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Comparative Map and Trait Viewer (CMTV): an integrated bioinformatic tool to construct consensus maps and compare QTL and functional genomics data across genomes and experiments

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Relation http://oar.icrisat.org/5737/
http://dx.doi.org/10.1007/s11103-004-4950-0
 
Title Comparative Map and Trait Viewer (CMTV): an integrated bioinformatic tool to construct consensus maps and compare QTL and functional genomics data across genomes and experiments
 
Creator Sawkins, M C
Farmer, A D
Hoisington, D A
Sullivan, J
Tolopko, A
Jiang, Z
Ribaut, J M
 
Subject Genetics and Genomics
Agriculture-Farming, Production, Technology, Economics
 
Description In the past few decades, a wealth of genomic data has been produced in a wide variety of species using a
diverse array of functional and molecular marker approaches. In order to unlock the full potential of the
information contained in these independent experiments, researchers need efficient and intuitive means to
identify common genomic regions and genes involved in the expression of target phenotypic traits across
diverse conditions. To address this need, we have developed a Comparative Map and Trait Viewer (CMTV)
tool that can be used to construct dynamic aggregations of a variety of types of genomic datasets. By
algorithmically determining correspondences between sets of objects on multiple genomic maps, the CMTV
can display syntenic regions across taxa, combine maps from separate experiments into a consensus map, or
project data from different maps into a common coordinate framework using dynamic coordinate translations
between source and target maps. We present a case study that illustrates the utility of the tool for
managing large and varied datasets by integrating data collected by CIMMYT in maize drought tolerance
research with data from public sources. This example will focus on one of the visualization features for
Quantitative Trait Locus (QTL) data, using likelihood ratio (LR) files produced by generic QTL analysis
software and displaying the data in a unique visual manner across different combinations of traits, environments
and crosses. Once a genomic region of interest has been identified, the CMTV can search and
display additional QTLs meeting a particular threshold for that region, or other functional data such as sets
of differentially expressed genes located in the region; it thus provides an easily used means for organizing
and manipulating data sets that have been dynamically integrated under the focus of the researcher’s
specific hypothesis.
 
Publisher Springer Netherlands
 
Date 2004
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Rights —
 
Identifier http://oar.icrisat.org/5737/1/PlantMolecularBiology_56_465%E2%80%93480_2004.pdf
Sawkins, M C and Farmer, A D and Hoisington, D A and Sullivan, J and Tolopko, A and Jiang, Z and Ribaut, J M (2004) Comparative Map and Trait Viewer (CMTV): an integrated bioinformatic tool to construct consensus maps and compare QTL and functional genomics data across genomes and experiments. Plant Molecular Biology, 56 (3). pp. 465-480. ISSN 1573-5028