find_common_de_genes_overlapping_dm_regions

MCP tool from MCP Genelab by sbl-sdsc

Identify DE genes whose promoter (or other region) is also differentially methylated — supports method-aware significance filtering and pooled-DM evidence across multiple methylation assays

How to use it

Project documentation lists find_common_de_genes_overlapping_dm_regions for the MCP Genelab MCP server. Add the server to your MCP client (Claude Desktop, Cursor, Windsurf and others), then check which tools your installed version makes available. Tool availability can depend on configuration and credentials. A server handshake does not verify this tool’s behavior. See the full listing for setup details.

Install MCP Genelab

$uvx mcp-genelab

FULL MCP GENELAB LISTING

Other tools in MCP Genelab (21)

clean_mermaid_diagram

Clean and validate a Mermaid class diagram of the KG schema

create_chat_transcript

Export the current chat as a formatted transcript

create_venn_diagram

Create a Venn diagram comparing DEGs / DMRs / DA organisms across 2 or 3 assays (also supports the expressionmethylation 2×2 grid variant); PNG returned inline and registered for resource fetch

create_volcano_plot

Generate a volcano plot of differential expression / methylation / abundance results; PNG returned inline and registered for resource fetch

fetch_plot

Re-fetch the canonical PNG bytes of a previously generated plot from the in-memory registry (last 8 plots, FIFO eviction). Returns the bytes as an EmbeddedResource so clients can render them inline. Safe to call repeatedly — no Cypher, no matplotlib, no re-render

find_common_differentially_abundant_organisms

Intersect differentially abundant organisms across multiple assays

find_common_differentially_expressed_genes

Intersect DEGs across multiple assays (up and down directions kept separate)

find_common_differentially_methylated_regions

Intersect DMRs across multiple assays, with optional MethylationRegion filters

find_differentially_abundant_organisms

Find organisms with differential abundance for a given assay (DESeq2 and/or ANCOM-BC)

find_differentially_expressed_genes

Find up/downregulated genes for a given assay (DESeq2)

find_differentially_methylated_regions

Find hyper/hypomethylated regions for a given assay, with optional inpromoter / inexon / inintron / distance filters

get_neo4j_schema

List all node types, their attributes, and relationships in the knowledge graph

get_node_metadata

Get descriptions of all node types from MetaNode entries

get_output_directory

Return the currently configured output directory

get_relationship_metadata

Get descriptions of all relationship types and their properties

get_save_script

Return a markdown block with multiple save options for a previously generated plot: right-click save, ask-LLM-client-to-save, or fetch via the plot:// resource URI

get_study_info

Get detailed information about a specific study and its assays (metadata + assay inventory)

query

Execute a read-only Cypher query on the Neo4j database. Fallback for questions the specialists don't cover — the DEFAULTINSTRUCTIONS policy directs the LLM to use specialist tools first

select_assays

Browse and filter assays by study, organism, technology, or measurement; resolve a factor pair to one or more assay IDs

set_output_directory

Set the user-facing directory where plots and CSV files should be saved

visualize_schema

Generate a visual schema diagram of the knowledge graph