ArticleGenome biology2006
Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans.
Article in Genome biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed, 63 citations in OpenAlex.
- Are Physicochemical Properties Shaping the Allergenic Potency of Plant Allergens?Clinical reviews in allergy & immunology · 2022Review
- The pentose phosphate pathway in industrially relevant fungi: crucial insights for bioprocessing.Applied microbiology and biotechnology · 2021Review
- Predicted Glycerol 3-Phosphate Dehydrogenase Homologs and the Glycerol Kinase GlcA Coordinately Adapt to Various Carbon Sources and Osmotic Stress inG3 (Bethesda, Md.) · 2018Article
- RNAseq analysis of Aspergillus fumigatus in blood reveals a just wait and see resting stage behavior.BMC genomics · 2015Article
- MIRA: mutual information-based reporter algorithm for metabolic networks.Bioinformatics (Oxford, England) · 2014Article
- An online system for metabolic network analysis.Database : the journal of biological databases and curation · 2014Article
- Trancriptional landscape of Aspergillus niger at breaking of conidial dormancy revealed by RNA-sequencing.BMC genomics · 2013Article
- The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum.PLoS computational biology · 2013Article
- Article
- Cytosolic NADPH balancing in Penicillium chrysogenum cultivated on mixtures of glucose and ethanol.Applied microbiology and biotechnology · 2011Article
- ATP-citrate lyase is required for production of cytosolic acetyl coenzyme A and development in Aspergillus nidulans.Eukaryotic cell · 2010Article
- Transcriptional regulation of gene expression clusters in motor neurons following spinal cord injury.BMC genomics · 2010Article
- Metabolic network topology reveals transcriptional regulatory signatures of type 2 diabetes.PLoS computational biology · 2010Article
- Metabolic and developmental effects resulting from deletion of the citA gene encoding citrate synthase in Aspergillus nidulans.Eukaryotic cell · 2010Article
- Uncovering transcriptional regulation of glycerol metabolism in Aspergilli through genome-wide gene expression data analysis.Molecular genetics and genomics : MGG · 2009Article
- Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content.Journal of bacteriology · 2009Review
- Studies of the production of fungal polyketides in Aspergillus nidulans by using systems biology tools.Applied and environmental microbiology · 2009Article
- Applications of genome-scale metabolic reconstructions.Molecular systems biology · 2009Review
- Context-specific metabolic networks are consistent with experiments.PLoS computational biology · 2008Article
- Analysis of Aspergillus nidulans metabolism at the genome-scale.BMC genomics · 2008Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAspergillus nidulans (the asexual form of Emericella nidulans) is a model organism for aspergilli, which are an important group of filamentous fungi that encompasses human and plant pathogens as well as industrial cell factories. Aspergilli have a highly diversified metabolism and, because of their medical, agricultural and biotechnological importance, it would be valuable to have an understanding of how their metabolism is regulated. We therefore conducted a genome-wide transcription analysis of A. nidulans grown on three different carbon sources (glucose, glycerol, and ethanol) with the objective of identifying global regulatory structures. Furthermore, we reconstructed the complete metabolic network of this organism, which resulted in linking 666 genes to metabolic functions, as well as assigning metabolic roles to 472 genes that were previously uncharacterized.
resultsThrough combination of the reconstructed metabolic network and the transcription data, we identified subnetwork structures that pointed to coordinated regulation of genes that are involved in many different parts of the metabolism. Thus, for a shift from glucose to ethanol, we identified coordinated regulation of the complete pathway for oxidation of ethanol, as well as upregulation of gluconeogenesis and downregulation of glycolysis and the pentose phosphate pathway. Furthermore, on change in carbon source from glucose to ethanol, the cells shift from using the pentose phosphate pathway as the major source of NADPH (nicotinamide adenine dinucleotide phosphatase, reduced form) for biosynthesis to use of the malic enzyme.
conclusionOur analysis indicates that some of the genes are regulated by common transcription factors, making it possible to establish new putative links between known transcription factors and genes through clustering.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.