PMID- 25378337
OWN - NLM
STAT- MEDLINE
DCOM- 20150629
LR  - 20220317
IS  - 1362-4962 (Electronic)
IS  - 0305-1048 (Print)
IS  - 0305-1048 (Linking)
VI  - 43
IP  - Database issue
DP  - 2015 Jan
TI  - APASdb: a database describing alternative poly(A) sites and selection of 
      heterogeneous cleavage sites downstream of poly(A) signals.
PG  - D59-67
LID - 10.1093/nar/gku1076 [doi]
AB  - Increasing amounts of genes have been shown to utilize alternative 
      polyadenylation (APA) 3'-processing sites depending on the cell and tissue type 
      and/or physiological and pathological conditions at the time of processing, and 
      the construction of genome-wide database regarding APA is urgently needed for 
      better understanding poly(A) site selection and APA-directed gene expression 
      regulation for a given biology. Here we present a web-accessible database, named 
      APASdb (http://mosas.sysu.edu.cn/utr), which can visualize the precise map and 
      usage quantification of different APA isoforms for all genes. The datasets are 
      deeply profiled by the sequencing alternative polyadenylation sites (SAPAS) 
      method capable of high-throughput sequencing 3'-ends of polyadenylated 
      transcripts. Thus, APASdb details all the heterogeneous cleavage sites downstream 
      of poly(A) signals, and maintains near complete coverage for APA sites, much 
      better than the previous databases using conventional methods. 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.
CI  - (c) The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic 
      Acids Research.
FAU - You, Leiming
AU  - You L
AD  - 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.
FAU - Wu, Jiexin
AU  - Wu J
AD  - 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.
FAU - Feng, Yuchao
AU  - Feng Y
AD  - 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.
FAU - Fu, Yonggui
AU  - Fu Y
AD  - 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.
FAU - Guo, Yanan
AU  - Guo Y
AD  - 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.
FAU - Long, Liyuan
AU  - Long L
AD  - 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.
FAU - Zhang, Hui
AU  - Zhang H
AD  - 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.
FAU - Luan, Yijie
AU  - Luan Y
AD  - 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.
FAU - Tian, Peng
AU  - Tian P
AD  - 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.
FAU - Chen, Liangfu
AU  - Chen L
AD  - 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.
FAU - Huang, Guangrui
AU  - Huang G
AD  - 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.
FAU - Huang, Shengfeng
AU  - Huang S
AD  - 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.
FAU - Li, Yuxin
AU  - Li Y
AD  - 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.
FAU - Li, Jie
AU  - Li J
AD  - 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.
FAU - Chen, Chengyong
AU  - Chen C
AD  - 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.
FAU - Zhang, Yaqing
AU  - Zhang Y
AD  - 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.
FAU - Chen, Shangwu
AU  - Chen S
AD  - 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.
FAU - Xu, Anlong
AU  - Xu A
AD  - 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 lssxal@mail.sysu.edu.cn.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20141106
PL  - England
TA  - Nucleic Acids Res
JT  - Nucleic acids research
JID - 0411011
RN  - 24937-83-5 (Poly A)
SB  - IM
MH  - Animals
MH  - *Databases, Nucleic Acid
MH  - Gene Expression
MH  - Humans
MH  - Internet
MH  - Mice
MH  - Poly A/analysis
MH  - *Polyadenylation
MH  - RNA Cleavage
MH  - Zebrafish/genetics
PMC - PMC4383914
EDAT- 2014/11/08 06:00
MHDA- 2015/06/30 06:00
PMCR- 2014/11/06
CRDT- 2014/11/08 06:00
PHST- 2014/11/08 06:00 [entrez]
PHST- 2014/11/08 06:00 [pubmed]
PHST- 2015/06/30 06:00 [medline]
PHST- 2014/11/06 00:00 [pmc-release]
AID - gku1076 [pii]
AID - 10.1093/nar/gku1076 [doi]
PST - ppublish
SO  - Nucleic Acids Res. 2015 Jan;43(Database issue):D59-67. doi: 10.1093/nar/gku1076. 
      Epub 2014 Nov 6.