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.