Connecting sequence and biology in the laboratory mouse.
The Mouse Genome Sequencing Consortium and the RIKEN Genome Exploration Research grouphave generated large sets of sequence data representing the mouse genome and transcriptome, respectively. These data provide a valuable foundation for genomic research. The challenges for the informatics community are how to integrate these data with the ever-expanding knowledge about the roles of genes and gene products in biological processes, and how to provide useful views to the scientific community. Public resources, such as the National Center for Biotechnology Information (NCBI; http://www.ncbi.nih.gov), and model organism databases, such as the Mouse Genome Informatics database (MGI; http://www.informatics.jax.org), maintain the primary data and provide connections between sequence and biology. In this paper, we describe how the partnership of MGI and NCBI LocusLink contributes to the integration of sequence and biology, especially in the context of the large-scale genome and transcriptome data now available for the laboratory mouse. In particular, we describe the methods and results of integration of 60,770 FANTOM2 mouse cDNAs with gene records in the databases of MGI and LocusLink.
Baldarelli
Richard M
RM
Mouse Genome Informatics Group, The Jackson Laboratory, Bar Harbor, Maine 04609, USA. rmb@informatics.jax.org
Hill
David P
DP
Blake
Judith A
JA
Adachi
Jun
J
Furuno
Masaaki
M
Bradt
Dirck
D
Corbani
Lori E
LE
Cousins
Sharon
S
Frazer
Kenneth S
KS
Qi
Dong
D
Yang
Longlong
L
Ramachandran
Sridhar
S
Reed
Deborah
D
Zhu
Yunxia
Y
Kasukawa
Takeya
T
Ringwald
Martin
M
King
Benjamin L
BL
Maltais
Lois J
LJ
McKenzie
Louise M
LM
Schriml
Lynn M
LM
Maglott
Donna
D
Church
Deanna M
DM
Pruitt
Kim
K
Eppig
Janan T
JT
Richardson
Joel E
JE
Kadin
Jim A
JA
Bult
Carol J
CJ
D000818:Animals; D001483:Base Sequence / Q000235:genetics* / Q000502:physiology; D019295:Computational Biology / Q000379:methods* / Q000706:statistics & numerical data; D003196:Computer Graphics / Q000706:statistics & numerical data / Q000639:trends; D018076:DNA, Complementary / Q000235:genetics / Q000502:physiology; D030541:Databases, Genetic / Q000706:statistics & numerical data / Q000639:trends; D005796:Genes / Q000235:genetics / Q000502:physiology; D016678:Genome; D020407:Internet / Q000706:statistics & numerical data / Q000639:trends; D051379:Mice
D018076:DNA, Complementary