SynthesisNucleic acids research2019
Updating genome annotation for the microbial cell factory Aspergillus niger using gene co-expression networks.
Synthesis in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 83 citations in OpenAlex.
- A network-based model of Aspergillus fumigatus elucidates regulators of development and defensive natural products of an opportunistic pathogen.Nucleic acids research · 2026Article
- The multipurpose cell factory Aspergillus niger can be engineered to produce hydroxylated collagen.Biotechnology for biofuels and bioproducts · 2025Article
- Comprehensive phenotypic analysis of multiple gene deletions of α-glucan synthase and Crh-transglycosylase gene families inCell surface (Amsterdam, Netherlands) · 2025Article
- Uncovering the transcriptional landscape of Fomes fomentarius during fungal-based material production through gene co-expression network analysis.Fungal biology and biotechnology · 2025Article
- Optimization of response surface methodology for the extraction of isoliquiritigenin fromFrontiers in pharmacology · 2025Article
- Enhanced extracellular production of Coprinopsis cinerea laccase Lcc9 in Aspergillus niger by gene expression cassette and bioprocess optimization.BMC biotechnology · 2024Article
- What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species.Genetics · 2024Article
- Breaking down barriers: comprehensive functional analysis of the Aspergillus niger chitin synthase repertoire.Fungal biology and biotechnology · 2024Article
- CryptoCEN: A Co-Expression Network for Cryptococcus neoformans reveals novel proteins involved in DNA damage repair.PLoS genetics · 2024Article
- The antifungal peptide AnAFP fromFrontiers in microbiology · 2024Article
- CryptoCEN: A Co-Expression Network forbioRxiv : the preprint server for biology · 2023Article
- Regression modelling of conditional morphogene expression links and quantifies the impact of growth rate, fitness and macromorphology with protein secretion in Aspergillus niger.Biotechnology for biofuels and bioproducts · 2023Article
- Insights into the genomic evolution and the alkali tolerance mechanisms ofMicrobial genomics · 2023Article
- Comprehensively dissecting the hub regulation of PkaC on high-productivity and pellet macromorphology in citric acid producing Aspergillus niger.Microbial biotechnology · 2022Article
- Evaluation ofJournal of fungi (Basel, Switzerland) · 2022Article
- Natural Variation and the Role of ZnMicroorganisms · 2022Article
- The importance of complete and high-quality genome sequences inFrontiers in fungal biology · 2022Article
- Machine learning prediction of novel pectinolytic enzymes inMicrobial genomics · 2021Article
- Leveraging machine learning essentiality predictions and chemogenomic interactions to identify antifungal targets.Nature communications · 2021Article
- Beyond the Biosynthetic Gene Cluster Paradigm: Genome-Wide Coexpression Networks Connect Clustered and Unclustered Transcription Factors to Secondary Metabolic Pathways.Microbiology spectrum · 2021Article
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Authors and funding
11 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A significant challenge in our understanding of biological systems is the high number of genes with unknown function in many genomes. The fungal genus Aspergillus contains important pathogens of humans, model organisms, and microbial cell factories. Aspergillus niger is used to produce organic acids, proteins, and is a promising source of new bioactive secondary metabolites. Out of the 14,165 open reading frames predicted in the A. niger genome only 2% have been experimentally verified and over 6,000 are hypothetical. Here, we show that gene co-expression network analysis can be used to overcome this limitation. A meta-analysis of 155 transcriptomics experiments generated co-expression networks for 9,579 genes (∼65%) of the A. niger genome. By populating this dataset with over 1,200 gene functional experiments from the genus Aspergillus and performing gene ontology enrichment, we could infer biological processes for 9,263 of A. niger genes, including 2,970 hypothetical genes. Experimental validation of selected co-expression sub-networks uncovered four transcription factors involved in secondary metabolite synthesis, which were used to activate production of multiple natural products. This study constitutes a significant step towards systems-level understanding of A. niger, and the datasets can be used to fuel discoveries of model systems, fungal pathogens, and biotechnology.
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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 Socratic graph.