How to deal with "///" in between gene symbols?

Question

[fatematuzzohara3]

Hello,

I am currently doing a project on 'identifying therapeutic genes related to hepatocellular carcinoma'. I have used GEO2r tool to screen the DEGs. However, I am getting genes name like "HSPB2-C11orf52///C11orf52///HSPB2" or "MIR1282///HYPK///SERF2". I wanted to know what this /// means. Should I separate them from "MIR1282///HYPK///SERF2" to MIR1282 HYPK SERF2, or should I keep it together as it is? Also there are some gene names like "LOC101930404" (uncharacterized LOC101930404). Should I remove these? It would be really great if someone could help me regarding this.

Thank you

[fracarb8]

They might be fusion genes between 2 adjacent genes.

Answer 1

[Kevin Blighe]

What fracarb8 says makes sense but may not account for every situation. At the HSPB2 locus, it looks like there's just a lot of 'complicated' transcription occurring:

https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr11%3A111902034%2D111929551&hgsid=1493203251_omalH4KPZAT1yl4YLjPMYIsHjmf9

You can choose to rename them to just the first gene mentioned in each sequence, if you wish, but then duplicates may be created. As the analyst, it is your role to make an executive decision about how to manage these.

Kevin

[fatematuzzohara3]

Thank you very much for the clarification