ArticleBMC bioinformatics2011
Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 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
10 citing papers in PubMed.
- Transkingdom Network Analysis (TkNA): a systems framework for inferring causal factors underlying host-microbiota and other multi-omic interactions.bioRxiv : the preprint server for biology · 2023Article
- Reference Module-Based Analysis of Ovarian Cancer Transcriptome Identifies Important Modules and Potential Drugs.Biochemical genetics · 2022Article
- Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host-Microbiota Interactions.Methods in molecular biology (Clifton, N.J.) · 2018Article
- Unexpected links reflect the noise in networks.Biology direct · 2016Article
- Review
- Differentially correlated genes in co-expression networks control phenotype transitions.F1000Research · 2016Article
- Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks.Gut · 2015Article
- Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists.Bioinformatics and biology insights · 2015Review
- Construction and comparison of gene co-expression networks shows complex plant immune responses.PeerJ · 2014Article
- Crosstalk between B lymphocytes, microbiota and the intestinal epithelium governs immunity versus metabolism in the gut.Nature medicine · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
backgroundDAPfinder and DAPview are novel BRB-ArrayTools plug-ins to construct gene coexpression networks and identify significant differences in pairwise gene-gene coexpression between two phenotypes.
resultsEach significant difference in gene-gene association represents a Differentially Associated Pair (DAP). Our tools include several choices of filtering methods, gene-gene association metrics, statistical testing methods and multiple comparison adjustments. Network results are easily displayed in Cytoscape. Analyses of glioma experiments and microarray simulations demonstrate the utility of these tools.
conclusionsDAPfinder is a new friendly-user tool for reconstruction and comparison of biological networks.
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.