When A Particular Gene Was Discovered Or Curated For The First Time

Question

[Ashutosh Pandey]

This question may be irrelevant for this forum.

Is there any way to know when was a particular gene discovered ? For example, for mouse genome there were lot of large scale EST studies during 1998-1999 and then the whole genome sequencing of mouse genome took place in 2002. There were lot of genes already known even before these large scale studies took place. I have this fun project where I am trying to find relation between number of articles associated with a gene and the number of years it has been known to the scientific community. I don't want to use PubMed (or the first paper for that gene) because a gene may have been known for a while but it might have taken 4-5 years before the first paper came out.

Thanks.

[JC]

it's a hard question, all the records in GenBank only report a possible date in the journal field, so you are directed to Pubmed.

[cdsouthan]

Not so, the primary mRNAs all have submission dates even if the RefSeqs have later dates

Afterthought, sorry if you meant the PubMed date is not always in the mRNA x-ref thats right. But UniProt entry will list the publication dates

[JC]

true, you can track the primary mRNAs with submission dates

[Ashutosh Pandey]

Hi JC and cdsouthan,

1) Can you tell me how can I get the mRNAs submission date for any gene? I mean which resource to use. I am good with eutils or parsing huge files but not sure about the resource to be used.

2) Also, do you think the "JOURNAL PUBMED" tag in GenBank entry would be of any use. I don't want to be too concerned about the actual date. For example if you click http://www.ncbi.nlm.nih.gov/nuccore/NM_010014.2 , then you can track that the first publication (though it may not be the actual first but at least it is according to GenBank) related to this mRNA is in 1996 (Scrambler, a new neurological mutation of the mouse with abnormalities of neuronal migration).

Thanks a lot.

Answer 1

[Istvan Albert]

I believe that the best possible answer is to use existing publications and mine those for answers.

Finding out just how long a someone may have been knowing about a gene before publishing it is probably impossible.

As with most scientific discoveries pinpointing the exact time and location is bound to lead to competing interpretation, this is more problematic when a final discovery is pieced together from partial knowledge that others have made available.

Answer 2

[cdsouthan]

Try the patent sequence databases. Between say 95 to 2000 many published filings (with dates on the patent sequence records) pre-date the first mRNA or paper. As Istvan says you have to have some kind of evidence to track. You can check for cases where EST coverage was high very early. I suspect very few people waited years, they knew they had to get the patent in, or the public mRNA out, asap

Some time back I did a related exercise where I used SRS to select "date range", "had mRNA" "had PubMed" "had word "novel" in title. This was selective for novel genes but many were not (i.e. they already had database entries from someone else)

This gives a bit of context

http://cdsouthan.blogspot.se/2012/07/gsk-buying-hgs-retroscopy.html