How to convert the position of probes into Gene symbol or Entrez_id(Platform GPL16110)
0
0
Entering edit mode
6 weeks ago
linhzye • 0

Hi,

I get the data table of "GPL16110" from GEO.

There is no information about the 'symbol', and I don't know how to convert the ID to gene symbol.

The only information I can get are "ID, Chr, Position, GC Score, SNP_ID, SPOT_ID", and the column of "ID" is the same with the column of "SPOT_ID".

The head of the Data table is below:

|ID       |Chr|Position  |GC Score    |SNP_ID|SPOT_ID   |
|GA008510|  Y |13311305|0.5193345  |         |GA008510|
|GA008524|  Y |21152701|0.5739997  |         |GA008524|
|GA008529|  Y |21154004|0.4872587  |         |GA008529|
|GA008532|  Y |28463253|0.5228286  |         |GA008532|
|GA026677|  Y |2722814  |0.00656162|         |GA026677|
|GA026703|  Y |13324571|0.4636189  |         |GA026703|
|GA026708|  Y |15053296|0.02973483|      |GA026708|


The description shows that

Chr: Chromosome on which the probe is located

Position: Position of the probe on chromosome

I wanna try to seek the gene symbol in the Database "hg19" from "genome-mysql.soe.ucsc.edu" by using the value of "Chr" and "Position".

So I use

select distinct name2  from refGene where chrom="chrY" and txStart>=28463253 and txEnd<=28463253;


to find the probe "GA008532"

But the result is

Empty set (0.31 sec)


How can I convert the probe into Gene symbol?

Thank you very much!

geo convert Platform GPL16110 symbol • 173 views
1
Entering edit mode

0
Entering edit mode

Thank you very much. At beginning I was puzzled that the post edit is too clean. With no toolbar at all and when I use "Enter" to separate the "tags", the web page is just submitting the post. And the format of post changes. So I guess maybe the post just use the "Markdown" grammar to write. Then I learn to use "Markdown" to fix the post.

After I see your comment, and I cannot click the "Add reply" buttom, I realized that maybe for my bad network that block some URL. Now I use the VPNs to surf the website. It seems work well.

Thank you for ur help.

0
Entering edit mode

Ahh, I'm guessing you're in China/Iran - users there have reported problems with certain website features. Sorry for my curt comment and please let me know if I can help some more.

0
Entering edit mode

Never mind. We should abey the rules in any forums. I am not familiar with it, so I will try my best to learn it.