10,020 research outputs found
Consensus clustering and functional interpretation of gene-expression data
Microarray analysis using clustering algorithms can suffer from lack of inter-method consistency in assigning related gene-expression profiles to clusters. Obtaining a consensus set of clusters from a number of clustering methods should improve confidence in gene-expression analysis. Here we introduce consensus clustering, which provides such an advantage. When coupled with a statistically based gene functional analysis, our method allowed the identification of novel genes regulated by NFκB and the unfolded protein response in certain B-cell lymphomas
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scAI: an unsupervised approach for the integrative analysis of parallel single-cell transcriptomic and epigenomic profiles.
Simultaneous measurements of transcriptomic and epigenomic profiles in the same individual cells provide an unprecedented opportunity to understand cell fates. However, effective approaches for the integrative analysis of such data are lacking. Here, we present a single-cell aggregation and integration (scAI) method to deconvolute cellular heterogeneity from parallel transcriptomic and epigenomic profiles. Through iterative learning, scAI aggregates sparse epigenomic signals in similar cells learned in an unsupervised manner, allowing coherent fusion with transcriptomic measurements. Simulation studies and applications to three real datasets demonstrate its capability of dissecting cellular heterogeneity within both transcriptomic and epigenomic layers and understanding transcriptional regulatory mechanisms
Discussion of: Treelets--An adaptive multi-scale basis for sparse unordered data
We would like to congratulate Lee, Nadler and Wasserman on their contribution
to clustering and data reduction methods for high and low situations. A
composite of clustering and traditional principal components analysis, treelets
is an innovative method for multi-resolution analysis of unordered data. It is
an improvement over traditional PCA and an important contribution to clustering
methodology. Their paper [arXiv:0707.0481] presents theory and supporting
applications addressing the two main goals of the treelet method: (1) Uncover
the underlying structure of the data and (2) Data reduction prior to
statistical learning methods. We will organize our discussion into two main
parts to address their methodology in terms of each of these two goals. We will
present and discuss treelets in terms of a clustering algorithm and an
improvement over traditional PCA. We will also discuss the applicability of
treelets to more general data, in particular, the application of treelets to
microarray data.Comment: Published in at http://dx.doi.org/10.1214/08-AOAS137F the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
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