One very common cause of confusion is use of the incorrect nomenclature to describe changes in the levels of genes, their mRNAs or the proteins that they encode. Constant changing from describing gene expression levels to protein levels and back again can also add to the confusion, especially because the names are often the same. Therefore, it needs to be completely clear to the reader exactly what level you are talking about.
Using proper nomenclature
Nomenclature differs among species, but generally gene names should be described in italics and protein names in normal font. Case (upper vs. lower) is often used to distinguish between species: generally, for mouse, rat and chicken, gene names are spelled with an upper case first letter and the rest in lower case; for humans, primates and some domestic species, gene names are spelled with all capital letters.
Descriptions of mRNAs generally use the gene name (levels of p53 mRNA), or you can refer to the mRNA "for" a given protein (levels of the mRNA for p53). The word "expression" is usually used to describe gene expression and can induce confusion when used to describe protein and mRNA levels. In most cases when referring to proteins, the word "expression" can simply be replaced with the word "level" (or "levels").
Be aware of the correct nomenclature for your species of subject and ensure that everywhere you refer to a protein, gene or mRNA by name in the text it is completely clear which of those you are referring to.
- "Expression of the Igf1 gene was increased in our transgenic mice." The use of italics and the word "gene" ensure that no confusion is possible here.
- "The levels of IGF1 mRNA were elevated in our patient group." This sentence uses correct nomenclature for human genes.
- "The serum IGF1 levels were elevated in the transgenic mice." Here, it is clear that the protein is being referred to. Capitals are appropriate in this case, even though the species is mouse, because it is the correct nomenclature for the mouse protein.