hgv_linktogprofile

hgv_linktogprofile links gene lists to g:GOSt (g:Profiler) to enable functional profiling and enrichment analysis across Gene Ontology (GO), pathways, and transcription factor binding sites for interpretation of high-throughput genomic data.

Key Features:

• Functional Profiling: Links gene lists to g:GOSt within g:Profiler to assess GO, pathway, and transcription factor binding site enrichments, including analyses at individual gene levels.
• Ranked and Co-expression Analysis Support: Supports analysis of ranked gene lists and integration with co-expression results to interpret high-throughput and next-generation sequencing datasets.
• Multiple Testing Correction: Applies advanced statistical methods for multiple testing correction, including a method tailored for complex GO structure.
• g:Convert: Converts identifiers across different databases to ensure identifier compatibility for downstream analyses.
• g:Orth: Identifies orthologous genes across species to support comparative genomics analyses.
• g:Sorter: Searches public gene expression datasets to find co-expressed genes for network and pathway exploration.
• Species Coverage and Data Updates: Provides data for 31 species with annotations updated from the Ensembl database.
• Integration and Reproducible Outputs: Integrates with g:Profiler workflows and provides simple textual outputs to support reproducibility and tracking of computational analyses.

Scientific Applications:

• Functional enrichment of gene sets: Interprets gene lists from high-throughput assays and next-generation sequencing via GO, pathway, and TFBS enrichment.
• Analysis of ranked and co-expression results: Interprets ranked gene lists and co-expression-derived gene sets to identify biologically relevant processes and regulators.
• Comparative genomics: Uses ortholog mapping to transfer functional interpretations across species.
• Identifier harmonization for multi-database studies: Resolves cross-database identifier issues to enable integrated analyses.

Methodology:

Links input gene lists to g:GOSt for enrichment analysis (GO, pathways, TFBS); applies multiple testing correction methods including a GO-structure-aware method; uses g:Convert for ID conversion, g:Orth for ortholog mapping, g:Sorter to query public expression datasets; and retrieves species annotations updated from Ensembl.