ArticleNature protocols2011
Comprehensive cluster analysis with Transitivity Clustering.
Article in Nature protocols, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 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
23 citing papers in PubMed.
- Guiding biomedical clustering with ClustEval.Nature protocols · 2018Article
- Novel 9-cis/all-trans β-carotene isomerases from plastidic oil bodies in Dunaliella bardawil catalyze the conversion of all-trans to 9-cis β-carotene.Plant cell reports · 2017Article
- The CopC Family: Structural and Bioinformatic Insights into a Diverse Group of Periplasmic Copper Binding Proteins.Biochemistry · 2016Article
- Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes.PLoS computational biology · 2016Article
- Comparing the performance of biomedical clustering methods.Nature methods · 2015Article
- Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity.Protein science : a publication of the Protein Society · 2015Article
- A multistage mathematical approach to automated clustering of high-dimensional noisy data.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Diversity of the metal-transporting P1B-type ATPases.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2014Article
- The path to triacylglyceride obesity in the sta6 strain of Chlamydomonas reinhardtii.Eukaryotic cell · 2014Article
- Bi-Force: large-scale bicluster editing and its application to gene expression data biclustering.Nucleic acids research · 2014Article
- BiCluE - Exact and heuristic algorithms for weighted bi-cluster editing of biomedical data.BMC proceedings · 2013Article
- CoPAP: Coevolution of presence-absence patterns.Nucleic acids research · 2013Article
- Ecogenomic perspectives on domains of unknown function: correlation-based exploration of marine metagenomes.PloS one · 2013Article
- Pythoscape: a framework for generation of large protein similarity networks.Bioinformatics (Oxford, England) · 2012Article
- A travel guide to Cytoscape plugins.Nature methods · 2012Article
- Uncovering the co-evolutionary network among prokaryotic genes.Bioinformatics (Oxford, England) · 2012Article
- The ins and outs of algal metal transport.Biochimica et biophysica acta · 2012Review
- DEFOG: discrete enrichment of functionally organized genes.Integrative biology : quantitative biosciences from nano to macro · 2012Article
- Fe sparing and Fe recycling contribute to increased superoxide dismutase capacity in iron-starved Chlamydomonas reinhardtii.The Plant cell · 2012Article
- Topological analysis and interactive visualization of biological networks and protein structures.Nature protocols · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Transitivity Clustering is a method for the partitioning of biological data into groups of similar objects, such as genes, for instance. It provides integrated access to various functions addressing each step of a typical cluster analysis. To facilitate this, Transitivity Clustering is accessible online and offers three user-friendly interfaces: a powerful stand-alone version, a web interface, and a collection of Cytoscape plug-ins. In this paper, we describe three major workflows: (i) protein (super)family detection with Cytoscape, (ii) protein homology detection with incomplete gold standards and (iii) clustering of gene expression data. This protocol guides the user through the most important features of Transitivity Clustering and takes ∼1 h to complete.
Indexed as
Identifiers
21372810What 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.