Abstract
BackgroundHigh-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.ResultsWe 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.ConclusionHere, 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.
Highlights
High-throughput technologies have opened new avenues to study biological processes and pathways
Adaptation of GeneTrail for the use of Arabidopsis thaliana In order to utilize GeneTrail for Arabidopsis thaliana, we extended GeneTrail such that, besides our supported default identifiers, Arabidopsis-specific identifiers (AGI gene codes from TAIR, transcript IDs from the ATH1 microarray) could be used
Experimental design In order to evaluate the GeneTrail tool for plant-specific analysis, we generated and used transcriptome data sets of nas4x-1 mutants compared to wild type plants grown under + and - Fe supply (Additional file 1, Figure S1)
Summary
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. For storing the vast amount of measured expression profiles, many freely available repositories have been developed, including the Gene Expression Omnibus (GEO) [1] or Stanford Microarray Database (SMD) [2]. It has become a routine habit for many researchers to consult published microarray expression data for theoretical modeling of regulatory networks involving their favourite genes prior to experimentation [3,4]. Specialized software tools like Genevestigator [4], the Botany Array Resource (BAR) [5], MapMan [6], ATTED-II [7,8] or VirtualPlant [9] for example have been developed to answer such complex questions in plants
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