and H. sapiens) are allowed for precise query, also fuzzy query by using keywords such as gene name, symbol and simple description is permitted. Clicking the button labeled ‘Example’ yields an example keyword suited for searching a selected dataset (Figure 2A), and the subsets and detail descriptions on the searched dataset can be unfolded by clicking the corresponding ‘+’-labeled icon (Figure 2B). Fuzzy search, using a fuzzy keyword of ‘chemokine’, may lead to a media page to list all the matched APA sites-contained genes in a dynamic table (Figure 2C), so as to facilitate the selective view of their corresponding APA information in a linked detail page (described next), but searching by using a precise keyword can give users quick access to the detailed page to view various types of information on APA sites and the related graphics.


APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals.

You L, Wu J, Feng Y, Fu Y, Guo Y, Long L, Zhang H, Luan Y, Tian P, Chen L, Huang G, Huang S, Li Y, Li J, Chen C, Zhang Y, Chen S, Xu A - Nucleic Acids Res. (2014)

Screen shot of the searching page and the media page resulting from a fuzzy query keyword of ‘chemokine’. (A) User retrieval interface designed to query datasets. (B) Descript list of datasets in retrieval interface. The List summarizes the released datasets and directs user's query. The ‘view’ button supports quick access to a example query of dataset and the ‘chr’ button links the browsing of dataset in a genome browser (Gbrowse). (C) List of APA sites-contained genes matching the fuzzy keyword of ‘chemokine’. Each icon displayed in ‘APAS’ column of the result table links a detail page to show more corresponding information of APA sites and the number highlighted in ‘APAS’ column indicates the number of APA-sites located in the transcript locus, and texts with hyperlinks 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 a genome browser. For direct viewing the example mentioned here, the reader is asked to refer to http://mosas.sysu.edu.cn/utr/search_APASdb.php?seqkeywords=chemokine.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC4383914&req=5

Figure 2: Screen shot of the searching page and the media page resulting from a fuzzy query keyword of ‘chemokine’. (A) User retrieval interface designed to query datasets. (B) Descript list of datasets in retrieval interface. The List summarizes the released datasets and directs user's query. The ‘view’ button supports quick access to a example query of dataset and the ‘chr’ button links the browsing of dataset in a genome browser (Gbrowse). (C) List of APA sites-contained genes matching the fuzzy keyword of ‘chemokine’. Each icon displayed in ‘APAS’ column of the result table links a detail page to show more corresponding information of APA sites and the number highlighted in ‘APAS’ column indicates the number of APA-sites located in the transcript locus, and texts with hyperlinks 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 a genome browser. For direct viewing the example mentioned here, the reader is asked to refer to http://mosas.sysu.edu.cn/utr/search_APASdb.php?seqkeywords=chemokine.
Mentions: Our ‘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. Currently, Ensembl id (for D. rerio) and UCSC id (for M. musculus and H. sapiens) are allowed for precise query, also fuzzy query by using keywords such as gene name, symbol and simple description is permitted. Clicking the button labeled ‘Example’ yields an example keyword suited for searching a selected dataset (Figure 2A), and the subsets and detail descriptions on the searched dataset can be unfolded by clicking the corresponding ‘+’-labeled icon (Figure 2B). Fuzzy search, using a fuzzy keyword of ‘chemokine’, may lead to a media page to list all the matched APA sites-contained genes in a dynamic table (Figure 2C), so as to facilitate the selective view of their corresponding APA information in a linked detail page (described next), but searching by using a precise keyword can give users quick access to the detailed page to view various types of information on APA sites and the related graphics.

Bottom Line: Furthermore, APASdb provides the quantification of a given APA variant among transcripts with different APA sites by computing their corresponding normalized-reads, making our database more useful.In addition, APASdb supports URL-based retrieval, browsing and display of exon-intron structure, poly(A) signals, poly(A) sites location and usage reads, and 3'-untranslated regions (3'-UTRs).Currently, APASdb involves APA in various biological processes and diseases in human, mouse and zebrafish.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou 510006, People's Republic of China School of Basic Medical Sciences, Beijing University of Chinese Medicine, Beijing 100029, People's Republic of China.

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Related in: MedlinePlus