Automated construction of high-density comparative maps between rat, human, and mouse

Anne E Kwitek; Peter J Tonellato; Dan Chen; Jo Gullings-Handley; Yongjian Samuel Cheng; Simon Twigger; Todd E Scheetz; Thomas L Casavant; Monika  Stoll; Marcelo A Nobrega; Masahide Shiozawa; M Bento Soares; Val C Sheffield; Howard J Jacob

doi:10.1101/gr.173701

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Automated construction of high-density comparative maps between rat, human, and mouse

Journal article

Open access

Peer reviewed

Automated construction of high-density comparative maps between rat, human, and mouse

Anne E Kwitek, Peter J Tonellato, Dan Chen, Jo Gullings-Handley, Yongjian Samuel Cheng, Simon Twigger, Todd E Scheetz, Thomas L Casavant, Monika Stoll, Marcelo A Nobrega, …

Genome research, Vol.11(11), pp.1935-1943

11/2001

DOI: 10.1101/gr.173701

PMCID: PMC311144

PMID: 11691858

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Abstract

Animal models have been used primarily as surrogates for humans, having similar disease-based phenotypes. Genomic organization also tends to be conserved between species, leading to the generation of comparative genome maps. The emergence of radiation hybrid (RH) maps, coupled with the large numbers of available Expressed Sequence Tags (ESTs), has revolutionized the way comparative maps can be built. We used publicly available rat, mouse, and human data to identify genes and ESTs with interspecies sequence identity (homology), identified their UniGene relationships, and incorporated their RH map positions to build integrated comparative maps with >2100 homologous UniGenes mapped in more than one species (approximately 6% of all mammalian genes). The generation of these maps is iterative and labor intensive; therefore, we developed a series of computer tools (not described here) based on our algorithm that identifies anchors between species and produces printable and on-line clickable comparative maps that link to a wide variety of useful tools and databases. The maps were constructed using sequence-based comparisons, thus creating "hooks" for further sequence-based annotation of human, mouse, and rat sequences. Currently, this map enables investigators to link the physiology of the rat with the genetics of the mouse and the clinical significance of the human.

Algorithms

Computational Biology - methods

Reproducibility of Results

Animals

Chromosome Mapping - methods

Humans

Databases, Genetic

Rats

Radiation Hybrid Mapping - methods

Mice

Expressed Sequence Tags

Details

Title: Subtitle: Automated construction of high-density comparative maps between rat, human, and mouse
Creators: Anne E Kwitek - Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA. ablack@mcw.edu
Peter J Tonellato
Dan Chen
Jo Gullings-Handley
Yongjian Samuel Cheng
Simon Twigger
Todd E Scheetz
Thomas L Casavant
Monika Stoll
Marcelo A Nobrega
Masahide Shiozawa
M Bento Soares
Val C Sheffield
Howard J Jacob
Resource Type: Journal article
Publication Details: Genome research, Vol.11(11), pp.1935-1943
DOI: 10.1101/gr.173701
PMID: 11691858
PMCID: PMC311144
NLM abbreviation: Genome Res
ISSN: 1088-9051
eISSN: 1549-5469
Publisher: United States
Grant note: HL59789-03 / NHLBI NIH HHS R01 HL064541 / NHLBI NIH HHS R01 HL9826-03 / NHLBI NIH HHS
Language: English
Date published: 11/2001
Academic Unit: Roy J. Carver Department of Biomedical Engineering; Electrical and Computer Engineering; Stead Family Department of Pediatrics; Iowa Neuroscience Institute; Medical Genetics and Genomics; Ophthalmology and Visual Sciences
Record Identifier: 9983979972902771

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