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.

GPL16110

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
ADD COMMENT
1
Entering edit mode

I just cleaned up your post. Please don't separate "tags" using spaces, use Enter/Return instead.

ADD REPLY
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.

ADD REPLY
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.

ADD REPLY
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.

ADD REPLY

Login before adding your answer.

Traffic: 2500 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6