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ERE database: a database of genomic maps and biological properties of endogenous retroviral elements in the C57BL/6J mouse genome.

Abstract Endogenous retroviral elements (EREs), a family of transposable elements, constitute a substantial fraction of mammalian genomes. It is expected that profiles of the ERE sequences and their genomic locations are unique for each individual. Comprehensive characterization of the EREs' genomic locations and their biological properties is essential for understanding their roles in the pathophysiology of the host. In this study, we identified and mapped putative EREs (a total of 111 endogenous retroviruses [ERVs] and 488 solo long terminal repeats [sLTRs]) within the C57BL/6J mouse genome. The biological properties of individual ERE isolates (both ERVs and sLTRs) were then characterized in the following aspects: transcription potential, tropism trait, coding potential, recombination event, integration age, and primer binding site for replication. In addition, a suite of database management system programs was developed to organize and update the data acquired from current and future studies and to make the data accessible via internet.
PMID
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Authors

Mayor MeshTerms

Databases, Genetic

Genome

Software

Keywords
Journal Title genomics
Publication Year Start
%A Kao, Damian; Hsu, Karen; Chiu, Sophia; Tu, Vince; Chew, Alex; Lee, Kang-Hoon; Lee, Young-Kwan; Kwon, Deug-Nam; Greenhalgh, David G.; Cho, Kiho
%T ERE database: a database of genomic maps and biological properties of endogenous retroviral elements in the C57BL/6J mouse genome.
%J Genomics, vol. 100, no. 3, pp. 157-161
%D 09/2012
%V 100
%N 3
%M eng
%B Endogenous retroviral elements (EREs), a family of transposable elements, constitute a substantial fraction of mammalian genomes. It is expected that profiles of the ERE sequences and their genomic locations are unique for each individual. Comprehensive characterization of the EREs' genomic locations and their biological properties is essential for understanding their roles in the pathophysiology of the host. In this study, we identified and mapped putative EREs (a total of 111 endogenous retroviruses [ERVs] and 488 solo long terminal repeats [sLTRs]) within the C57BL/6J mouse genome. The biological properties of individual ERE isolates (both ERVs and sLTRs) were then characterized in the following aspects: transcription potential, tropism trait, coding potential, recombination event, integration age, and primer binding site for replication. In addition, a suite of database management system programs was developed to organize and update the data acquired from current and future studies and to make the data accessible via internet.
%K Animals, Binding Sites, Chromosome Mapping, DNA Primers, Databases, Genetic, Endogenous Retroviruses, Genome, Mice, Mice, Inbred C57BL, Open Reading Frames, Phylogeny, Promoter Regions, Genetic, Recombination, Genetic, Regulatory Elements, Transcriptional, Sequence Analysis, DNA, Software, Terminal Repeat Sequences, Transcription, Genetic
%P 157
%L 161
%Y 10.1016/j.ygeno.2012.06.002
%W PHY
%G AUTHOR
%R 2012......100..157K

@Article{Kao2012,
author="Kao, Damian
and Hsu, Karen
and Chiu, Sophia
and Tu, Vince
and Chew, Alex
and Lee, Kang-Hoon
and Lee, Young-Kwan
and Kwon, Deug-Nam
and Greenhalgh, David G.
and Cho, Kiho",
title="ERE database: a database of genomic maps and biological properties of endogenous retroviral elements in the C57BL/6J mouse genome.",
journal="Genomics",
year="2012",
month="Sep",
day="09",
volume="100",
number="3",
pages="157--161",
keywords="Animals",
keywords="Binding Sites",
keywords="Chromosome Mapping",
keywords="DNA Primers",
keywords="Databases, Genetic",
keywords="Endogenous Retroviruses",
keywords="Genome",
keywords="Mice",
keywords="Mice, Inbred C57BL",
keywords="Open Reading Frames",
keywords="Phylogeny",
keywords="Promoter Regions, Genetic",
keywords="Recombination, Genetic",
keywords="Regulatory Elements, Transcriptional",
keywords="Sequence Analysis, DNA",
keywords="Software",
keywords="Terminal Repeat Sequences",
keywords="Transcription, Genetic",
abstract="Endogenous retroviral elements (EREs), a family of transposable elements, constitute a substantial fraction of mammalian genomes. It is expected that profiles of the ERE sequences and their genomic locations are unique for each individual. Comprehensive characterization of the EREs' genomic locations and their biological properties is essential for understanding their roles in the pathophysiology of the host. In this study, we identified and mapped putative EREs (a total of 111 endogenous retroviruses [ERVs] and 488 solo long terminal repeats [sLTRs]) within the C57BL/6J mouse genome. The biological properties of individual ERE isolates (both ERVs and sLTRs) were then characterized in the following aspects: transcription potential, tropism trait, coding potential, recombination event, integration age, and primer binding site for replication. In addition, a suite of database management system programs was developed to organize and update the data acquired from current and future studies and to make the data accessible via internet.",
issn="1089-8646",
doi="10.1016/j.ygeno.2012.06.002",
url="http://www.ncbi.nlm.nih.gov/pubmed/22691267",
language="eng"
}

