TraPS-VarI

TraPS-VarI identifies genetic variants that alter phosphotyrosine-based signaling motifs within transmembrane proteins to evaluate their potential impact on immune cell signaling.

Key Features:

• Focus on Transmembrane Proteins: TraPS-VarI targets transmembrane proteins, with emphasis on proteins expressed in haematopoietic immune cells (myeloid and lymphoid).
• Detection of TBSM Alterations: It detects mutations that alter phosphotyrosine-based signaling motifs (TBSMs) including ITAM, ITIM, and STAT3-recruiting YxxQ motifs.
• Comprehensive Mutation Mapping: The tool maps individual mutations within transmembrane protein sequences to identify alterations that affect signaling motifs.
• Mutation Type Identification: TraPS-VarI identifies non-synonymous mutations, including stop-insertions and frameshifts, within coding regions of membrane proteins.

Scientific Applications:

• Patient- and Cell Line-specific Variant Analysis: Enables identification of patient-specific or cell line-specific mutations in transmembrane proteins that may modulate signaling.
• Cancer Immunotherapy Research: Supports analysis of how genetic variations in transmembrane proteins alter immune receptor signaling relevant to cancer immunotherapy.

Methodology:

Uses genome sequencing data to identify non-synonymous mutations, including stop-insertions and frameshifts, in coding regions of membrane proteins and maps them onto transmembrane protein sequences to assess impacts on phosphotyrosine-based signaling motifs.