Create a Gene-List using QuickGO

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Create a list of genes sharing a Gene Ontology annotation


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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[1] 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 [2]) or Bioconductor packages and [R][3] tools (for more advanced users).

Access QuickGo and search for Membrane receptors in human

Handicon.png Consider viewing the videos and following the training material present on the site


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Type some search keyword and identify the best hit (here GO:0098802)


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click it and move to the dedicated page


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change to the 'Protein Annotation' TAB</br> click on the 'Filter' icon on the right


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move to the 'taxon' TAB and check the box for human to restrict the search to human genes (proteins)


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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)


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in the resulting window, change to 'Protein Annotation' and review the results
when satisfied, click on the 'Download icon' on the right


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select Tab separated values from the drop-down menu


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Select gzip to speed up download (or not if you cannot unzip files on your laptop)


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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.


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then select the column of symbols and copy them to a new worksheet


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re-select the column and use 'Data/Sort' to sort them alphabetically (all duplicates follow each other after this step)


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re-select the same column and now call 'Data/Filter' => 'Advanced Filter'


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check 'Unique records only' and click OK


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copy the resulting area again

Technical.png the current selection is not OK as it still contains the hidden duplicates, you need to re-select the area by clicking on teh top symbol, moving to the last row and shift-clicking the last symbol


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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)

Handicon.png this basic workflow can be used for any combination of GO queries

Compare your list with other lists

You are now good to go crossing this list with your data or other lists and find overlap; a good easy way to compare lists of gene names is Venny[4]

As a dummy example, we searched for GO:0006915 apoptotic process and used the two lists to look for overlap.


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download exercise files

Download exercise files here.

Use the right application to open the files present in result-files
References:
  1. ↑ https://www.ebi.ac.uk/QuickGO/
  2. ↑ http://www.psb.ugent.be/cbd/papers/BiNGO/Tutorial.html
  3. ↑ https://www.bioconductor.org/help/workflows/annotation-data/
  4. ↑ http://bioinfogp.cnb.csic.es/tools/venny/


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