OMnalysis

OMnalysis performs integrative analysis of differential gene and protein expression data to provide pathway enrichment, network-based pathway analysis, visualization, and literature integration for biological interpretation.

Key Features:

• Data Compatibility: Accepts tabular inputs from edgeR, DESeq2, MaxQuant Perseus, and other R packages and processes lists of differentially expressed genes or proteins with metrics including log fold change, count per million, P-value, and q-value.
• Visualization Capabilities: Generates multiple image types for data visualization with customizable image dimensions.
• Statistical Analysis Tools: Implements seven methods for multiple hypothesis testing correction and supports gene ontology analyses and network topology–based pathway analysis.
• Pathway Enrichment and Database Integration: Integrates KEGG, Reactome, PANTHER, biocarta, NCI-Nature Pathway Interaction Database, PharmGKB, and STRINGdb for pathway enrichment analyses.
• Literature Integration: Fetches relevant literature from PubMed to associate identified biomarkers with published evidence.

Scientific Applications:

• Genomics, Transcriptomics, and Proteomics: Analysis of differentially expressed genes and proteins across genomics, transcriptomics, and proteomics studies.
• Biomarker Discovery: Identification of candidate biomarkers from differential expression results.
• Functional Interpretation and Pathway Analysis: Functional interpretation of differential expression via pathway enrichment and network topology–based analyses to elucidate biological mechanisms.
• Translational Research and Target Identification: Supporting identification of potential therapeutic targets and contextualization of results with PubMed literature for disease mechanism studies and personalized medicine.

Methodology:

Accepts tabular inputs from edgeR, DESeq2, MaxQuant Perseus and other R packages; processes lists of differentially expressed genes/proteins with log fold change, count per million, P-value, and q-value; applies seven multiple hypothesis testing correction methods; performs gene ontology and network topology–based pathway analysis; queries KEGG, Reactome, PANTHER, biocarta, NCI-Nature Pathway Interaction Database, PharmGKB, and STRINGdb for enrichment; retrieves PubMed literature; and generates multiple image types with customizable dimensions.