In sigven/oncoEnrichR: Cancer-dedicated gene set interpretation

Input data

The main input to oncoEnrichR is a list of human genes, typically the top ranked hits from a high-throughput screen. The gene list can be provided by using any of the following identifiers:

• Primary gene symbols (e.g. KRAS)
• Entrez gene IDs (e.g. 3845)
• Uniprot accessions (e.g. P01116)
• Ensembl gene identifiers (e.g. ENSG00000133703)
• Ensembl transcript identifiers (e.g. ENST00000311936)
• Ensembl protein identifiers (e.g. ENSP00000308495)
• RefSeq transcript identifiers (e.g. NM_004985)
• RefSeq peptide identifiers (e.g. NP_004976)

The type of identifier used should be specified using the --query_id_type argument. Similarly, if a background gene set is specified (through the --bgset argument, for use in enrichment analysis), the identifier type should be set with the --bgset_id_type argument.

If the user submits gene symbols which are no longer considered as primary gene symbols, oncoEnrichR attempts to map such cases as synonyms/aliases for the primary gene symbols.

Number of input genes

In order to keep the size of the HTML output report at a manageable level, there is currently an upper limit of

• n = 1000

genes that can be used as input to the tool. When running the tool through Galaxy, the limitation with respect to the number of input genes is stricter (n = 200). Note also that if the number of input genes is very low (i.e. n = 1-5), some analysis modules are not applicable for analysis (functional enrichment, protein-protein interaction network etc).

IMPORTANT NOTE: Due to its large size, the HTML report can be slow to load when generating full reports with the maximum number of genes (n = 1000). We generally recommend to use oncoEnrichR with smaller querysets (< 500), as this will produce reports that can be more efficiently loaded and viewed. If you want to submit a query that pushes the limit (n = 1000), we recommend that you carefully configure the report contents/modules, in that sense producing more managable reports.

sigven/oncoEnrichR documentation built on March 5, 2025, 7:49 p.m.