Literature DB >> 16009995

Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses.

Björn Usadel1, Axel Nagel, Oliver Thimm, Henning Redestig, Oliver E Blaesing, Natalia Palacios-Rojas, Joachim Selbig, Jan Hannemann, Maria Conceição Piques, Dirk Steinhauser, Wolf-Rüdiger Scheible, Yves Gibon, Rosa Morcuende, Daniel Weicht, Svenja Meyer, Mark Stitt.   

Abstract

MapMan is a user-driven tool that displays large genomics datasets onto diagrams of metabolic pathways or other processes. Here, we present new developments, including improvements of the gene assignments and the user interface, a strategy to visualize multilayered datasets, the incorporation of statistics packages, and extensions of the software to incorporate more biological information including visualization of corresponding genes and horizontal searches for similar global responses across large numbers of arrays.

Mesh：

Year:  2005        PMID： 16009995      PMCID： PMC1176394          DOI： 10.1104/pp.105.060459

Source DB:  PubMed          Journal:  Plant Physiol        ISSN： 0032-0889            Impact factor:   8.340


  28 in total

1.  Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks.

Authors:  Paul Grosu; Jeffrey P Townsend; Daniel L Hartl; Duccio Cavalieri
Journal:  Genome Res       Date:  2002-07       Impact factor: 9.043

2.  MetaGeneAlyse: analysis of integrated transcriptional and metabolite data.

Authors:  Carsten O Daub; Sebastian Kloska; Joachim Selbig
Journal:  Bioinformatics       Date:  2003-11-22       Impact factor: 6.937

3.  Microarray analysis of the nitrate response in Arabidopsis roots and shoots reveals over 1,000 rapidly responding genes and new linkages to glucose, trehalose-6-phosphate, iron, and sulfate metabolism.

Authors:  Rongchen Wang; Mamoru Okamoto; Xiujuan Xing; Nigel M Crawford
Journal:  Plant Physiol       Date:  2003-06       Impact factor: 8.340

4.  Detection of genes with tissue-specific expression patterns using Akaike's information criterion procedure.

Authors:  Koji Kadota; Shin-Ichiro Nishimura; Hidemasa Bono; Shugo Nakamura; Yoshihide Hayashizaki; Yasushi Okazaki; Katsutoshi Takahashi
Journal:  Physiol Genomics       Date:  2003-02-06       Impact factor: 3.107

5.  Metabolite profiling for plant functional genomics.

Authors:  O Fiehn; J Kopka; P Dörmann; T Altmann; R N Trethewey; L Willmitzer
Journal:  Nat Biotechnol       Date:  2000-11       Impact factor: 54.908

6.  A probabilistic functional network of yeast genes.

Authors:  Insuk Lee; Shailesh V Date; Alex T Adai; Edward M Marcotte
Journal:  Science       Date:  2004-11-26       Impact factor: 47.728

7.  Genomic analysis of the nitrate response using a nitrate reductase-null mutant of Arabidopsis.

Authors:  Rongchen Wang; Rudolf Tischner; Rodrigo A Gutiérrez; Maren Hoffman; Xiujuan Xing; Mingsheng Chen; Gloria Coruzzi; Nigel M Crawford
Journal:  Plant Physiol       Date:  2004-08-27       Impact factor: 8.340

Review 8.  Genome-wide reprogramming of primary and secondary metabolism, protein synthesis, cellular growth processes, and the regulatory infrastructure of Arabidopsis in response to nitrogen.

Authors:  Wolf-Rüdiger Scheible; Rosa Morcuende; Tomasz Czechowski; Christina Fritz; Daniel Osuna; Natalia Palacios-Rojas; Dana Schindelasch; Oliver Thimm; Michael K Udvardi; Mark Stitt
Journal:  Plant Physiol       Date:  2004-09       Impact factor: 8.340

9.  The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community.

Authors:  Seung Yon Rhee; William Beavis; Tanya Z Berardini; Guanghong Chen; David Dixon; Aisling Doyle; Margarita Garcia-Hernandez; Eva Huala; Gabriel Lander; Mary Montoya; Neil Miller; Lukas A Mueller; Suparna Mundodi; Leonore Reiser; Julie Tacklind; Dan C Weems; Yihe Wu; Iris Xu; Daniel Yoo; Jungwon Yoon; Peifen Zhang
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

10.  MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes.

Authors:  Oliver Thimm; Oliver Bläsing; Yves Gibon; Axel Nagel; Svenja Meyer; Peter Krüger; Joachim Selbig; Lukas A Müller; Seung Y Rhee; Mark Stitt
Journal:  Plant J       Date:  2004-03       Impact factor: 6.417
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  257 in total

1.  Laser microdissection unravels cell-type-specific transcription in arbuscular mycorrhizal roots, including CAAT-box transcription factor gene expression correlating with fungal contact and spread.

