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Performance comparison of dimensionality reduction methods on RNA-Seq data from the GTEx project.

Ho-Sik Seok1

  • 1Department of Computer and Communications Engineering, Kangwon National University, Chuncheon-si, Gangwon-do, 24341, South Korea. hsseok@kangwon.ac.kr.

Genes & Genomics
|December 14, 2019
PubMed
Summary

Dimensionality reduction methods like LLE, t-SNE, and SE offer superior clustering performance on RNA-Seq data compared to PCA and MDS. Applying both linear and non-linear techniques is recommended for intuitive data understanding.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Bioinformatics datasets often feature a high dimensionality (many features) with limited samples, hindering intuitive comprehension.
  • Dimensionality reduction and manifold learning offer solutions, but method selection remains crucial.

Purpose of the Study:

  • To evaluate the performance of various dimensionality reduction techniques on RNA-Seq data.
  • To compare linear methods (PCA, MDS) with non-linear methods (LLE, SE, t-SNE).

Main Methods:

  • Applied dimensionality reduction methods including Locally Linear Embedding (LLE), Multi-dimensional Scaling (MDS), Principal Component Analysis (PCA), Spectral Embedding (SE), and t-distributed Stochastic Neighbor Embedding (t-SNE).
  • Utilized RNA-Seq data from the Genotype-Tissue Expression (GTEx) project.
Keywords:
ClusteringDimensionality reductionManifold learningRNA-SeqThe genotype-tissue expression (GTEx) project

Related Experiment Videos

  • Assessed performance using k-means clustering in reduced dimensions (2, 3, and 4).

    • Main Results:

    • Each dimensionality reduction method generated distinct reduced spaces.
    • Non-linear methods (LLE, t-SNE, SE) outperformed linear methods (PCA, MDS) in k-means clustering accuracy.
    • Visualization revealed unique characteristics for each method in the reduced space.

    Conclusions:

    • Non-linear dimensionality reduction techniques show promise for analyzing complex bioinformatics data.
    • Combining linear and non-linear methods can enhance intuitive understanding of high-dimensional datasets.