ArticleBioinformatics (Oxford, England)2013
Network2Canvas: network visualization on a canvas with enrichment analysis.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 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
24 citing papers in PubMed.
- Gene Set Knowledge Discovery with Enrichr.Current protocols · 2021Article
- H4K20me3 methyltransferase SUV420H2 shapes the chromatin landscape of pluripotent embryonic stem cells.Development (Cambridge, England) · 2020Article
- BMAL1 coordinates energy metabolism and differentiation of pluripotent stem cells.Life science alliance · 2020Article
- Genomic Integrity Safeguards Self-Renewal in Embryonic Stem Cells.Cell reports · 2019Article
- Oncogenic role of SFRP2 in p53-mutant osteosarcoma development via autocrine and paracrine mechanism.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- H4K20me3 co-localizes with activating histone modifications at transcriptionally dynamic regions in embryonic stem cells.BMC genomics · 2018Article
- KDM5B decommissions the H3K4 methylation landscape of self-renewal genes during trophoblast stem cell differentiation.Biology open · 2018Article
- Pulmonary endothelial cell DNA methylation signature in pulmonary arterial hypertension.Oncotarget · 2017Article
- Comparative Analyses of Signature Genes in Acute Rejection and Operational Tolerance.Immune network · 2017Article
- Estrogen modulates mesenchyme-epidermis interactions in the adult nipple.Development (Cambridge, England) · 2017Article
- Revealing cancer subtypes with higher-order correlations applied to imaging and omics data.BMC medical genomics · 2017Article
- Kaposi's sarcoma-associated herpesvirus infection promotes differentiation and polarization of monocytes into tumor-associated macrophages.Cell cycle (Georgetown, Tex.) · 2017Article
- SMYD5 regulates H4K20me3-marked heterochromatin to safeguard ES cell self-renewal and prevent spurious differentiation.Epigenetics & chromatin · 2017Article
- Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration.Nature neuroscience · 2016Article
- Fetal liver hematopoietic stem cell niches associate with portal vessels.Science (New York, N.Y.) · 2016Article
- Publisher’s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction.Computational biology and chemistry · 2015Article
- Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets.Bioinformatics (Oxford, England) · 2014Article
- Article
- Lean Big Data integration in systems biology and systems pharmacology.Trends in pharmacological sciences · 2014Article
- LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures.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
5 authors.
Funding
Abstract
motivationNetworks are vital to computational systems biology research, but visualizing them is a challenge. For networks larger than ∼100 nodes and ∼200 links, ball-and-stick diagrams fail to convey much information. To address this, we developed Network2Canvas (N2C), a web application that provides an alternative way to view networks. N2C visualizes networks by placing nodes on a square toroidal canvas. The network nodes are clustered on the canvas using simulated annealing to maximize local connections where a node's brightness is made proportional to its local fitness. The interactive canvas is implemented in HyperText Markup Language (HTML)5 with the JavaScript library Data-Driven Documents (D3). We applied N2C to visualize 30 canvases made from human and mouse gene-set libraries and 6 canvases made from the Food and Drug Administration (FDA)-approved drug-set libraries. Given lists of genes or drugs, enriched terms are highlighted on the canvases, and their degree of clustering is computed. Because N2C produces visual patterns of enriched terms on canvases, a trained eye can detect signatures instantly. In summary, N2C provides a new flexible method to visualize large networks and can be used to perform and visualize gene-set and drug-set enrichment analyses. AVAILABILITY: N2C is freely available at http://www.maayanlab.net/N2C and is open source. CONTACT: avi.maayan@mssm.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.