There is a tutorial on using neo4j Cypher query here.
To retrieve all human pathways for a single gene (for example: P36897, the Uniprot identifier for TGFR1)
MATCH (n)-[:referenceDatabase]->(rd:ReferenceDatabase)
WHERE toLower(rd.displayName) = toLower("UniProt") AND (n.identifier = "P36897" OR n.variantIdentifier ="P36897" OR "P36897" IN n.geneName OR "P36897" IN n.name)
WITH DISTINCT n
MATCH (pe:PhysicalEntity)-[:referenceEntity|referenceSequence|crossReference|referenceGene*]->(n)
WITH DISTINCT pe
MATCH (rle:ReactionLikeEvent)-[:input|output|catalystActivity|physicalEntity|entityFunctionalStatus|diseaseEntity|regulatedBy|regulator|hasComponent|hasMember|hasCandidate|repeatedUnit*]->(pe)
WITH DISTINCT rle
MATCH (:Species{taxId:"9606"})<-[:species]-(p:pathway)-[:hasevent]->(rle)
RETURN DISTINCT p
ORDER BY p.stId
If you have a list of genes, we suggest using UNWIND neo4j cypher to flatten your list back to individual items and then execute the query.