TEspeX

TEspeX quantifies transposable element expression at the consensus level from Illumina RNA-seq short reads while excluding signals originating from exonized TE fragments.

Key Features:

• Consensus-Level Quantification: Provides quantification of TE expression at the consensus sequence level to represent genuine TE activity.
• Exonized Fragment Exclusion: Avoids biases introduced by exonized TE fragments embedded within canonical coding or non-coding transcripts.
• Illumina RNA-seq Compatibility: Operates on Illumina RNA-seq short reads as input for transcriptomic TE quantification.
• Implementation: Implemented in Python 3 as a computational pipeline for TE expression analysis.

Scientific Applications:

• Gene Regulation: Enables investigation of how TE transcription contributes to gene regulatory networks by providing accurate TE expression measurements.
• Genome Evolution: Facilitates studies of the evolutionary impact of TEs on genome structure and function through consensus-level expression profiling.
• Disease Mechanisms: Supports analyses of TE activity in disease contexts, including cancer, where TEs may contribute to genomic instability and oncogene activation.

Methodology:

Consensus-level quantification from Illumina RNA-seq short reads with explicit exclusion of exonized TE fragments; implemented as a Python 3 pipeline.