%0 Journal Article
%T ERE database: a database of genomic maps and biological properties of endogenous retroviral elements in the C57BL/6J mouse genome.
%A Kao, Damian
%A Hsu, Karen
%A Chiu, Sophia
%A Tu, Vince
%A Chew, Alex
%A Lee, Kang-Hoon
%A Lee, Young-Kwan
%A Kwon, Deug-Nam
%A Greenhalgh, David G.
%A Cho, Kiho
%J Genomics
%D 2012
%8 Sep 09
%V 100
%N 3
%@ 1089-8646
%G eng
%F Kao2012
%X Endogenous retroviral elements (EREs), a family of transposable elements, constitute a substantial fraction of mammalian genomes. It is expected that profiles of the ERE sequences and their genomic locations are unique for each individual. Comprehensive characterization of the EREs' genomic locations and their biological properties is essential for understanding their roles in the pathophysiology of the host. In this study, we identified and mapped putative EREs (a total of 111 endogenous retroviruses [ERVs] and 488 solo long terminal repeats [sLTRs]) within the C57BL/6J mouse genome. The biological properties of individual ERE isolates (both ERVs and sLTRs) were then characterized in the following aspects: transcription potential, tropism trait, coding potential, recombination event, integration age, and primer binding site for replication. In addition, a suite of database management system programs was developed to organize and update the data acquired from current and future studies and to make the data accessible via internet.
%K Animals
%K Binding Sites
%K Chromosome Mapping
%K DNA Primers
%K Databases, Genetic
%K Endogenous Retroviruses
%K Genome
%K Mice
%K Mice, Inbred C57BL
%K Open Reading Frames
%K Phylogeny
%K Promoter Regions, Genetic
%K Recombination, Genetic
%K Regulatory Elements, Transcriptional
%K Sequence Analysis, DNA
%K Software
%K Terminal Repeat Sequences
%K Transcription, Genetic
%U http://dx.doi.org/10.1016/j.ygeno.2012.06.002
%U http://www.ncbi.nlm.nih.gov/pubmed/22691267
%P 157-161

PT Journal
AU Kao, D
   Hsu, K
   Chiu, S
   Tu, V
   Chew, A
   Lee, K
   Lee, Y
   Kwon, D
   Greenhalgh, DG
   Cho, K
TI ERE database: a database of genomic maps and biological properties of endogenous retroviral elements in the C57BL/6J mouse genome.
SO Genomics
PD Sep
PY 2012
BP 157
EP 161
VL 100
IS 3
DI 10.1016/j.ygeno.2012.06.002
LA eng
DE Animals; Binding Sites; Chromosome Mapping; DNA Primers; Databases, Genetic; Endogenous Retroviruses; Genome; Mice; Mice, Inbred C57BL; Open Reading Frames; Phylogeny; Promoter Regions, Genetic; Recombination, Genetic; Regulatory Elements, Transcriptional; Sequence Analysis, DNA; Software; Terminal Repeat Sequences; Transcription, Genetic
AB Endogenous retroviral elements (EREs), a family of transposable elements, constitute a substantial fraction of mammalian genomes. It is expected that profiles of the ERE sequences and their genomic locations are unique for each individual. Comprehensive characterization of the EREs' genomic locations and their biological properties is essential for understanding their roles in the pathophysiology of the host. In this study, we identified and mapped putative EREs (a total of 111 endogenous retroviruses [ERVs] and 488 solo long terminal repeats [sLTRs]) within the C57BL/6J mouse genome. The biological properties of individual ERE isolates (both ERVs and sLTRs) were then characterized in the following aspects: transcription potential, tropism trait, coding potential, recombination event, integration age, and primer binding site for replication. In addition, a suite of database management system programs was developed to organize and update the data acquired from current and future studies and to make the data accessible via internet.
ER

