ArticleNucleic acids research2011
Unraveling networks of co-regulated genes on the sole basis of genome sequences.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 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
25 citing papers in PubMed, 36 citations in OpenAlex.
- Inferring fungal cis-regulatory networks from genome sequences via unsupervised and interpretable representation learning.Genetics · 2026Article
- Integrative transcriptomic and genomic insights into diabetic kidney disease: evidence from multi-omics analysis and experimental validation.Renal failure · 2025Article
- Human Sterols Are Overproduced, Stored and Excreted in Yeasts.International journal of molecular sciences · 2024Article
- RhizoBindingSites v2.0 Is a Bioinformatic Database of DNA Motifs Potentially Involved in Transcriptional Regulation Deduced From Their Genomic Sites.Bioinformatics and biology insights · 2024Article
- RSAT 2022: regulatory sequence analysis tools.Nucleic acids research · 2022Article
- Increased biosynthesis of acetyl-CoA in the yeast Saccharomyces cerevisiae by overexpression of a deregulated pantothenate kinase gene and engineering of the coenzyme A biosynthetic pathway.Applied microbiology and biotechnology · 2021Article
- RhizoBindingSites, a Database of DNA-Binding Motifs in Nitrogen-Fixing Bacteria Inferred Using a Footprint Discovery Approach.Frontiers in microbiology · 2020Article
- Limits to a classic paradigm: most transcription factors in E. coli regulate genes involved in multiple biological processes.Nucleic acids research · 2019Article
- RSAT 2018: regulatory sequence analysis tools 20th anniversary.Nucleic acids research · 2018Article
- Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses.Scientific reports · 2016Article
- An overview of bioinformatics methods for modeling biological pathways in yeast.Briefings in functional genomics · 2016Review
- Following the Footsteps of Chlamydial Gene Regulation.Molecular biology and evolution · 2015Article
- Classifying pairs with trees for supervised biological network inference.Molecular bioSystems · 2015Article
- RSAT 2015: Regulatory Sequence Analysis Tools.Nucleic acids research · 2015Article
- Article
- Evolutionary genomics of Borrelia burgdorferi sensu lato: findings, hypotheses, and the rise of hybrids.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2014Review
- Converting the yeast arginine can1 permease to a lysine permease.The Journal of biological chemistry · 2014Article
- Promoter type influences transcriptional topography by targeting genes to distinct nucleoplasmic sites.Journal of cell science · 2013Article
- Yeast gene CMR1/YDL156W is consistently co-expressed with genes participating in DNA-metabolic processes in a variety of stringent clustering experiments.Journal of the Royal Society, Interface · 2013Article
- A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks.BMC genomics · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With the growing number of available microbial genome sequences, regulatory signals can now be revealed as conserved motifs in promoters of orthologous genes (phylogenetic footprints). A next challenge is to unravel genome-scale regulatory networks. Using as sole input genome sequences, we predicted cis-regulatory elements for each gene of the yeast Saccharomyces cerevisiae by discovering over-represented motifs in the promoters of their orthologs in 19 Saccharomycetes species. We then linked all genes displaying similar motifs in their promoter regions and inferred a co-regulation network including 56,919 links between 3171 genes. Comparison with annotated regulons highlights the high predictive value of the method: a majority of the top-scoring predictions correspond to already known co-regulations. We also show that this inferred network is as accurate as a co-expression network built from hundreds of transcriptome microarray experiments. Furthermore, we experimentally validated 14 among 16 new functional links between orphan genes and known regulons. This approach can be readily applied to unravel gene regulatory networks from hundreds of microbial genomes for which no other information is available except the sequence. Long-term benefits can easily be perceived when considering the exponential increase of new genome sequences.
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.