iSyTE

iSyTE integrates transcriptomic data and proteomic profiling to prioritize genes and proteins associated with lens development and cataract disease via comparative proteome analysis.

Key Features:

• Transcriptome–proteome integration: Combines transcriptome data with proteomic profiling to enhance gene discovery for eye-related diseases such as cataracts.
• Proteomic profiling (MS/MS): Uses high-throughput tandem mass spectrometry (MS/MS) to generate a global protein expression profile of the mouse lens at embryonic day 14.5.
• In silico WB-subtraction: Implements an in silico whole-embryonic-body (WB) subtraction approach to identify lens-enriched proteins by comparative analysis against a WB reference proteome.
• Reference dataset: Employs proteome data from the entire mouse whole embryonic body (WB) as the comparative reference dataset.
• Quantitative filtering criteria: Applies an average spectral count threshold of ≥ 2.5, a fold enrichment cut-off of ≥ 2.0, and a false discovery rate (FDR) of < 0.01 to define significant lens enrichment.
• Lens proteome characterization: Identified 2,371 lens-expressed proteins and 422 proteins with significantly enriched expression in the lens under the stated criteria.
• Candidate prioritization: Ranks candidates with the top 20% representing high-priority proteins, including known cataract-linked genes and novel potential regulators of lens development and homeostasis.

Scientific Applications:

• Cataract gene discovery: Prioritizes candidate genes and proteins implicated in human cataract and other eye diseases by integrating transcriptomic and proteomic evidence.
• Identification of lens-enriched proteins: Detects proteins with lens-specific or enriched expression using comparative proteomics against whole embryonic body data.
• Prioritization of developmental regulators: Highlights novel candidate regulators of lens development and homeostasis for further functional study.
• Comparative proteomics for tissue specificity: Enables tissue-specific enrichment analysis through in silico subtraction and statistical filtering.

Methodology:

Integration of transcriptome data with proteomic profiling by high-throughput tandem mass spectrometry (MS/MS); generation of a global protein expression profile for mouse lens at embryonic day 14.5; in silico WB-subtraction comparing lens proteome to whole embryonic body (WB) proteome; filtering using average spectral count ≥ 2.5, fold enrichment ≥ 2.0 and FDR < 0.01; selection and ranking of top 20% prioritized candidates.