Authors:  Claudia Hogekamp; Damaris Arndt; Patrícia A Pereira; Jörg D Becker; Natalija Hohnjec; Helge Küster
Journal:  Plant Physiol       Date:  2011-10-27       Impact factor: 8.340

2.  Transcriptomic resilience to global warming in the seagrass Zostera marina, a marine foundation species.

Authors:  Susanne U Franssen; Jenny Gu; Nina Bergmann; Gidon Winters; Ulrich C Klostermeier; Philip Rosenstiel; Erich Bornberg-Bauer; Thorsten B H Reusch
Journal:  Proc Natl Acad Sci U S A       Date:  2011-11-14       Impact factor: 11.205

3.  PAMP (pathogen-associated molecular pattern)-induced changes in plasma membrane compartmentalization reveal novel components of plant immunity.

Authors:  Nana F Keinath; Sylwia Kierszniowska; Justine Lorek; Gildas Bourdais; Sharon A Kessler; Hiroko Shimosato-Asano; Ueli Grossniklaus; Waltraud X Schulze; Silke Robatzek; Ralph Panstruga
Journal:  J Biol Chem       Date:  2010-09-15       Impact factor: 5.157

4.  Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function.

Authors:  Takayuki Tohge; Alisdair R Fernie
Journal:  Nat Protoc       Date:  2010-06-10       Impact factor: 13.491

5.  Mutations in the Arabidopsis homolog of LST8/GβL, a partner of the target of Rapamycin kinase, impair plant growth, flowering, and metabolic adaptation to long days.

Authors:  Manon Moreau; Marianne Azzopardi; Gilles Clément; Thomas Dobrenel; Chloé Marchive; Charlotte Renne; Marie-Laure Martin-Magniette; Ludivine Taconnat; Jean-Pierre Renou; Christophe Robaglia; Christian Meyer
Journal:  Plant Cell       Date:  2012-02-03       Impact factor: 11.277

6.  Mapping metabolic and transcript temporal switches during germination in rice highlights specific transcription factors and the role of RNA instability in the germination process.

Authors:  Katharine A Howell; Reena Narsai; Adam Carroll; Aneta Ivanova; Marc Lohse; Björn Usadel; A Harvey Millar; James Whelan
Journal:  Plant Physiol       Date:  2008-12-12       Impact factor: 8.340

7.  Integrated transcript and metabolite profiling reveals coordination between biomass size and nitrogen metabolism in Arabidopsis F1 hybrids.

Authors:  Naoya Sugi; Quynh Thi Ngoc Le; Makoto Kobayashi; Miyako Kusano; Hiroshi Shiba
Journal:  Plant Biotechnol (Tokyo)       Date:  2021-03-25       Impact factor: 1.133

8.  Arabidopsis DPB3-1, a DREB2A interactor, specifically enhances heat stress-induced gene expression by forming a heat stress-specific transcriptional complex with NF-Y subunits.

Authors:  Hikaru Sato; Junya Mizoi; Hidenori Tanaka; Kyonosin Maruyama; Feng Qin; Yuriko Osakabe; Kyoko Morimoto; Teppei Ohori; Kazuya Kusakabe; Maika Nagata; Kazuo Shinozaki; Kazuko Yamaguchi-Shinozaki
Journal:  Plant Cell       Date:  2014-12-09       Impact factor: 11.277

9.  Additional amphivasal bundles in pedicel pith exacerbate central fruit dominance and induce self-thinning of lateral fruitlets in apple.

Authors:  Jean-Marc Celton; Emmanuelle Dheilly; Marie-Charlotte Guillou; Fabienne Simonneau; Marjorie Juchaux; Evelyne Costes; François Laurens; Jean-Pierre Renou
Journal:  Plant Physiol       Date:  2014-02-18       Impact factor: 8.340

10.  Conserved transcriptional regulatory programs underlying rice and barley germination.

Authors:  Li Lin; Shulan Tian; Shawn Kaeppler; Zongrang Liu; Yong-Qiang Charles An
Journal:  PLoS One       Date:  2014-02-18       Impact factor: 3.240
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