APCluster: an R package for affinity propagation clustering

Bodenhofer, Ulrich; Kothmeier, Andreas; Hochreiter, Sepp

doi:10.1093/bioinformatics/btr406

Cited by 442 publications

(324 citation statements)

References 15 publications

Supporting

Mentioning

321

Contrasting

Unclassified

Order By: Relevance

“…The kohonen R package (Wehrens and Buydens 2007) was used for training the SOM with custom modifications to the plotting functions following . We then clustered the codebook vectors of the 140 units in the SOM using affinity propagation clustering (Frey and Dueck 2007) as implemented in the apcluster R package (Bodenhofer et al 2011). For details, see Supplemental Methods.…”

Section: Self-organizing Maps For Integrative Gene Expression Analysismentioning

confidence: 99%

Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans

et al. 2015

View full text Add to dashboard Cite

Elucidating the consequences of genetic differences between humans is essential for understanding phenotypic diversity and personalized medicine. Although variation in RNA levels, transcription factor binding, and chromatin have been explored, little is known about global variation in translation and its genetic determinants. We used ribosome profiling, RNA sequencing, and mass spectrometry to perform an integrated analysis in lymphoblastoid cell lines from a diverse group of individuals. We find significant differences in RNA, translation, and protein levels suggesting diverse mechanisms of personalized gene expression control. Combined analysis of RNA expression and ribosome occupancy improves the identification of individual protein level differences. Finally, we identify genetic differences that specifically modulate ribosome occupancy-many of these differences lie close to start codons and upstream ORFs. Our results reveal a new level of gene expression variation among humans and indicate that genetic variants can cause changes in protein levels through effects on translation.

show abstract

Section: Self-organizing Maps For Integrative Gene Expression Analysismentioning

confidence: 99%

Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans

et al. 2015

View full text Add to dashboard Cite

show abstract

“…The method chosen for calculation is a method called by Frey and Dueck (2007) as Baffinity propagation,^which takes the measures of similarity between pairs of data points as input and simultaneously considers all data points as potential exemplars. The affinity propagation method was implemented in System R as a package APCluster (Bodenhofer et al 2011). This method provides individual selection of the number of clusters, suitable for the particular field of precipitation classes.…”

Section: Methodsmentioning

confidence: 99%

Comparison of selected methods of analysis for reconstructed fields of precipitation in climate scenarios over Poland

Konca-Kędzierska

2015

Theor Appl Climatol

View full text Add to dashboard Cite

Obtaining information about future climate change is essential to the development of adaptation strategies, but no less a significant problem than gathering the data is assessing its credibility. The task of assessing the credibility of scenarios is solved by evaluating climate models in the referenced period. Methods of comparing meteorological fields in the grid points often lead to an overestimation of the error for precipitation. The way precipitation effects the environment-a much wider concern than just where the precipitation occurs-allows for the assumption of some tolerance in the verification of its location. The main objective of this study is to find a way to evaluate climate scenarios without taking into account the details of location and intensity of precipitation. One of the methods for a less restrictive examination of compatibility of precipitation fields is to compare their properties in the neighborhood of the point rather than the value at the point. Maps of climate indices and probabilities of exceeding some threshold are evaluated. The second method is a cluster approach, and each field of precipitation is replaced by a set of clusters found in the phase space {(lon,lat,cl)}, where cl is the class of precipitation. Instead of comparing the fields of precipitation, it deals with the set of exemplars of the clusters. Further analysis concerns the spatial distribution of exemplars within a selected class of precipitation. This generalized description allows for comparison between precipitation fields with tolerance in respect to exact location and intensity. Comparison with such descriptions allows one to assess whether two given fields have a similar property in a very general sense.

show abstract

“…Unless stated all heatmaps were constructed using affinity propagation clustering with pairwise similarities as correlations and negative correlations taken into account 47 .…”

Section: Clusteringmentioning

confidence: 99%

Whippet: an efficient method for the detection and quantification of alternative splicing reveals extensive transcriptomic complexity

Sterne-Weiler

Weatheritt

Best

et al. 2017

Preprint

View full text Add to dashboard Cite

Alternative splicing (AS) is a widespread process underlying the generation of transcriptomic and proteomic diversity in metazoans. Major challenges in comprehensively detecting and quantifying patterns of AS are that RNA-seq datasets are expanding near exponentially, while existing analysis tools are computationally inefficient and ineffective at handling complex splicing patterns. Here, we describe Whippet, a method that rapidly, and with minimal hardware requirements, models and quantifies splicing events of any complexity without significant loss of accuracy.Using an entropic measure of splicing complexity, Whippet reveals that approximately 33% of human protein coding genes contain complex AS events that result in substantial expression of multiple splice isoforms. These events frequently affect tandem arrays of folded protein domains. Remarkably, high-entropy AS events are more prevalent in tumour relative to matched normal tissues, and these differences correlate with increased expression of proto-oncogenic splicing factors. Whippet thus affords the rapid and accurate analysis of AS events of any complexity, and as such will facilitate biomedical research.

show abstract

APCluster: an R package for affinity propagation clustering

Cited by 442 publications

References 15 publications

Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans

Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans

Comparison of selected methods of analysis for reconstructed fields of precipitation in climate scenarios over Poland

Whippet: an efficient method for the detection and quantification of alternative splicing reveals extensive transcriptomic complexity

Contact Info

Product

Resources

About