ArticleBMC systems biology2009
Ranges of control in the transcriptional regulation of Escherichia coli.
Article in BMC systems biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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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.
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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.
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Who cites it
8 citing papers in PubMed, 18 citations in OpenAlex.
- Relationship between the Chromosome Structural Dynamics and Gene Expression-A Chicken and Egg Dilemma?Microorganisms · 2022Review
- Composition of Transcription Machinery and Its Crosstalk with Nucleoid-Associated Proteins and Global Transcription Factors.Biomolecules · 2021Review
- Chromosomal origin of replication coordinates logically distinct types of bacterial genetic regulation.NPJ systems biology and applications · 2020Article
- Coherent Domains of Transcription Coordinate Gene Expression During Bacterial Growth and Adaptation.Microorganisms · 2019Review
- Chromosomal organization of transcription: in a nutshell.Current genetics · 2018Review
- Effect of database drift on network topology and enrichment analyses: a case study for RegulonDB.Database : the journal of biological databases and curation · 2016Article
- Optimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation.BMC bioinformatics · 2015Article
- Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli.PLoS computational biology · 2010Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe positioning of genes in the genome is an important evolutionary degree of freedom for organizing gene regulation. Statistical properties of these distributions have been studied particularly in relation to the transcriptional regulatory network. The systematics of gene-gene distances then become important sources of information on the control, which different biological mechanisms exert on gene expression.
resultsHere we study a set of categories, which has to our knowledge not been analyzed before. We distinguish between genes that do not participate in the transcriptional regulatory network (i.e. that are according to current knowledge not producing transcription factors and do not possess binding sites for transcription factors in their regulatory region), and genes that via transcription factors either are regulated by or regulate other genes. We find that the two types of genes ("isolated" and "regulatory" genes) show a clear statistical repulsion and have different ranges of correlations. In particular we find that isolated genes have a preference for shorter intergenic distances.
conclusionsThese findings support previous evidence from gene expression patterns for two distinct logical types of control, namely digital control (i.e. network-based control mediated by dedicated transcription factors) and analog control (i.e. control based on genome structure and mediated by neighborhood on the genome).
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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.