The basics

The results for the template 'Gene --> Orthologues + GO terms of these orthologues' shows the starting gene, orthologous genes and organism names with details of each GO term applied to the orthologous genes. Orthologue data in FlyMine come from InParanoid. Note that 'main' means the best hit in the other organism, 'secondary' denotes paralogues of the best hit.

Summary buttons at the top of each column allow you to view some summary statistics. For names and identifiers it will tell you about unique values, numerical data gives the min, max, mean and standard deviation. In case of the example abobe, the summary button for the column 'Orthologue > GO annotation > name' shows you the most commonly occurring GO terms applied to orthologues of the original gene. (Note: it only shows the first 10 rows of summary).

Exporting and saving results

- All results pages have a number of export options:

Currently, either the entire results table or specific columns can be exported. If nothing is selected, the entire data set will be exported. If you do not wish to export certain columns these can be hidden using the small double arrow in the column header.

If the results table contains a column with objects that have a nucleotide or amino acid sequence, it is possible to export all sequences from that column in FASTA format. Currently, the FASTA export option will export the sequences belonging to objects in the first visible (i.e. not hidden) column only. Columns can be moved to the first position by using the arrows in the header. If objects appear more than once in the column, the sequence will only be exported once.

- Results pages also allow you to save your data to a new list or add them to an existing list:

Select the required data and either add it to an existing list or save it to a new list. Selecting the check boxes next to the column headings will select the entire column for saving. Alternatively, individual items can be saved by selecting check-boxes next to the items. Currently, a list can only contain one column. However, if you have multiple columns for the same item (eg a column for gene identifier and one for gene symbol), all related columns become highlighted when you select the checkbox next to one. This is because you are saving the actual item (eg the gene) to a list, not just the identifier.

Changing the output

To change the output of the results table, click on 'query' at the top of the results page:

This will display the template form again, and

will display the template query in the FlyMine Query Builder.