I am performing GO enrichment analysis on PPI network clusters and encountering high mapping failure in clusterProfiler::bitr(). I would appreciate any clarifications on whether this indicates a flaw in my workflow.

Workflow

Downloaded interaction data from HIPPIE (TAB format).

Filtered interactions with score >= 0.70.

Imported only the protein names (e.g., ITA7, ERBB2) into Cytoscape to build the network.

Selected a predefined gene list in the network and constructed a first-neighbor subnetwork.

Ran MCODE to detect clusters.

Exported the top 5 clusters as CSV files.

Attempted GO enrichment in R using clusterProfiler:

Issue

I receive warnings such as:

Warning: 1: In bitr(gene1, fromType = "SYMBOL", toType = "ENTREZID", OrgDb = org.Hs.eg.db) : 81.13% of input gene IDs are fail to map... 2: In bitr(gene1, fromType = "SYMBOL", toType = "ENTREZID", OrgDb = org.Hs.eg.db) : 41.03% of input gene IDs are fail to map...

The cluster gene names look like this:

RL37A RS16 PRS8.... etc.

Is the mapping failure due to incorrect identifier type selection rather than an error in clusterProfiler?. Should I instead use the Entrez ID columns from the original HIPPIE TAB file for enrichment?

I would appreciate any guidance on the correct way to handle HIPPIE-derived identifiers for downstream GO/KEGG analysis.