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This was a new and interesting question, one I haven’t seen before. Are there resources specifically highlighting essential genes in fly? I can see how a dedicated set of these would be useful, and how it could be challenging to extract that from other, more broad, tools and collections.
Question: database of gene essentiality in Drosophila?
I am looking for annotation of gene essentiality in Drosophila. The ideal resource would be a knockout or a RNAi screening which would tell me, for every gene, whether its deletion or silencing is lethal or not.
I saw that there are many resources online, from flybase to UCSC, but I could not find any annotation on gene essentiality there. There are also a lot of screenings published, but they all seem to be related to specific conditions (e.g. exposure to a DNA damaging factor, stress, etc..), but I could not find any screening in which no special conditions were applied. In general, I not familiar with Drosophila, and I am not sure what an expert in the field would use. Which resource do you recommend me?
–Giovanni M Dall’Olio
Giovanni found a couple of answers and brought them over, but if you know of any other useful collections it would be handy to have that information. I know there are various species knock-out projects, and likely more to come. But I was not familiar with the OGEE (Online GEne Essentiality Database) set. It’s not limited to flies, btw. And as I was reading up on OGEE, I saw a reference in PubMed to another essential gene database that was new to me: DEG, Database of Essential Genes. Reading up on that now too.
Chen W.H., M. J. Lercher & P. Bork (2011). OGEE: an online gene essentiality database, Nucleic Acids Research, 40 (D1) D901-D906. DOI: http://dx.doi.org/10.1093/nar/gkr986
Luo H., Lin Y., Gao F., Zhang C.T. & Zhang R. (2013). DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements., Nucleic acids research, PMID: http://www.ncbi.nlm.nih.gov/pubmed/24243843