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I am computer scientist working on machine learning methods applied to predicting missing Gene Ontology annotations. In many papers, I wrote that my computational methods are very useful to suggest to the biologists on which gene functions they should address their research, because my software need less resources (a simple laptop connected to a database) and less time (e.g. with a dataset of all the Homo sapiens Gene Ontology annotations: about 3 hours) than their biological experiments.

Now a reviewer asked me to be more precise. Truly, how much does an in vitro experiment to biologically validate a human Gene Ontology annotation run by biologists cost?

How much money, broadly?

How much time?

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Wow that can vary from a couple of months and a few thousand dollars to a lifetime and millions of dollars. I can give a couple of examples, but this is an extremely broad question. Wet science is not cheap might be the message here.

Gene Ontology terms are meant to cover all biological roles known for genes. Terms are added and retire regularly. They embody thousands of person-years of work to establish the framework of what is going on in cells. At the same time its a limited vocabulary of gene behavior. It doesn't represent a complete catalog of all known gene behaviors (e.g. in such detail that it could only be the property of a specific gene) and it is also uneven in the level of its detail of its leaf terms. Its an ontology that is manually assembled and edited and therefore subjective.

I just did an overview of GO 1.2. there are 34153 unique GO terms. That's easily 10s of thousands of separate assays, so picking a group of important ones might be useful. There are also lots of orphan GO terms, where only one gene is currently attached to the term.

For GO annotations, a simple and typical case is a metabolic gene which has a high homology to a known gene and you are only trying to verify that biological role, and you have a functioning biological laboratory.

A breakdown might be:

  • clone the gene ( \$200 to \$1000 and up): order primers, use PCR to insert the gene into a plasmid or get the gene synthesized if you have to, transform it into bacteria, ideally sequence it to make sure you have it right.
  • purify the protein ( \$500 maybe). Run a check culture to see if the protein is produced, then run a full culture with induction, lyse it and then purify on an affinity chromatography column. you may need to run a second column to get the protein pure.
  • do a kinetics study with mass spectroscopic validation of the products (minimally about \$300). Cost involves reagents - if you have an assay you can use a UV/Vis spectrophotometer this can be simple, if not it can be much more expensive. This part will vary with the enzyme you are looking at.

Hopefully you get all these steps right the first time. Salaries are not included in this cost.

The more complicated the GO term, the more difficult the work will be - they are not all equal. If the protein function can't be verified in isolation, but must be in situ (i.e. in the living organism). Then you start to get into time. What if your gene is involved in protein routing through the golgi apparatus and modulates the function of other proteins for instance? That's going to require a very specialized and difficult set of experiments that should involve someone with experience in that field.

Finding GO annotations which are not clear from sequence similarity - unknown functions or new genes which reflect previously unestablished GO Terms could cost even more and take a good deal longer.

Still, high throughput studies are being done to find and validate electronic GO annotations. And with that scale, the cost per experiment will go down. Take a look at Olga Troyanskaya's research for an example of such an effort.

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Can you please escape the $ signs with \$ to prevent SX going into the math mode? –  Chris Dec 16 '13 at 10:34
    
thanks - got it. –  shigeta Dec 16 '13 at 10:36
    
@shigeta Thanks a lot, that is what I was looking for. And for the example you give the \$ prices, can you also give a broad time schedule? –  DavideChicco.it Dec 16 '13 at 21:10
    
Hi David, If you had a well equipped laboratory, but without high throughput scaling, It could take 2-3 weeks per enzyme in the simple case. Also the costs of the reagents will vary - they can be expensive... –  shigeta Dec 17 '13 at 4:34
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