Dataset Information

ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking.

ABSTRACT:

Unlabelled

Unsupervised class discovery is a highly useful technique in cancer research, where intrinsic groups sharing biological characteristics may exist but are unknown. The consensus clustering (CC) method provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset. ConsensusClusterPlus implements the CC method in R and extends it with new functionality and visualizations including item tracking, item-consensus and cluster-consensus plots. These new features provide users with detailed information that enable more specific decisions in unsupervised class discovery.

Availability

ConsensusClusterPlus is open source software, written in R, under GPL-2, and available through the Bioconductor project (http://www.bioconductor.org/).

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Wilkerson MD

PROVIDER: S-EPMC2881355 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking.

Wilkerson Matthew D MD Hayes D Neil DN

Bioinformatics (Oxford, England) 20100428 12

<h4>Unlabelled</h4>Unsupervised class discovery is a highly useful technique in cancer research, where intrinsic groups sharing biological characteristics may exist but are unknown. The consensus clustering (CC) method provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset. ConsensusClusterPlus implements the CC method in R and extends it with new functionality and visualizations including item tracking, item-consensus and cluster-conse ...[more]

PMID: 20427518

Similar Datasets

Project description:Many ribosomally synthesized and posttranslationally modified peptide classes (RiPPs) are reliant on a domain called the RiPP recognition element (RRE). The RRE binds specifically to a precursor peptide and directs the posttranslational modification enzymes to their substrates. Given its prevalence across various types of RiPP biosynthetic gene clusters (BGCs), the RRE could theoretically be used as a bioinformatic handle to identify novel classes of RiPPs. In addition, due to the high affinity and specificity of most RRE-precursor peptide complexes, a thorough understanding of the RRE domain could be exploited for biotechnological applications. However, sequence divergence of RREs across RiPP classes has precluded automated identification based solely on sequence similarity. Here, we introduce RRE-Finder, a new tool for identifying RRE domains with high sensitivity. RRE-Finder can be used in precision mode to confidently identify RREs in a class-specific manner or in exploratory mode to assist in the discovery of novel RiPP classes. RRE-Finder operating in precision mode on the UniProtKB protein database retrieved ∼25,000 high-confidence RREs spanning all characterized RRE-dependent RiPP classes, as well as several yet-uncharacterized RiPP classes that require future experimental confirmation. Finally, RRE-Finder was used in precision mode to explore a possible evolutionary origin of the RRE domain. The results suggest RREs originated from a co-opted DNA-binding transcriptional regulator domain. Altogether, RRE-Finder provides a powerful new method to probe RiPP biosynthetic diversity and delivers a rich data set of RRE sequences that will provide a foundation for deeper biochemical studies into this intriguing and versatile protein domain.IMPORTANCE Bioinformatics-powered discovery of novel ribosomal natural products (RiPPs) has historically been hindered by the lack of a common genetic feature across RiPP classes. Herein, we introduce RRE-Finder, a method for identifying RRE domains, which are present in a majority of prokaryotic RiPP biosynthetic gene clusters (BGCs). RRE-Finder identifies RRE domains 3,000 times faster than current methods, which rely on time-consuming secondary structure prediction. Depending on user goals, RRE-Finder can operate in precision mode to accurately identify RREs present in known RiPP classes or in exploratory mode to assist with novel RiPP discovery. Employing RRE-Finder on the UniProtKB database revealed several high-confidence RREs in novel RiPP-like clusters, suggesting that many new RiPP classes remain to be discovered.

Project description:BackgroundHigher levels of functional health in older adults leads to higher quality of life and improves the ability to age-in-place. Tracking functional health objectively could help clinicians to make decisions for interventions in case of health deterioration. Even though several geriatric assessments capture several aspects of functional health, there is limited research in longitudinally tracking personalized functional health of older adults using a combination of these assessments.MethodsWe used geriatric assessment data collected from 150 older adults to develop and validate a functional health prediction model based on risks associated with falls, hospitalizations, emergency visits, and death. We used mixed effects logistic regression to construct the model. The geriatric assessments included were Activities of Daily Living (ADL), Instrumental Activities of Daily Living (IADL), Mini-Mental State Examination (MMSE), Geriatric Depression Scale (GDS), and Short Form 12 (SF12). Construct validators such as fall risks associated with model predictions, and case studies with functional health trajectories were used to validate the model.ResultsThe model is shown to separate samples with and without adverse health event outcomes with an area under the receiver operating characteristic curve (AUC) of?>?0.85. The model could predict emergency visit or hospitalization with an AUC of 0.72 (95% CI 0.65-0.79), fall with an AUC of 0.86 (95% CI 0.83-0.89), fall with hospitalization with an AUC of 0.89 (95% CI 0.85-0.92), and mortality with an AUC of 0.93 (95% CI 0.88-0.97). Multiple comparisons of means using Turkey HSD test show that model prediction means for samples with no adverse health events versus samples with fall, hospitalization, and death were statistically significant (p?<?0.001). Case studies for individual residents using predicted functional health trajectories show that changes in model predictions over time correspond to critical health changes in older adults.ConclusionsThe personalized functional health tracking may provide clinicians with a longitudinal view of overall functional health in older adults to help address the early detection of deterioration trends and decide appropriate interventions. It can also help older adults and family members take proactive steps to improve functional health.

Dataset Information

ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking.

Unlabelled

Availability

Supplementary information

Publications

ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets