ArticleBMC bioinformatics2010
NeatMap--non-clustering heat map alternatives in R.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers, 2 of them syntheses that pooled it.
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
44 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Induction of a common microglia gene expression signature by aging and neurodegenerative conditions: a co-expression meta-analysis.Acta neuropathologica communications · 2015Pooled it
- Background gene expression networks significantly enhance drug response prediction by transcriptional profiling.The pharmacogenomics journal · 2012Pooled it
- Interplay between disinfection and the enigmatic diplomonad parasite Spironucleus salmonicida in Atlantic salmon.Scientific reports · 2026Article
- Characterization of bacterial communities of ewe's vaginal tract and its potential impact on reproductive efficiency.Animal microbiome · 2025Article
- Bacterial communities of fungus-growing ant queens are species-specific and suggest vertical transmission.PloS one · 2025Article
- eDNA metabarcoding reveals biodiversity and depth stratification patterns of dinoflagellate assemblages within the epipelagic zone of the western Coral Sea.BMC ecology and evolution · 2024Article
- Degenerative Cervical Myelopathy induces sex-specific dysbiosis in mice.Frontiers in microbiology · 2023Article
- The Rhizobial Microbiome from the Tropical Savannah Zones in Northern Côte d'Ivoire.Microorganisms · 2021Article
- FreshwatermSystems · 2021Article
- The Composition of the Microbiota in the Full-Term Fetal Gut and Amniotic Fluid: A Bovine Cesarean Section Study.Frontiers in microbiology · 2021Article
- Three Candidate Probiotic Strains Impact Gut Microbiota and Induce Anergy in Mice with Cow's Milk Allergy.Applied and environmental microbiology · 2020Article
- Identifying an Eight-Gene Signature to Optimize Overall Survival Prediction of Esophageal Adenocarcinoma Using Bioinformatics Analysis of ceRNA Network.OncoTargets and therapy · 2020Article
- Article
- Microbial communities of the house fly Musca domestica vary with geographical location and habitat.Microbiome · 2019Article
- Article
- Emerging from the ice-fungal communities are diverse and dynamic in earliest soil developmental stages of a receding glacier.Environmental microbiology · 2019Article
- Bayesian Unidimensional Scaling for visualizing uncertainty in high dimensional datasets with latent ordering of observations.BMC bioinformatics · 2017Article
- Type 1 Diabetes: Urinary Proteomics and Protein Network Analysis Support Perturbation of Lysosomal Function.Theranostics · 2017Article
- Molecular mechanisms and the conflict between courtship and aggression in three-spined sticklebacks.Molecular ecology · 2016Article
- From Mouth to Model: CombiningFrontiers in microbiology · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe clustered heat map is the most popular means of visualizing genomic data. It compactly displays a large amount of data in an intuitive format that facilitates the detection of hidden structures and relations in the data. However, it is hampered by its use of cluster analysis which does not always respect the intrinsic relations in the data, often requiring non-standardized reordering of rows/columns to be performed post-clustering. This sometimes leads to uninformative and/or misleading conclusions. Often it is more informative to use dimension-reduction algorithms (such as Principal Component Analysis and Multi-Dimensional Scaling) which respect the topology inherent in the data. Yet, despite their proven utility in the analysis of biological data, they are not as widely used. This is at least partially due to the lack of user-friendly visualization methods with the visceral impact of the heat map.
resultsNeatMap is an R package designed to meet this need. NeatMap offers a variety of novel plots (in 2 and 3 dimensions) to be used in conjunction with these dimension-reduction techniques. Like the heat map, but unlike traditional displays of such results, it allows the entire dataset to be displayed while visualizing relations between elements. It also allows superimposition of cluster analysis results for mutual validation. NeatMap is shown to be more informative than the traditional heat map with the help of two well-known microarray datasets.
conclusionsNeatMap thus preserves many of the strengths of the clustered heat map while addressing some of its deficiencies. It is hoped that NeatMap will spur the adoption of non-clustering dimension-reduction algorithms.
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.