<p>Hi, I'm a computer scientist working on PPI networks. I'm trying to understand the concept of synonym. How are synonyms defined and how can one conclude that 2 gene names are synonyms? </p>

<p>I thought they would be the same or almost same, having very similar sequence and interactions but I found counter examples. For example I'm wondering how this situation does exist:</p>

<p>I found a gene in Homo Sapiens called MEN1 (official symbol). When I look at its synonyms, I see SCG2 which is the official symbol of a gene also in Homo Sapiens.</p>

<p>There are 2 genes. They are both in Homo Sapiens and they are synonyms. Their interactions are completely different.</p>

<p>I could not find much information about this issue. I'd like to know the definition of synonym and if I can assume two genes that are synonyms are the same for some specific cases.</p>

<p>Synonyms are a curation issue. Alternative names are generated from a variety of situations: some are different labs stumbling on to the same gene, some are simple differences between characters (MEN1, MEN 1, MEN-1). Sometimes large-scale projects generated some form of coded designation (such as 1200015E08Rik, a mouse example). </p>
<p>Alternate names are collected by curation teams at various places. Some come from papers read by curators. Some would have come from computational sources. Most of them are shared around, but there may be some sources that have some name that others don't. </p>
<p>There are nomenclature standards that are supposed to be used, and there are committees that establish the rules and assign official names and symbols. However, some people refuse to use those names in publications and revert to their preferred name.</p>
<p>The official name/symbols shouldn't have duplicates. But the synonyms might--so what you are seeing with SCG2 could certainly be 2 different genes. </p>
<p>EDIT: If you are new to this arena maybe you should see some nomenclature stuff. Here's the mouse stuff, maintained by Jax, where I learned about it:
<a href="http://www.informatics.jax.org/mgihome/nomen/index.shtml">http://www.informatics.jax.org/mgihome/nomen/index.shtml</a></p>
<p>Here's the HUGO site for human <a href="http://www.genenames.org/">http://www.genenames.org/</a></p>