Create a Gene-List using QuickGO
Create a list of genes sharing a Gene Ontology annotation
You may need a list of all annotated receptors in order to cross it with your list of experimentally identified genes and prioritise the receptors among them.
This QuickGO tutorial is avery basic example of what you can do. More advanced tools exist to enrich you gene lists using GO knowledge, please refer to Bingo (a Cytoscape plugin ) or Bioconductor packages and [R] tools (for more advanced users).
Access QuickGo and search for Membrane receptors in human
Type some search keyword and identify the best hit (here GO:0098802)
click it and move to the dedicated page
change to the 'Protein Annotation' TAB</br> click on the 'Filter' icon on the right
move to the 'taxon' TAB and check the box for human to restrict the search to human genes (proteins)
change to the 'GO identifier' TAB and review the possible further restrictions
when satisfied, click on 'submit' at the bottom of the screen (the search starts NOW)
in the resulting window, change to 'Protein Annotation' and review the results
when satisfied, click on the 'Download icon' on the right
select Tab separated values from the drop-down menu
Select gzip to speed up download (or not if you cannot unzip files on your laptop)
The files probably named associations.tsv.gz is now in your download folder
Cleanup the obtained data and extract unique gene symbols
The table contains a lot of information, including a column of gene symbols with duplicate rows for a given genes. We need a list of unique symbols to proceed with other applications. This can easily be done using Excel as shown below.
first open the tsv file in excel.
then select the column of symbols and copy them to a new worksheet
re-select the column and use 'Data/Sort' to sort them alphabetically (all duplicates follow each other after this step)
re-select the same column and now call 'Data/Filter' => 'Advanced Filter'
check 'Unique records only' and click OK
copy the resulting area again
Paste the resulting clipboard in a new worksheet or in some text file and keep it preciously. Name your file with a meaningful name (eg the hsGO-0098802_list.txt)
Compare your list with other lists
As a dummy example, we searched for GO:0006915 apoptotic process and used the two lists to look for overlap.
download exercise files
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