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23 Οκτ 2013 (πριν από 3 χρόνια και 11 μήνες)

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Author(s):

Wu, LC (Wu, Li
-
Ching); Horng, JT (Horng, Jorng
-
Tzong); Chen, YA (Chen,
Yong
-
An)

Title:

A Computation to Integrate the Analysis of Genetic Variations Occurring within
Regulatory Elements and Their Possible Effects

Source:

JOURNAL OF COMPUTATION
AL BIOLOGY, 16 (12): 1731
-
1747 2009

Language:

English

Document Type:

Article

Author Keywords:

genetic variation; SNP; TFBS

KeyWords Plus:

MICRORNA TARGETS; WEB TOOL; SNPS; SEQUENCES; PREDICTION;
DATABASE; GENOME; LEVEL

Abstract:

Single nucleotide poly
morphisms (SNPs) and short tandem repeats (STRs) are the
most common genetic variations, are widespread within genomes, and form the diversity
within species. These genetic vari ations affect many regulatory elements such as transcription
factor binding sit
es (TFBSs), DNA methylation sites on CpG islands, and microRNA target
sites; these elements have been found to play major as well as indirect roles in regulati ng gene
expression. Currently, systems are available to display such genetic variation occurring
within
regulatory elements. To understand and displ ay all the potential vari ation described above, we
have developed a web
-
based system tool, the Regulatory Element and Genetic Variation
Viewer (REGV Viewer [REGV]), which provides a friendly web interface
for users and shows
genetic variation information within regulatory elements by either inputting a gene list or
selecting a chromosome by name. Moreover, our tool not only supports logic operation
queries, but after a query is submitted, it also shows a hi
gh
-
throughput simulation, including
combined data, statistical graphs, and graphical views of the genetic variants and regulatory
elements. Additionally, when the SNP variation occurs within TFBSs and if the SNP allele
frequency and TFBS position weight ma
trices (PWMs) are available, our system will show the
new putative TFBSs resulting from the SNP variation.

Addresses:

[Horng, Jorng
-
Tzong; Chen, Yong
-
An] Natl Cent Univ, Dept Comp Sci & Informat
Engn, Jhongli 32001, Taoyuan County, Taiwan; [Wu, Li
-
Ching;
Horng, Jorng
-
Tzong] Natl Cent
Univ, Inst Syst Biol & Bioinformat, Jhongli 32001, Taoyuan County, Taiwan; [Horng,
Jorng
-
Tzong] Asia Univ, Dept Bioinformat, Taichung, Taiwan

Reprint Address:

Horng, JT, Natl Cent Univ, Dept Comp Sci & Informat Engn, 300 Jhon
gda
Rd, Jhongli 32001, Taoyuan County, Taiwan.

E
-
mail Address:

horng@db.csie.ncu.edu.tw

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Cited Reference Count:

20

Times Cited:

0

Publisher:

MARY ANN LIEBERT INC

Publis
her Address:

140 HUGUENOT STREET, 3RD FL, NEW ROCHELLE, NY 10801 USA

ISSN:

1066
-
5277

DOI:

10.1089/cmb.2008.0247

29
-
char Source Abbrev.:

J COMPUT BIOLOGY

ISO Source Abbrev.:

J. Comput. Biol.

Source Item Page Count:

17

Subject Category:

Biochemical Res
earch Methods; Biotechnology & Applied Microbiology;
Computer Science, Interdisciplinary Applications; Mathematical & Computational Biology;
Statistics & Probability

ISI Document Delivery No.:

545CG