PMID- 22691267
OWN - NLM
STAT- MEDLINE
DA  - 20120827
DCOM- 20130104
LR  - 20150317
IS  - 1089-8646 (Electronic)
IS  - 0888-7543 (Linking)
VI  - 100
IP  - 3
DP  - 2012 Sep
TI  - ERE database: a database of genomic maps and biological properties of endogenous 
      retroviral elements in the C57BL/6J mouse genome.
PG  - 157-61
LID - 10.1016/j.ygeno.2012.06.002 [doi]
AB  - Endogenous retroviral elements (EREs), a family of transposable elements,
      constitute a substantial fraction of mammalian genomes. It is expected that
      profiles of the ERE sequences and their genomic locations are unique for each
      individual. Comprehensive characterization of the EREs' genomic locations and
      their biological properties is essential for understanding their roles in the
      pathophysiology of the host. In this study, we identified and mapped putative
      EREs (a total of 111 endogenous retroviruses [ERVs] and 488 solo long terminal
      repeats [sLTRs]) within the C57BL/6J mouse genome. The biological properties of
      individual ERE isolates (both ERVs and sLTRs) were then characterized in the
      following aspects: transcription potential, tropism trait, coding potential,
      recombination event, integration age, and primer binding site for replication. In
      addition, a suite of database management system programs was developed to
      organize and update the data acquired from current and future studies and to make
      the data accessible via internet.
CI  - Copyright (c) 2012 Elsevier Inc. All rights reserved.
FAU - Kao, Damian
AU  - Kao D
AD  - Burn Research, Shriners Hospitals for Children Northern California, Sacramento,
      CA 95817, USA.
FAU - Hsu, Karen
AU  - Hsu K
FAU - Chiu, Sophia
AU  - Chiu S
FAU - Tu, Vince
AU  - Tu V
FAU - Chew, Alex
AU  - Chew A
FAU - Lee, Kang-Hoon
AU  - Lee KH
FAU - Lee, Young-Kwan
AU  - Lee YK
FAU - Kwon, Deug-Nam
AU  - Kwon DN
FAU - Greenhalgh, David G
AU  - Greenhalgh DG
FAU - Cho, Kiho
AU  - Cho K
LA  - eng
GR  - R01 GM071360/GM/NIGMS NIH HHS/United States
GR  - R01GM071360/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20120609
PL  - United States
TA  - Genomics
JT  - Genomics
JID - 8800135
RN  - 0 (DNA Primers)
SB  - IM
MH  - Animals
MH  - Binding Sites
MH  - Chromosome Mapping/*methods
MH  - DNA Primers/chemistry
MH  - *Databases, Genetic
MH  - Endogenous Retroviruses/classification/*genetics
MH  - *Genome
MH  - Mice
MH  - Mice, Inbred C57BL
MH  - Open Reading Frames
MH  - Phylogeny
MH  - Promoter Regions, Genetic
MH  - Recombination, Genetic
MH  - Regulatory Elements, Transcriptional
MH  - Sequence Analysis, DNA/methods
MH  - *Software
MH  - Terminal Repeat Sequences
MH  - Transcription, Genetic
PMC - PMC3428438
MID - NIHMS389524
OID - NLM: NIHMS389524
OID - NLM: PMC3428438
EDAT- 2012/06/14 06:00
MHDA- 2013/01/05 06:00
CRDT- 2012/06/14 06:00
PHST- 2012/01/25 [received]
PHST- 2012/05/31 [revised]
PHST- 2012/06/04 [accepted]
PHST- 2012/06/09 [aheadofprint]
AID - S0888-7543(12)00109-7 [pii]
AID - 10.1016/j.ygeno.2012.06.002 [doi]
PST - ppublish
SO  - Genomics. 2012 Sep;100(3):157-61. doi: 10.1016/j.ygeno.2012.06.002. Epub 2012 Jun
      9.
TY  - JOUR
AU  - Kao, Damian
AU  - Hsu, Karen
AU  - Chiu, Sophia
AU  - Tu, Vince
AU  - Chew, Alex
AU  - Lee, Kang-Hoon
AU  - Lee, Young-Kwan
AU  - Kwon, Deug-Nam
AU  - Greenhalgh, David G.
AU  - Cho, Kiho
PY  - 2012/Sep/09
TI  - ERE database: a database of genomic maps and biological properties of endogenous retroviral elements in the C57BL/6J mouse genome.
JO  - Genomics
SP  - 157
EP  - 161
VL  - 100
IS  - 3
KW  - Animals
KW  - Binding Sites
KW  - Chromosome Mapping
KW  - DNA Primers
KW  - Databases, Genetic
KW  - Endogenous Retroviruses
KW  - Genome
KW  - Mice
KW  - Mice, Inbred C57BL
KW  - Open Reading Frames
KW  - Phylogeny
KW  - Promoter Regions, Genetic
KW  - Recombination, Genetic
KW  - Regulatory Elements, Transcriptional
KW  - Sequence Analysis, DNA
KW  - Software
KW  - Terminal Repeat Sequences
KW  - Transcription, Genetic
N2  - Endogenous retroviral elements (EREs), a family of transposable elements, constitute a substantial fraction of mammalian genomes. It is expected that profiles of the ERE sequences and their genomic locations are unique for each individual. Comprehensive characterization of the EREs' genomic locations and their biological properties is essential for understanding their roles in the pathophysiology of the host. In this study, we identified and mapped putative EREs (a total of 111 endogenous retroviruses [ERVs] and 488 solo long terminal repeats [sLTRs]) within the C57BL/6J mouse genome. The biological properties of individual ERE isolates (both ERVs and sLTRs) were then characterized in the following aspects: transcription potential, tropism trait, coding potential, recombination event, integration age, and primer binding site for replication. In addition, a suite of database management system programs was developed to organize and update the data acquired from current and future studies and to make the data accessible via internet.
SN  - 1089-8646
UR  - http://dx.doi.org/10.1016/j.ygeno.2012.06.002
UR  - http://www.ncbi.nlm.nih.gov/pubmed/22691267
ID  - Kao2012
ER  - 
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