Scholarlink

Background <p>Allele Specific Expression analysis is an important tool for integrating genome and transcriptome data. It quantifies expression variation between the two haplotypes of a diploid individual distinguished by heterozygous sites, and is a powerful tool to estimate <i>cis-</i>regulatory diversity of alleles. Clustering algorithms can be used to identify patterns or groups of genes/samples based on their expression profiles. Depending on the structure of the data, different existing clustering algorithm can be adapted to allele specific expression data. However, no <i>ad-hoc</i> procedure has been developed.</p> Results <p>In this work, we begin defining an expression matrix capturing allele expressions from an RNA-sequencing experiment. On this matrix, we develop a novel two-phase unsupervised clustering procedure, built on top of a spectral clustering algorithm, whose aim is to partition the population into groups of similar individuals, according to their allelic expression. As case-studies, the approach is used to cluster 98 cultivars representative of the variability observed in Vitis vinifera, starting from read counts of genes of chromosome 1 of leaves, and to analyze allele-specific count data from a CASTxMRL F1 hybrid mice dataset.</p> Conclusion <p>Using the above mentioned real case-studies as well as generated synthetic data, we see that our algorithm shows significant robustness and outperforms other standard clustering techniques.</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

A two-phase clustering procedure based on allele specific expression

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年4月1日

查看全文
  • Roberto Pagliarini,
  • Francesco Nascimben,
  • Alberto Policriti

摘要

Background

Allele Specific Expression analysis is an important tool for integrating genome and transcriptome data. It quantifies expression variation between the two haplotypes of a diploid individual distinguished by heterozygous sites, and is a powerful tool to estimate cis-regulatory diversity of alleles. Clustering algorithms can be used to identify patterns or groups of genes/samples based on their expression profiles. Depending on the structure of the data, different existing clustering algorithm can be adapted to allele specific expression data. However, no ad-hoc procedure has been developed.

Results

In this work, we begin defining an expression matrix capturing allele expressions from an RNA-sequencing experiment. On this matrix, we develop a novel two-phase unsupervised clustering procedure, built on top of a spectral clustering algorithm, whose aim is to partition the population into groups of similar individuals, according to their allelic expression. As case-studies, the approach is used to cluster 98 cultivars representative of the variability observed in Vitis vinifera, starting from read counts of genes of chromosome 1 of leaves, and to analyze allele-specific count data from a CASTxMRL F1 hybrid mice dataset.

Conclusion

Using the above mentioned real case-studies as well as generated synthetic data, we see that our algorithm shows significant robustness and outperforms other standard clustering techniques.