Cluster analysis on high dimensional RNA-seq data with applications to cancer research – An evaluation study

Clustering of gene expression data is widely used to identify novel subtypes of cancer. Plenty of clustering approaches have been proposed, but there is a lack of knowledge regarding their relative merits and how data characteristics influence the performance. Umeå University researchers evaluate how cluster analysis choices affect the performance by studying four publicly available human cancer data sets: breast, brain, kidney and stomach cancer. In particular, they focus on how the sample size, distribution of subtypes and sample heterogeneity affect the performance.

In general, increasing the sample size had limited effect on the clustering performance, e.g. for the breast cancer data similar performance was obtained for n = 40 as for n = 330. The relative distribution of the subtypes had a noticeable effect on the ability to identify the disease subtypes and data with disproportionate cluster sizes turned out to be difficult to cluster. Both the choice of clustering method and selection method affected the ability to identify the subtypes, but the relative performance varied between data sets, making it difficult to rank the approaches. For some data sets, the performance was substantially higher when the clustering was based on data from only one sex compared to data from a mixed population. This suggests that homogeneous data are easier to cluster than heterogeneous data and that clustering males and females individually may be beneficial and increase the chance to detect novel subtypes. It was also observed that the performance often differed substantially between females and males.

Principal component analysis to visualize separation between subtypes

rna-seq

Figures based on the first two principal components, where the subtypes are marked in different colors; Breast: ER+(red) and ER-(blue), Brain: IDHnocodel (red) and IDHcodel (blue), Kidney: type 1(red) and type 2(blue), Stomach: CIN (red) and MSI (blue).

The number of samples seems to have a limited effect on the performance while the heterogeneity, at least with respect to sex, is important for the performance. Hence, by analyzing the genders separately, the possible loss caused by having fewer samples could be outweighed by the benefit of a more homogeneous data.

Vidman L, Källberg D, Rydén P (2019) Cluster analysis on high dimensional RNA-seq data with applications to cancer research – An evaluation study. PLoS ONE 14(12): e0219102. [article]

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