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Creating a list from an external source List analysis page

The example list check matches 7 genes successfully but contains 3 discrepancies - two low quality matches and a converted type:

  1. Low quality matches: A low quality match is one that does not match the main identifiers in the database but which was found by searching the synonyms. In this case Dsix3 and FBgn0011647 are old (or secondary) identifiers. However, it has found the genes that we want so we can add both to our list by clicking on 'add' in the last column.

  2. Converting types: When we uploaded our list we specified that we wanted to make a list of genes. However one item in our list is actually a protein identifier (PAX6_DROME). FlyMine has found this protein in the database along with the gene that encodes it. It is not possible to make a list of mixed 'types' but we can now add the gene for this protein to our list.

  3. Duplicate genes: You may also see discrepancies called 'Duplicate genes'. This can occur if, for example, you have gene symbols in your list and the symbol is found in more than one organism. Such discrepancies can be avoided by using the optional organism constraint on the list upload page. It will also happen when two gene symbols differ in case, since FlyMine is not case-sensitive.

In any of these case, all occurrences of the gene will be listed and you can select the one you intended to be in your list. Once you are happy with your list you can give it a name, eg. eye_genes_dmel, and press Save list.

[list_confirm.png]

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Creating a list from an external source List analysis page