ArticleBMC bioinformatics2012
Regulatory network operations in the Pathway Tools software.
Article in BMC bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 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
7 citing papers in PubMed.
- A spermidine riboswitch class in bacteria exploits a close variant of an aptamer for the enzyme cofactor S-adenosylmethionine.Cell reports · 2023Article
- Pathway Tools Visualization of Organism-Scale Metabolic Networks.Metabolites · 2021Article
- Untargeted metabolomics studies employing NMR and LC-MS reveal metabolic coupling betweenMetabolomics : Official journal of the Metabolomic Society · 2015Article
- Article
- A computational platform to maintain and migrate manual functional annotations for BioCyc databases.BMC systems biology · 2014Article
- Clinical proteomic biomarkers: relevant issues on study design & technical considerations in biomarker development.Clinical and translational medicine · 2014Article
- The Genome Database for Rosaceae (GDR): year 10 update.Nucleic acids research · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
backgroundBiologists are elucidating complex collections of genetic regulatory data for multiple organisms. Software is needed for such regulatory network data.
resultsThe Pathway Tools software supports storage and manipulation of regulatory information through a variety of strategies. The Pathway Tools regulation ontology captures transcriptional and translational regulation, substrate-level regulation of enzyme activity, post-translational modifications, and regulatory pathways. Regulatory visualizations include a novel diagram that summarizes all regulatory influences on a gene; a transcription-unit diagram, and an interactive visualization of a full transcriptional regulatory network that can be painted with gene expression data to probe correlations between gene expression and regulatory mechanisms. We introduce a novel type of enrichment analysis that asks whether a gene-expression dataset is over-represented for known regulators. We present algorithms for ranking the degree of regulatory influence of genes, and for computing the net positive and negative regulatory influences on a gene.
conclusionsPathway Tools provides a comprehensive environment for manipulating molecular regulatory interactions that integrates regulatory data with an organism's genome and metabolic network. Curated collections of regulatory data authored using Pathway Tools are available for Escherichia coli, Bacillus subtilis, and Shewanella oneidensis.
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.