Dear all :
I downloaded a data set from http://comppi.linkgroup.hu/downloads (Integrated protein-protein interaction dataset / C elegans) but it does not have a label if they are essential or not, How could I get these labels? I found out some of them in " http://ogee.medgenius.info " but many of them don't exist in this site.
Thank you for your time.
Assuming that for you essential means loss of function is lethal, here is how you can go:
- On the WormBase site, go to Tools > Ontology browser
- In the phenotype ontology (bottom of the page) look for phenotype "lethal" (variant > development variant > organism development variant > lethal)
- click on "lethal"
- In the tree at the bottom of the page, the term becomes highlighted in green and next to it you have the number of gene products annotated with this term
- Click on this and you get a list of the corresponding genes.
I really appreciate for your answer and consideration. I only want to find out is this WBgene of specific protein essential or not like this site : http://ogee.medgenius.info/browse/Caenorhabditis%20elegans but this site does not have many of WBgene IDs.
From this link, the data corresponds to only one publication testing ~11000 genes and essentiality is defined as embryonic lethality or sterility. You can get this also from Wormbase by selecting the relevant phenotypes in the way I explained above. The difference is that WormBase data is collected and curated over many different screens and experiments so will be more comprehensive.
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A protein is only essential in some context, i.e. what is it essential for ? The reference for C. elegans is Wormbase. You could search there for "essential" genes.
Thank you for your reply, the dataset that I have, many of them do not have WBGene ID and when I find these IDs of proteins I could not find labels either in this site.
You'll have to convert your protein IDs to gene IDs
Most of the proteins have gene ID(i.e. WBGene00003576) but I could not find more than half of gene ID is essential or not like these ones : P03949 WBGene00000018 Q23500 WBGene00000040 Q95ZL1 WBGene00000066 ... I really do not know what to do ?!
I am not sure I understand the problem. WBGene00000040 has no phenotype and lethal phenotypes are reported as not observed for WBGene00000018. However, WBGene00000066 is reported as embryonic lethal. See my answer below for a way of doing it.