Enrichment analysis

Description

Enrichment analysis in genome-wide gene studies is essential to find biological functions that are particularly abundant in a group of genes more than would be expected by chance.

Here we provide the enrichment analysis tool to find out whether a target gene list is enriched in any of the predefined ecDNA gene sets. Overrepresentation analysis (ORA) and gene set enrichment analysis (GSEA) are two predominant methods, and they have been integrated into this tool.

ORA tests whether a gene set is overrepresented in an experimentally-derived gene list. GSEA tests whether genes of a gene set accumulate at the top or bottom of the full gene vector ordered by a specific metric, such as direction and magnitude of expression change.

Input (user gene list)

Input format

Text input

File upload

Text input

Please enter gene symbols, one per line, in the text area above. Gene symbols cannot contain spaces. For single-column input, enter only the gene symbol. For two-column input, separate the gene symbol and its corresponding numeric value with a space, tab, or comma. Please note that GSEA requires two-column input.

Please follow the above guidlines when preparing your input data.

Enrichment setting

Method

Background

To use

None: all genes in all ecDNA gene sets.
All known human gene: all human genes from the GENCODE database.
Specify a number: the number of total expressed genes. It assumes that all your genes could be found in background.
Input a gene list (recommended): defined by your experment, such as the expressed genes in your experiment.

ecDNA setting (optional)

ecDNA oncogene ⓘ

Yes

ecDNA gene score

≥

ecDNA hits

≥

ecDNA copy number

≥

≤

ecDNA size (bp)

≤

Analysis

Output

Results will be shown here