ArticleNature protocols2009
Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet.
Article in Nature protocols, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 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
13 citing papers in PubMed.
- Molecular networks in Network Medicine: Development and applications.Wiley interdisciplinary reviews. Systems biology and medicine · 2020Review
- CMRegNet-An interspecies reference database for corynebacterial and mycobacterial regulatory networks.BMC genomics · 2015Article
- Corynebacterium glutamicum promoters: a practical approach.Microbial biotechnology · 2013Review
- Arabitol metabolism of Corynebacterium glutamicum and its regulation by AtlR.Journal of bacteriology · 2012Article
- CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands.Nucleic acids research · 2012Article
- Complete genome sequence of Corynebacterium variabile DSM 44702 isolated from the surface of smear-ripened cheeses and insights into cheese ripening and flavor generation.BMC genomics · 2011Article
- A combined approach for comparative exoproteome analysis of Corynebacterium pseudotuberculosis.BMC microbiology · 2011Article
- Article
- Quinone-dependent D-lactate dehydrogenase Dld (Cg1027) is essential for growth of Corynebacterium glutamicum on D-lactate.BMC microbiology · 2010Article
- On the power and limits of evolutionary conservation--unraveling bacterial gene regulatory networks.Nucleic acids research · 2010Review
- The Zur regulon of Corynebacterium glutamicum ATCC 13032.BMC genomics · 2010Article
- Mechanisms and evolution of control logic in prokaryotic transcriptional regulation.Microbiology and molecular biology reviews : MMBR · 2009Review
- MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations.Genome biology · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
CoryneRegNet is the reference database and analysis platform for corynebacterial gene regulatory networks. It provides web-based access to integrated data on gene regulatory interactions of corynebacteria relevant to human medicine and biotechnology, Escherichia coli and Mycobacterium tuberculosis. To facilitate the analysis and reconstruction of the corresponding networks, CoryneRegNet provides user-friendly interfaces for bioinformatics analysis and network visualization tools. This protocol describes four major workflows: (1) querying the regulatory network of a gene of interest, (2) prediction and interspecies transfer of gene regulatory interactions, (3) visualization and comparison of predicted or known networks and (4) integration of gene expression data analysis and visualization. This protocol guides the user through the most important features of CoryneRegNet and takes 45-60 min to complete.
Indexed as
Identifiers
19498379What 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.