ProLiC (Protein List Comparator)

ProLiC compares protein lists to identify correspondences across datasets and support multi-OMICS biomarker discovery by handling changing database accession numbers and incorporating measured sequence and peptide information.

Key Features:

• Accession-based comparison: Performs simple comparisons between protein lists using database accession numbers.
• Sequence- and peptide-aware analysis: Incorporates measured sequence and peptide information into list comparisons.
• Robust handling of accession changes: Addresses varying or changing database accession numbers when matching proteins across lists.
• Multi-list comparison: Compares an arbitrary number of protein lists in a single analysis.
• Biomarker identification and ranking: Supports identification and ranking of candidate biomarkers from comparative results.
• Advanced comparison beyond linear regression: Enables comparisons that go beyond simple linear regression analyses.
• Annotation and multivariate analysis support: Produces outputs usable for annotation and multivariate analysis workflows.
• Integration with external workflows: Compatible with CrossPlatformCommander for semi-automated integration into multi-OMICS pipelines.

Scientific Applications:

• Multi-OMICS integration: Facilitates integration of Proteomics with other omics layers such as Transcriptomics in comparative analyses.
• Biomarker discovery: Supports discovery and ranking of biomarkers across proteomic datasets.
• Cross-database and longitudinal comparisons: Enables comparison of datasets affected by changing database accession numbers.
• Application in disease-focused projects: Has been applied within workflows such as the PROFILE project for liver disease multi-OMICS research.
• Preparation for multivariate analyses: Generates comparison outputs suitable for downstream annotation and multivariate analysis.

Methodology:

Performs simple accession-based comparisons and analyses that incorporate measured sequence and peptide information to compare arbitrary numbers of protein lists, supports ranking of biomarkers, enables outputs for annotation and multivariate analysis, and is compatible with CrossPlatformCommander and PROFILE multi-OMICS workflows.