These gene symbol are from where? What source?

Question

[cfarmeri]

I have gene symbol list like following.

2-Sep
Hist2h4
5-Mar
Nupr1
7-Sep
5-Mar
15-Sep
11-Sep
Egam-1c

I have not ever seen "2-Sep" and "5-Mar" . These gene symbol are from where? you know?

Furthermore, do you know some ID conversion application able to change the above gene symbol to Ensemble ID.

[GenoMax]

Change the format on the column to "text" in excel and the transformation should get fixed. Then get that list out of Excel ASAP.

[gangireddy]

They are two different columns and you are viewing date and geneId columns together.

[zx8754]

How to avoid conversion of gene symbols to date format in Excel

Answer 1

[Devon Ryan]

Congrats, someone used Excel on the dataset!

https://nsaunders.wordpress.com/2012/10/22/gene-name-errors-and-excel-lessons-not-learned/

[cfarmeri]

Thanks Ryan! This URL looks so useful.

But This gene symbol list is downloaded from GEO ftp. I open this list file by "cat" UNIX command directly not use Excel.

This is responsible for the data contributor...

[Chris Miller]

Yep, that happens sometimes. I've seen published manuscripts with "10-Sep" listed as a gene. It's really exhibit A of why you shouldn't use excel.

Answer 2

[Chris Miller]

Here's a translation table, courtesy of Deanna Church:

[Devon Ryan]

Wow, some of those I could have predicted. But how the heck does C11orf40 get turned into 1-Nov?!?

[Chris Miller]

My best guess is that some of these are things that happen with non-english settings, but ¯_(ツ)_/¯

[cfarmeri]

Miller, thank you so much!

This table gives assistance to me.

[Данил]

Also MARC1 ->1-Mar and MARC2 -> 2-Mar

[Данил]

SELENOF -> SEP15

Answer 3

[igor]

Excel.

There is even a paper about this phenomenon: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-5-80

[cfarmeri]

thanks!

Script to scan for SymbolMutation error in this paper fig4 is so useful.