ArticleBMC genomics2009
BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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
14 citing papers in PubMed, 25 citations in OpenAlex.
- On the Consistency between Gene Expression and the Gene Regulatory Network ofNetwork and systems medicine · 2021Article
- E. coli gene regulatory networks are inconsistent with gene expression data.Nucleic acids research · 2019Article
- Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies.BMC bioinformatics · 2015Article
- CytoASP: a Cytoscape app for qualitative consistency reasoning, prediction and repair in biological networks.BMC systems biology · 2015Article
- A model for gene deregulation detection using expression data.BMC systems biology · 2015Article
- Network reconstruction based on proteomic data and prior knowledge of protein connectivity using graph theory.PloS one · 2015Article
- Using a large-scale knowledge database on reactions and regulations to propose key upstream regulators of various sets of molecules participating in cell metabolism.BMC systems biology · 2014Article
- Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks.Cell communication and signaling : CCS · 2013Article
- Detecting and removing inconsistencies between experimental data and signaling network topologies using integer linear programming on interaction graphs.PLoS computational biology · 2013Article
- A travel guide to Cytoscape plugins.Nature methods · 2012Article
- Regulatory network operations in the Pathway Tools software.BMC bioinformatics · 2012Article
- Using answer set programming to integrate RNA expression with signalling pathway information to infer how mutations affect ageing.PloS one · 2012Article
- Localizing potentially active post-transcriptional regulations in the Ewing's sarcoma gene regulatory network.BMC systems biology · 2010Article
- The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms.Briefings in bioinformatics · 2010Review
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 at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe method most commonly used to analyse regulatory networks is the in silico simulation of fluctuations in network components when a network is perturbed. Nevertheless, confronting experimental data with a regulatory network entails many difficulties, such as the incomplete state-of-art of regulatory knowledge, the large-scale of regulatory models, heterogeneity in the available data and the sometimes violated assumption that mRNA expression is correlated to protein activity.
resultsWe have developed a plugin for the Cytoscape environment, designed to facilitate automatic reasoning on regulatory networks. The BioQuali plugin enhances user-friendly conversions of regulatory networks (including reference databases) into signed directed graphs. BioQuali performs automatic global reasoning in order to decide which products in the network need to be up or down regulated (active or inactive) to globally explain experimental data. It highlights incomplete regions in the network, meaning that gene expression levels do not globally correlate with existing knowledge on regulation carried by the topology of the network.
conclusionThe BioQuali plugin facilitates in silico exploration of large-scale regulatory networks by combining the user-friendly tools of the Cytoscape environment with high-performance automatic reasoning algorithms. As a main feature, the plugin guides further investigation regarding a system by highlighting regions in the network that are not accurately described and merit specific study.
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.