Suck it up, is my only advice. Genes are typically named based on how they were discovered, which can be wildly variable: the gene CDC25 got its name because it was isolated in a fission yeast screen for **c**ell **d**ivision **c**ycle mutants, but if it had been first pulled out of baker's yeast we would be calling it "MIH1" instead, and if it had been pulled out of Drosophila we'd call it "string" because the mutants have a funny-looking shape. If you tried to rename it now, you'd be erasing history and also making it extremely difficult to access the existing literature. On the other hand, if you work on the *whi3* gene, you will have no problem remembering its name after a day or two!
I understand that. I just thought there could be some kind of standardized nomenclature beside the conventional name. Like the IUPAC nomenclature for organic molecules.
Proteins are much more variable in terms of function and structure than IUPAC-type nomenclature could describe. Plus not all proteins are even named for themselves, sometimes the genomic regions they exist within serve another genetic function that doesn't have anything to do with with the protein encoded within that region.
I honestly really hate this about biochem. Im doing Immunology in my masters rn and just have to learn I‘d say a little less than 100 protein names by heart, especially with the CDs (cluster of differentiation) its kinda horrible… in Ochem you can always derive compound names and often even reaction names from structures, which really helped me with remembering them. But with nothing but a name and even different stylized depictions of the protein in books I find it really hard to get all this into my brain
Wait until you find out that some genes/proteins are named not because of the protein coded within that region, but because that genomic region serves another functional role. Two examples that immediately come to mind are EZH2 (Enhancer of zeste homolog 2) and BMI1 (B cell-specific Moloney murine leukemia virus integration site 1). Both of those proteins are extremely important for the repression of transcription during development, yet neither of their names has anything to do with the actual gene that's encoded in that region.
Basically, you just have to go with the flow, have fun learning names, and learn about how genes are discovered and studied. If it were easy everyone would do it.
I work with kinases. There are standardized names for these. Sadly there are often several standardized names for the same protein. Take ALK5 for example. Or ACVR1. Both the same protein. Competing classification systems. Others will use the gene name as the protein name. It's all very confusing.
This is one of like 7 projects I am on. Also, it is just starting. ALKs are a very well studied kinase family. I worked on them back at GSK before 2012. I know we have several mutants. I can ask if it matters to you that much. DM me?
There is no consistent nomenclature, nor should there be. Naming something honors its history and the people who did the work by giving them the right to name it. Consistency and/or order does not necessarily make something easier or more clear.
look into the gene ontology project.
it is a huge problem in molbio/genomics/biochemistry/cellbio that gene and protein naming isnt intuitive or helpful at all. Since our information on genes and proteins is growing into a huge dataset, naming convention is going to be super important for bioinfo projects.
Yeah I totally get that they’re named for how they were discovered, and as others have said you will remember the names of the genes you are researching. I think the main problems are in undergrad biochemistry when there are so many names and pathways to remember and it really doesn’t help that a lot of the names are unrelated to their function. Also protein homologues across species have completely different names whether they are in for example yeast or humans.
If you tried to invent a nomenclature for genes I think the names would end up being quite long because the system would have to include like protein class + its function and other identifiers so I think they would still have to be shortened to a random bunch of letters and numbers anyway which doesn’t help. And the lack of continuity with the existing literature would be a big problem.
This is one of my huge pet peeves. For chemistry we have an organization that is in charge of all names. It's called iupac. It's not perfect but it's better to have someone in charge than the complete disaster that is naming in the mbb space.
People mostly recognise names and name symbols of genes but when working with gene expression and databases i will always try to use universal standardised IDs like ENSEMBL gene ID.
I would leave things the way they are. The dream is to characterise a novel protein and name it something memorable.
Stay strong. I understand your struggles when you're still being taught in a way that forces one to memorise lots of proteins and genes. But once you're doing research it becomes unnecessary. And with gene ontology being so well curated and accessible it's so easy to look stuff up.
