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:

	##Mar 13, 2015
	##Some 'date-names' are aliases and map to more than one gene
	#symbol date name
	SEPT1 1-Sep
	SEPT2 2-Sep
	SEPT3 3-Sep
	SEPT4 4-Sep
	SEPT5 5-Sep
	SEPT6 6-Sep
	SEPT7 7-Sep
	SEPT8 8-Sep
	SEPT9 9-Sep
	SEPT10 10-Sep
	SEPT11 11-Sep
	SEPT12 12-Sep
	SEPT13 13-Sep
	SEPT14 14-Sep
	POU2F2 2-Oct
	SLC22A2 2-Oct
	POU5F1 3-Oct
	POU5F1 4-Oct
	POU3F1 6-Oct
	SLC22A16 6-Oct
	POU3F2 7-Oct
	POU3F4 9-Oct
	POU2F3 11-Oct
	DEC1 1-Dec
	MARCH1 1-Mar
	MARCH2 2-Mar
	MARCH3 3-Mar
	MARCH4 4-Mar
	MARCH5 5-Mar
	MARCH6 6-Mar
	MARCH7 7-Mar
	MARCH8 8-Mar
	MARCH9 9-Mar
	MARCH10 10-Mar
	MARCH11 11-Mar
	FEB1 1-Feb
	FEB2 2-Feb
	FEB5 5-Feb
	FEB6 6-Feb
	FEB7 7-Feb
	FEB9 9-Feb
	FEB10 10-Feb
	FAM215A 2-Apr
	ATRAID 3-Apr
	MAGEH1 1-Apr
	PRKCD 1-May
	CTGF 2-Nov
	C11orf40 1-Nov

view raw ExcelMangledGenes hosted with ❤ by GitHub

[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.