TITLE

Transcriptome analysis by GeneTrail revealed regulation of functional categories in response to alterations of iron homeostasis in Arabidopsis thaliana

AUTHOR(S)
Schuler, Mara; Keller, Andreas; Backes, Christina; Philippar, Katrin; Lenhof, Hans-Peter; Bauer, Petra
PUB. DATE
January 2011
SOURCE
BMC Plant Biology;2011, Vol. 11 Issue 1, p87
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: High-throughput technologies have opened new avenues to study biological processes and pathways. The interpretation of the immense amount of data sets generated nowadays needs to be facilitated in order to enable biologists to identify complex gene networks and functional pathways. To cope with this task multiple computer-based programs have been developed. GeneTrail is a freely available online tool that screens comparative transcriptomic data for differentially regulated functional categories and biological pathways extracted from common data bases like KEGG, Gene Ontology (GO), TRANSPATH and TRANSFAC. Additionally, GeneTrail offers a feature that allows screening of individually defined biological categories that are relevant for the respective research topic. Results: We have set up GeneTrail for the use of Arabidopsis thaliana. To test the functionality of this tool for plant analysis, we generated transcriptome data of root and leaf responses to Fe deficiency and the Arabidopsis metal homeostasis mutant nas4x-1. We performed Gene Set Enrichment Analysis (GSEA) with eight meaningful pairwise comparisons of transcriptome data sets. We were able to uncover several functional pathways including metal homeostasis that were affected in our experimental situations. Representation of the differentially regulated functional categories in Venn diagrams uncovered regulatory networks at the level of whole functional pathways. Over-Representation Analysis (ORA) of differentially regulated genes identified in pairwise comparisons revealed specific functional plant physiological categories as major targets upon Fe deficiency and in nas4x-1. Conclusion: Here, we obtained supporting evidence, that the nas4x-1 mutant was defective in metal homeostasis. It was confirmed that nas4x-1 showed Fe deficiency in roots and signs of Fe deficiency and Fe sufficiency in leaves. Besides metal homeostasis, biotic stress, root carbohydrate, leaf photosystem and specific cell biological categories were discovered as main targets for regulated changes in response to - Fe and nas4x-1. Among 258 differentially expressed genes in response to - Fe and nas4x-1 five functional categories were enriched covering metal homeostasis, redox regulation, cell division and histone acetylation. We proved that GeneTrail offers a flexible and user-adapted way to identify functional categories in large-scale plant transcriptome data sets. The distinguished feature that allowed analysis of individually assembled functional categories facilitated the study of the Arabidopsis thaliana transcriptome.
ACCESSION #
62641701

 

Related Articles

  • The transcriptome of Arabidopsis thaliana during systemic acquired resistance. Maleck, Klaus; Levine, Aaron; Eulgem, Thomas; Morgan, Allen; Schmid, Jürg; Lawton, Kay A.; Dangl, Jeffery L.; Dietrich, Robert A. // Nature Genetics;Dec2000, Vol. 26 Issue 4, p403 

    Infected plants undergo transcriptional reprogramming during initiation of both local defence and systemic acquired resistance (SAR). We monitored gene-expression changes in Arabidopsis thaliana under 14 different SAR-inducing or SAR-repressing conditions using a DNA microarray representing...

  • Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana. Kusano, Miyako; Fukushima, Atsushi; Arita, Masanori; Jonsson, Pär; Moritz, Thomas; Kobayashi, Makoto; Hayashi, Naomi; Tohge, Takayuki; Saito, Kazuki // BMC Systems Biology;2007, Vol. 1, p53 

    Background: Metabolites are not only the catalytic products of enzymatic reactions but also the active regulators or the ultimate phenotype of metabolic homeostasis in highly complex cellular processes. The modes of regulation at the metabolome level can be revealed by metabolic networks. We...

  • Arabidopsis PAI gene arrangements, cytosine methylation and expression. Melquist, Stacey; Luff, Bradley // Genetics;Sep99, Vol. 153 Issue 1, p401 

    Studies mechanisms of PAI gene duplication and relationship between gene arrangement and methylation of Arabidopsis thaliana. Identification of PAI genes at Wassilewskija and Columbia ecotypes; Correlation between gene structure and onset of cytosine methylation; Genetic tools in understanding...

  • Gene expression: Mapping QTLs for genomic stochastic noise. Casci, Tanita // Nature Reviews Genetics;Nov2011, Vol. 12 Issue 11, p742 

    The article discusses research conducted by J. M. Jimenez-Gomez and colleagues on genomic analysis of quantitative trait locus (QTL) and genes changing natural variation in stochastic noise in Arabidopsis thaliana.

  • Chromosome synapsis in Arabidopsis: analysis of the transverse filament protein ZYP1 reveals novel functions for the synaptonemal complex. Osman, Kim; Sanchez-Moran, Eugenio; Higgins, James D.; Jones, Gareth H.; Franklin, F. Chris H. // Chromosoma;Jun2006, Vol. 115 Issue 3, p212 

    With respect to history, plants have provided an ideal system for cytogenetical analysis of the synaptonemal complex (SC). However, until recently, the identification of the genes that encode the SC in plants has proved elusive. In recent years, Arabidopsis thaliana was developed as a model...

  • Gene coexpression clusters and putative regulatory elements underlying seed storage reserve accumulation in Arabidopsis. Peng, Fred Y.; Weselake, Randall J. // BMC Genomics;2011, Vol. 12 Issue 1, p286 

    Background: In Arabidopsis, a large number of genes involved in the accumulation of seed storage reserves during seed development have been characterized, but the relationship of gene expression and regulation underlying this physiological process remains poorly understood. A more holistic view...

  • TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation. Bernard, Virginie; Brunaud, Véronique; Lecharny, Alain // BMC Genomics;2010, Vol. 11, p166 

    Background: The TATA-box and TATA-variants are regulatory elements involved in the formation of a transcription initiation complex. Both have been conserved throughout evolution in a restricted region close to the Transcription Start Site (TSS). However, less than half of the genes in model...

  • Latest news about the sulfurtransferase protein family of higher plants. Papenbrock, Jutta; Guretzki, Sebastian; Henne, Melina // Amino Acids;Jun2011, Vol. 41 Issue 1, p43 

    Sulfurtransferases/rhodaneses (Str) comprise a group of enzymes widely distributed in all phyla which catalyze in vitro the transfer of a sulfur atom from suitable sulfur donors to nucleophilic sulfur acceptors. The best characterized Str is bovine rhodanese (EC 2.8.1.1) which catalyses in vitro...

  • DELLA-Induced Early Transcriptional Changes during Etiolated Development in Arabidopsis thaliana. Gallego-Bartolome, Javier; Alabadí, David; Blázquez, Miguel A. // PLoS ONE;2011, Vol. 6 Issue 8, p1 

    The hormones gibberellins (GAs) control a wide variety of processes in plants, including stress and developmental responses. This task largely relies on the activity of the DELLA proteins, nuclear-localized transcriptional regulators that do not seem to have DNA binding capacity. The...

Share

Read the Article

Courtesy of VIRGINIA BEACH PUBLIC LIBRARY AND SYSTEM

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics