CoTrEx

CoTrEx analyzes transcriptome-wide gene expression and regulatory variation in normal colon tissue to support functional interpretation of genetic associations related to colon health.

Key Features:

• Exhaustive visualization and analysis: Provides detailed visualization and analysis of gene expression profiles across the transcriptome of normal colon tissue.
• Integration of BarcUVa-Seq and GTEx: Incorporates gene expression data from the BarcUVa-Seq and GTEx projects.
• Expression and splicing QTLs (e/sQTLs): Includes sets of e/sQTLs to aid functional annotation of single nucleotide polymorphisms (SNPs) identified in genome-wide association studies (GWAS).
• Gene expression prediction models: Provides prediction models used as reference panels for transcriptome-wide association studies (TWAS) to nominate susceptibility genes.
• Regulatory and co-expression networks: Integrates regulatory and co-expression networks to study gene–gene relationships and network context.

Scientific Applications:

• Functional annotation of GWAS loci: Uses e/sQTLs to assign putative regulatory consequences to SNPs from GWAS.
• Transcriptome-wide association studies (TWAS): Applies gene expression prediction models and reference panels to prioritize candidate susceptibility genes for colon-related traits.
• Investigation of genetic susceptibility: Supports analysis of genetic contributions to complex traits and diseases affecting colon health.
• Study of regulatory mechanisms: Enables exploration of regulatory interactions and co-expression modules relevant to colorectal biology.

Methodology:

Integrates and analyzes large-scale gene expression data from BarcUVa-Seq and GTEx, identifies expression and splicing QTLs (e/sQTLs), generates gene expression prediction models for TWAS, and explores regulatory and co-expression networks.