Some preliminary results on relation between triplet composition and tissue source in larch total transcriptome

TL;DR

This study explores the structure of Siberian larch transcriptome, revealing geometric patterns and tissue-specific differences, and compares real and surrogate transcriptomes to understand tissue-related variations.

Contribution

It introduces a novel analysis of transcriptome structuredness using clustering and geometric methods, highlighting tissue-specific differences and discrepancies between real and surrogate transcriptomes.

Findings

Identified tetrahedron-like structure in transcriptome fragment distribution

Found relative similarity among classes based on Chargaff's discrepancy

Observed significant differences between real and surrogate transcriptomes

Abstract

We studied the structuredness ensemble of transcriptome of Siberian larch. The clusters in 64-dimensional space were identified with $K$-means technique, where the objects to be clusterized are the different fragments of the genome. A tetrahedron like structure in distribution of these fragments was found. Chargaff's discrepancy measure was determined for each class, as well as that latter between the classes. It reveals a relative similitude of the classes. The results have been compared to those obtained for specific transcriptome of each tissue. Also, a surrogate transcriptome has been developed comprising the contigs assembled for specific tissues; that latter has been compared with the real total transcriptome, and significant difference has been observed.