Clustering of RNA-Seq samples: Comparison study on cancer data

Author(s)

Jaskowiak, Pablo Andretta ^[1] ; Costa, Ivan G. ^[2] ; Campello, Ricardo J. G. B. ^{[3, 4]}

Affiliation

^[1] Univ Fed Santa Catarina, Joinville, SC - Brazil

^[2] Rhein Westfal TH Aachen, Med Sch, Inst Biomed Engn, IZKF Computat Biol Res Grp, Aachen - Germany

^[3] Univ Sao Paulo, Inst Math & Comp Sci, Sao Carlos, SP - Brazil

^[4] James Cook Univ, Coll Sci & Engn, Townsville, Qld - Australia

• Document type: Journal article
• Source: METHODS; v. 132, p. 42-49, JAN 1 2018.
• Web of Science Citations: 3

Abstract

RNA-Seq is becoming the standard technology for large-scale gene expression level measurements, as it offers a number of advantages over microarrays. Standards for RNA-Seq data analysis are, however, in its infancy when compared to those of microarrays. Clustering, which is essential for understanding gene expression data, has been widely investigated w.r.t. microarrays. In what concerns the clustering of RNA-Seq data, however, a number of questions remain open, resulting in a lack of guidelines to practitioners. Here we evaluate computational steps relevant for clustering cancer samples via an empirical analysis of 15 mRNA-seq datasets. Our evaluation considers strategies regarding expression estimates, number of genes after non-specific filtering and data transformations. We evaluate the performance of four clustering algorithms and twelve distance measures, which are commonly used for gene expression analysis. Results support that clustering cancer samples based on a gene quantification should be preferred. The use of non-specific filtering leading to a small number of features (1,000) presents, in general, superior results. Data should be log-transformed previously to cluster analysis. Regarding the choice of clustering algorithms, Average-Linkage and k-medoids provide, in general, superior recoveries. Although specific cases can benefit from a careful selection of a distance measure, Symmetric Rank Magnitude correlation provides consistent and sound results in different scenarios. (C) 2017 Elsevier Inc. All rights reserved. (AU)

• FAPESP's process: 11/04247-5 - Gene Selection and Clustering Validation in Gene Expression Data
• Grantee: Pablo Andretta Jaskowiak
• Support Opportunities: Scholarships in Brazil - Doctorate