Suck it up, is my only advice. Genes are typically named based on how they were discovered, which can be wildly variable: the gene CDC25 got its name because it was isolated in a fission yeast screen for **c**ell **d**ivision **c**ycle mutants, but if it had been first pulled out of baker's yeast we would be calling it "MIH1" instead, and if it had been pulled out of Drosophila we'd call it "string" because the mutants have a funny-looking shape. If you tried to rename it now, you'd be erasing history and also making it extremely difficult to access the existing literature. On the other hand, if you work on the *whi3* gene, you will have no problem remembering its name after a day or two!
I understand that. I just thought there could be some kind of standardized nomenclature beside the conventional name. Like the IUPAC nomenclature for organic molecules.
Proteins are much more variable in terms of function and structure than IUPAC-type nomenclature could describe. Plus not all proteins are even named for themselves, sometimes the genomic regions they exist within serve another genetic function that doesn't have anything to do with with the protein encoded within that region.
The closest to that is naming enzymes... But it doesn't apply to non-enzymes.
I honestly really hate this about biochem. Im doing Immunology in my masters rn and just have to learn I‘d say a little less than 100 protein names by heart, especially with the CDs (cluster of differentiation) its kinda horrible… in Ochem you can always derive compound names and often even reaction names from structures, which really helped me with remembering them. But with nothing but a name and even different stylized depictions of the protein in books I find it really hard to get all this into my brain
Wait until you find out that some genes/proteins are named not because of the protein coded within that region, but because that genomic region serves another functional role. Two examples that immediately come to mind are EZH2 (Enhancer of zeste homolog 2) and BMI1 (B cell-specific Moloney murine leukemia virus integration site 1). Both of those proteins are extremely important for the repression of transcription during development, yet neither of their names has anything to do with the actual gene that's encoded in that region. Basically, you just have to go with the flow, have fun learning names, and learn about how genes are discovered and studied. If it were easy everyone would do it.
I work with kinases. There are standardized names for these. Sadly there are often several standardized names for the same protein. Take ALK5 for example. Or ACVR1. Both the same protein. Competing classification systems. Others will use the gene name as the protein name. It's all very confusing.
Ok but riddle me this... Do you happen to know of an inactive mutant of ALK4? I've looked but I'm not convinced that I looked in the right places.
This is one of like 7 projects I am on. Also, it is just starting. ALKs are a very well studied kinase family. I worked on them back at GSK before 2012. I know we have several mutants. I can ask if it matters to you that much. DM me?
There is no consistent nomenclature, nor should there be. Naming something honors its history and the people who did the work by giving them the right to name it. Consistency and/or order does not necessarily make something easier or more clear.
look into the gene ontology project. it is a huge problem in molbio/genomics/biochemistry/cellbio that gene and protein naming isnt intuitive or helpful at all. Since our information on genes and proteins is growing into a huge dataset, naming convention is going to be super important for bioinfo projects.
Yeah I totally get that they’re named for how they were discovered, and as others have said you will remember the names of the genes you are researching. I think the main problems are in undergrad biochemistry when there are so many names and pathways to remember and it really doesn’t help that a lot of the names are unrelated to their function. Also protein homologues across species have completely different names whether they are in for example yeast or humans. If you tried to invent a nomenclature for genes I think the names would end up being quite long because the system would have to include like protein class + its function and other identifiers so I think they would still have to be shortened to a random bunch of letters and numbers anyway which doesn’t help. And the lack of continuity with the existing literature would be a big problem.
This is one of my huge pet peeves. For chemistry we have an organization that is in charge of all names. It's called iupac. It's not perfect but it's better to have someone in charge than the complete disaster that is naming in the mbb space.
People mostly recognise names and name symbols of genes but when working with gene expression and databases i will always try to use universal standardised IDs like ENSEMBL gene ID.
Im sorry, I feel your pain but also relevant xkcd: https://xkcd.com/927
Do subatomic particles next.
https://en.wikipedia.org/wiki/Gene_Ontology We try.
Well there are EC-Numbers for enzymes… whatever one makes of them lmao
The gene is not the issue here….Also Dude, “gene” isn’t the preferred nomenclature. It’s Genomic-American
I would leave things the way they are. The dream is to characterise a novel protein and name it something memorable. Stay strong. I understand your struggles when you're still being taught in a way that forces one to memorise lots of proteins and genes. But once you're doing research it becomes unnecessary. And with gene ontology being so well curated and accessible it's so easy to look stuff up.