Perform GO and KEGG functional enrichment using HOMER from genomic regions (BED/narrowPeak/broadPeak) or gene lists, and produce R-based barplot/dotplot visualizations. Use this skill when you want to perform GO and KEGG functional enrichment using HOMER from genomic regions or just want to link genomic region to genes.
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Perform GO and KEGG functional enrichment using HOMER from genomic regions (BED/narrowPeak/broadPeak) or gene lists, and produce R-based barplot/dotplot visualizations. Use this skill when you want to perform GO and KEGG functional enrichment using HOMER from genomic regions or just want to link genomic region to genes.
Functional Enrichment (HOMER + R)
Overview
Validate input: Accept BED/peak files with genomic coordinates or gene lists; check format and genome assembly.
Map regions to genes: Convert regions to a unique gene set using HOMER annotatePeaks.pl.
Run GO enrichment: Use HOMER findGO.pl (or annotatePeaks.pl -go) for BP/MF/CC.
Run KEGG enrichment: Use HOMER findGO.pl -kegg (or annotatePeaks.pl -kegg).
Collect outputs: Save tidy tables for downstream plotting and a compact summary of top terms.
Visualize in R: Create barplots and dotplots (GO/KEGG) with ggplot2 from standardized outputs.
QC & troubleshooting: Provide checks for genome mismatch, chromosome naming, and low-signal inputs.
Inputs & Outputs
Inputs (choose one):
Option 1: Input is a genomic region file (BED/narrowPeak/broadPeak)
Genomic region formats supported:
BED files: Standard genomic interval format
narrowPeak: narrow peak format
broadPeak: broad peak format
Option 2: Input is a gene list (txt)
gene_list.txt with one official gene symbol per line (no header). And an optional with one official gene symbol per line (no header).
output_bed: the path to save the standardized BED file
The tool will:
Standardize the chromosome names in the BED file.
Return the path of the standardized BED file.
Step 4 (Optional): Convert gene ID to gene symbol
This step is optional. Only perform this step if the input file is a gene list file. If the input file is a BED file, skip this step.
Call:
mcp__mygene-tools__convert_gene_ids_mygene
With:
input_ids_file: the user-provided gene list file. May end with .txt.
scopes: the source ID type for mygene (e.g., 'ensembl.gene', 'symbol', 'entrezgene', 'uniprot', or a comma-separated list).
fields: the comma-separated target fields to retrieve from mygene (e.g., 'symbol,ensembl.gene,uniprot,entrezgene').
species: the species for mygene (e.g., 'human', 'mouse', 'zebrafish', or NCBI taxon ID like '9606').
out_file: the path to save the converted gene list file. In this skill, it is the full path of the ${sample}_functional_enrichment directory returned by mcp__project-init-tools__project_init
batch_size: the batch size for mygene.querymany (default 1000).
The tool will:
Convert the gene ID to gene symbol.
Return the path of the converted gene list file.
Step 5: GO enrichment analysis
Option 1: from genomic regions file
Only if the input file is a BED file. If the input file is a gene list, call tools in Option 2.
annotate the genomic regions using Homer's annotatePeaks.pl with -go option. If user also provides a background genome region file, like a control peak file, also call this tool for the background genome region file. Use a different ${sample} as the sample name for the background sample.
Call:
mcp__homer-tools__annotate_genomic_features
With:
sample: the user-provided sample name
proj_dir: directory to save the genomic feature annotation results. In this skill, it is the full path of the ${sample}_functional_enrichment directory returned by mcp__project-init-tools__project_init
regions_bed: the user-provided regions file in BED format. May end with .bed, .narrowPeak, .broadPeak, etc.
genome: the user-provided genome assembly, e.g. hg38, mm10, danRer11
ann: "custom homer annotation file (created by assignGenomeAnnotation.pl), (default: None).
size_given: keep original region sizes (default: True)
cpg: include CpG information (default: False)
go: True to perform GO enrichment analysis.
The tool will:
Annotate the genomic regions using Homer's annotatePeaks.pl.
Return the path of the annotated regions file under ${proj_dir}/results/ directory, and the path to the log file under ${proj_dir}/logs/ directory.
(optional) extract the genes from the annotated regions file if neccessary for future analysis or the target gene list is requested by user. If not requested, skip this step.
Call:
mcp__file-format-tools__extract_gene_list
With:
sample: the user-provided sample name
proj_dir: directory to save the genomic feature annotation results. In this skill, it is the full path of the ${sample}_functional_enrichment directory returned by mcp__project-init-tools__project_init
The tool will:
Extract the genes from the annotated regions file.
Return the path of the gene list file under ${proj_dir}/tables/ directory.
${proj_dir}/tables/${sample}.gene_list.txt
Option 2: from gene list file
Only if the input file is a gene list file. If the input file is a BED file, call tools in Option 1.
Call:
mcp__homer-tools__gene_function_enrichment
With:
sample: the user-provided sample name
proj_dir: directory to save the GO & KEGG enrichment results. In this skill, it is the full path of the ${sample}_functional_enrichment directory returned by mcp__project-init-tools__project_init
gene_list_file: the user-provided gene list file. May end with .txt.
organism: the user-provided organism name, e.g. human, mouse, zebrafish, etc.
background_gene_list_file: the user-provided background gene list file. May end with .txt. If not provided, set this parameter to None.
The tool will:
Find the GO enrichment for the gene list.
Return the path of the GO & KEGG enrichment results under ${proj_dir}/results/ directory.
${proj_dir}/results/biological_process.txt
${proj_dir}/results/kegg.txt
... other GO and KEGG enrichment results files.
Return the path of the log file under ${proj_dir}/logs/ directory.
proj_dir: directory to save the GO & KEGG enrichment results. In this skill, it is the full path of the ${sample}_functional_enrichment directory returned by mcp__project-init-tools__project_init
go_results_file: the user-provided GO results file. May be ${proj_dir}/results/biological_process.txt or ${proj_dir}/results/molecular_function.txt or ${proj_dir}/results/cellular_component.txt, etc. This could be the GO results file under the ${proj_dir}/results/ directory returned by mcp__homer-tools__gene_function_enrichment.
The tool will:
Visualize the GO & KEGG enrichment results in barplot and dotplot.
Return the path of the barplot file under ${proj_dir}/plots/ directory.
${proj_dir}/plots/${sample}.GO_barplot.pdf
Alternative direct from BED annotatePeaks.pl peaks.bed hg38 -go results/{run}/tables/go_dir -genomeOntology annotatePeaks.pl peaks.bed hg38 -kegg results/{run}/tables/kegg_dir
Notes & Best Practices
Genome & naming: Ensure the HOMER genome key matches the species; chromosome naming must be consistent (chr1 vs 1).
BED format: Tab-delimited, ≥3 columns, 0-based coordinates, no header.
Multiple testing: Prefer FDR (BH) if provided; otherwise fallback to P-value.
Background set: -bg helps reduce bias; choose a reasonable universe (e.g., all expressed or all accessible regions → genes).
Direct-from-BED: annotatePeaks.pl -go/-kegg is convenient; the gene-list route yields uniform TSVs for plotting.
Troubleshooting
Many NAs after annotation: Check genome version, chromosome naming, BED formatting, and headers.
Empty/weak enrichment: Ensure sufficient genes (suggest ≥50), verify species of symbols, tune thresholds or background.
Column name drift: HOMER versions may differ; adjust R column mappings if needed.
