Run enrichment analysis on 2 groups of sequences with different annotation files.

Run enrichment analysis on 2 groups of sequences with different annotation files.

It is possible to perform a Fisher Exact Test on the 2 groups even if the annotation is in different files (.annot).

First, both .annot files (group 1 and group 2) need to be loaded into Blast2GO.
The test and reference set have to be generated according to the groups you want to compare. These are normal text files with the sequence name in one column.

Example:
TestSet (group1.txt)
Seq1
Seq2
Seq3

RefSet (group2.txt)
Seq4
Seq2
Seq5

The following steps describe how to load both annotation files into OmicsBox and how to create the reference and test sets in order to compare two groups.

1) Load the .annot file of group 1 in OmicsBox Add the .annot file of group 2 to the already loaded project (File > Load > Load Annotation Add to existing Project).
2) Generate the test set for group 1 and the reference set for group 2. These lists of sequence IDs have to be in .txt format.
3) Once the .annot files are loaded into OmicsBox and both files have been created it is possible to execute Fisher’s Exact test on these 2 groups;
-> go to Functional Analysis > Enrichment Analysis > Fisher’s Exact Test and now select group1.txt as Test set and group2.txt as Reference set.

Remember that the Fisher’s Exact Test implementation is sensitive in the direction of the test: the sequences that are present in group1 and also in group2 will be deleted from group2, but not from group1.
If you have sequences in common in both lists (e.g. Seq2) and you want to perform a test which is insensitive to the direction of the comparison, select the option Remove double IDs when performing the test.

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