Given a list of gene ids, obtain the pathway information, perform pathway analysis using
Hyper-geometric test to identify significantly enriched pathways.
Pathway descriptions and hypergeometric test
- The pathway descriptions are coming from MaizeCyc.
- Hypergeometic test to identify significantly enriched pathways
includes one-sided fisher exact test and corrected multiple test, with p-values
- The one-sided fisher exact test is done to compute whether
the overlap between the sample set and the background set is significant, meaning the
overlap between the lists is not due to chance. The lower the p-value the less likely
that there is a random overlap
- The multiple test correction is performed to eliminate the error,
observing a false-positive result. The p-value is calculated by multiplying each p-value by
the number of comparisons made and using the modified p-value to indicate significance.
Steps to follow
- Use the dropdown labeled Against the background of.
The default list is all maize genes. You can select from your saved list of genes too.
- Use the dropdown menu to select a previously saved gene list
and click on Analyze Pathway
If there are no saved gene list files, it shows a message saying 'No saved gene lists'
- Click on Example set of gene ids.
to populate the box with example set of gene ids
OR type in the desired list of gene ids in the box with one gene id per line.
- Click on
- Wait for the page to load the pathway hypergeometric test
results in tabular format
column 1: Gene id
column 2: Pathway it belongs
column 3: One-sided Fisher's exact test (p-value)
column 4: Multiple test corrected (p-value)
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