A-Lister

A-Lister analyzes and compares differentially expressed omics entities across multiple pairwise comparisons using filtering criteria and set-based operations.

Key Features:

• Multi-Omics Differential Expression Support: Processes differentially expressed entities including genes (DEGs), proteins (DEPs), and methylated positions or regions (DMPs/DMRs).
• Compatibility with Differential Expression Tools: Accepts delimited text outputs generated by DESeq2, edgeR, Cuffdiff, and limma.
• Threshold-Based Filtering: Filters entities using statistical criteria including p-value, q-value, fold change, and fold-change direction.
• Set Operation Analysis: Performs set operations including intersection, fuzzy intersection, difference, and union across entity lists from multiple comparisons.
• Generic Name List Processing: Supports analysis of arbitrary delimited text files containing lists of entity identifiers for comparative set-based queries.

Scientific Applications:

• Comparative Differential Expression Analysis: Identifies overlapping or distinct differentially expressed entities across multiple experimental conditions or timepoints.
• Multi-Omics Data Integration: Compares gene, protein, and DNA methylation datasets to identify shared molecular signals.
• Biomarker Candidate Identification: Refines large differential expression datasets to smaller subsets of candidate genes, proteins, or methylation sites for downstream analysis.

Methodology:

A-Lister parses delimited differential expression output files, filters entities based on statistical thresholds and fold-change direction, and performs set operations including intersection, fuzzy intersection, difference, and union across multiple pairwise comparison datasets.