Very often you will get a gene list from genomic or proteomic data. For example,
To follow up with the gene list, a common step is to figure out what are the functional categories that are over-represented (enriched) in the gene list. There are many tools to do that. Some of these tools are web-based, e.g. DAVID is one of the most commonly used web-based tools. We like the functional enrichment tools provided with HOMER, but it is only available in command line. Therefore, we have build a web-based interface for this tool.
Tips for using the tool
To run a new analysis, go to the Functional Enrichment Tool page, choose species, paste your list (either gene symbol or common IDs like RefSeq, Ensembl will work), and click submit. The analysis will typically finish within a minute. You can also copy the URL for the page and check the results later. The results page has bar chart summary, and link to a big table listing all enriched categories. In addition, you can download text result file for each of the GO category at the top of the page.
Here are a few unique features about this tool.
1) Easy to use. Just upload your gene list to the website, the tool will take care of everything.
You can enter a variety of IDs (gene symbols, locus ID, RefSeq or Ensembl IDs) or even mix them. Most times you can simply select whole genome as the background if you have genome-wide data. If your assay only detects a subset of genes in the genome, you can enter the detectable gene list as the background.
2) Comprehensive coverage of functional categories. One click gives you answers for many biological questions.
As an example, we get a gene list which are highly expressed in metastasis cells vs. primary cells for prostate cancer. Running the web-based tool gives us this result. As you can see, the top functional category is WU_CELL_MIGRATION, which fits very well with the notion that these genes are likely involved in metastasis. Note WU_CELL_MIGRATION is from MSigDB, which is actually not available in many common tools like DAVID.