A guide to using MapMan to visualize and compare Omics data in plants:
a case study in the crop species, Maize
B. Usadel, F. Poree, A. Nagel, M. Lohse, A. Czedik-Eysenberg, and M. Stitt. Plant Cell Environ, 32 (9):
1211-29(September 2009)Usadel, Bjorn Poree, Fabien Nagel, Axel Lohse, Marc Czedik-Eysenberg,
Angelika Stitt, Mark Comparative Study Research Support, Non-U.S.
Gov't United States Plant, cell & environment Plant Cell Environ.
2009 Sep;32(9):1211-29. Epub 2009 Mar 24..
Abstract
MapMan is a software tool that supports the visualization of profiling
data sets in the context of existing knowledge. Scavenger modules
generate hierarchical and essentially non-redundant gene ontologies
('mapping files'). An ImageAnnotator module visualizes the data on
a gene-by-gene basis on schematic diagrams ('maps') of biological
processes. The PageMan module uses the same ontologies to statistically
evaluate responses at the pathway or processes level. The generic
structure of MapMan also allows it to be used for transcripts, proteins,
enzymes and metabolites. MapMan was developed for use with Arabidopsis,
but has already been extended for use with several other species.
These tools are available as downloadable and web-based versions.
After providing an introduction to the scope and use of MapMan, we
present a case study where MapMan is used to analyse the transcriptional
response of the crop plant maize to diurnal changes and an extension
of the night. We then explain how MapMan can be customized to visually
and systematically compare responses in maize and Arabidopsis. These
analyses illustrate how MapMan can be used to analyse and compare
global transcriptional responses between phylogenetically distant
species, and show that analyses at the level of functional categories
are especially useful in cross-species comparisons.
Usadel, Bjorn Poree, Fabien Nagel, Axel Lohse, Marc Czedik-Eysenberg,
Angelika Stitt, Mark Comparative Study Research Support, Non-U.S.
Gov't United States Plant, cell & environment Plant Cell Environ.
2009 Sep;32(9):1211-29. Epub 2009 Mar 24.
%0 Journal Article
%1 Usadel2009
%A Usadel, B.
%A Poree, F.
%A Nagel, A.
%A Lohse, M.
%A Czedik-Eysenberg, A.
%A Stitt, M.
%D 2009
%J Plant Cell Environ
%K *Genome, *Software Arabidopsis/genetics/metabolism Chromosome Genetic Genomics/*methods Mapping Photoperiod Plant Plant/genetics RNA, Transcription, Zea mays/*genetics/metabolism
%N 9
%P 1211-29
%T A guide to using MapMan to visualize and compare Omics data in plants:
a case study in the crop species, Maize
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19389052
%V 32
%X MapMan is a software tool that supports the visualization of profiling
data sets in the context of existing knowledge. Scavenger modules
generate hierarchical and essentially non-redundant gene ontologies
('mapping files'). An ImageAnnotator module visualizes the data on
a gene-by-gene basis on schematic diagrams ('maps') of biological
processes. The PageMan module uses the same ontologies to statistically
evaluate responses at the pathway or processes level. The generic
structure of MapMan also allows it to be used for transcripts, proteins,
enzymes and metabolites. MapMan was developed for use with Arabidopsis,
but has already been extended for use with several other species.
These tools are available as downloadable and web-based versions.
After providing an introduction to the scope and use of MapMan, we
present a case study where MapMan is used to analyse the transcriptional
response of the crop plant maize to diurnal changes and an extension
of the night. We then explain how MapMan can be customized to visually
and systematically compare responses in maize and Arabidopsis. These
analyses illustrate how MapMan can be used to analyse and compare
global transcriptional responses between phylogenetically distant
species, and show that analyses at the level of functional categories
are especially useful in cross-species comparisons.
@article{Usadel2009,
abstract = {MapMan is a software tool that supports the visualization of profiling
data sets in the context of existing knowledge. Scavenger modules
generate hierarchical and essentially non-redundant gene ontologies
('mapping files'). An ImageAnnotator module visualizes the data on
a gene-by-gene basis on schematic diagrams ('maps') of biological
processes. The PageMan module uses the same ontologies to statistically
evaluate responses at the pathway or processes level. The generic
structure of MapMan also allows it to be used for transcripts, proteins,
enzymes and metabolites. MapMan was developed for use with Arabidopsis,
but has already been extended for use with several other species.
These tools are available as downloadable and web-based versions.
After providing an introduction to the scope and use of MapMan, we
present a case study where MapMan is used to analyse the transcriptional
response of the crop plant maize to diurnal changes and an extension
of the night. We then explain how MapMan can be customized to visually
and systematically compare responses in maize and Arabidopsis. These
analyses illustrate how MapMan can be used to analyse and compare
global transcriptional responses between phylogenetically distant
species, and show that analyses at the level of functional categories
are especially useful in cross-species comparisons.},
added-at = {2010-12-14T18:12:02.000+0100},
author = {Usadel, B. and Poree, F. and Nagel, A. and Lohse, M. and Czedik-Eysenberg, A. and Stitt, M.},
biburl = {https://www.bibsonomy.org/bibtex/22967fcf70956b8b4a24648e594adfd60/pharmawuerz},
endnotereftype = {Journal Article},
interhash = {b0b75471ce3152547d80d7a6c81e74b3},
intrahash = {2967fcf70956b8b4a24648e594adfd60},
issn = {1365-3040 (Electronic) 1365-3040 (Linking)},
journal = {Plant Cell Environ},
keywords = {*Genome, *Software Arabidopsis/genetics/metabolism Chromosome Genetic Genomics/*methods Mapping Photoperiod Plant Plant/genetics RNA, Transcription, Zea mays/*genetics/metabolism},
month = Sep,
note = {Usadel, Bjorn Poree, Fabien Nagel, Axel Lohse, Marc Czedik-Eysenberg,
Angelika Stitt, Mark Comparative Study Research Support, Non-U.S.
Gov't United States Plant, cell \& environment Plant Cell Environ.
2009 Sep;32(9):1211-29. Epub 2009 Mar 24.},
number = 9,
pages = {1211-29},
shorttitle = {A guide to using MapMan to visualize and compare Omics data in plants:
a case study in the crop species, Maize},
timestamp = {2010-12-14T18:12:34.000+0100},
title = {A guide to using MapMan to visualize and compare Omics data in plants:
a case study in the crop species, Maize},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19389052},
volume = 32,
year = 2009
}