Question: Determining Up and Down regulated genes from GEO GDS4296
0
gravatar for hAjmal
4.8 years ago by
hAjmal40
hAjmal40 wrote:

Hi All, How to see if the genes are up or down regulated in the publicly available dataset GDS4296 which contains analysis from cell lines from 9 different cancer tissue of origin types (Breast, Central Nervous System, Colon, Leukemia, Melanoma, Non-Small Cell Lung, Ovarian, Prostate, and Renal) from the NCI-60 panel? Regards

geo regulation R gene • 1.6k views
ADD COMMENTlink written 4.8 years ago by hAjmal40

Have you tried the GEO2R option available from within GEO? That a quick and easy method that tends to work well enough.

ADD REPLYlink written 4.8 years ago by Devon Ryan98k

Yes I have looked into that, but what I dont understand is what will be the control(no cancer) group?

ADD REPLYlink written 4.8 years ago by hAjmal40

Control is the group of samples, with which you will have to compare the patient samples. For each tissue, there should be different controls.

ADD REPLYlink written 4.8 years ago by Deepak Tanwar4.1k

Thats where I find it confusing. I want to analyze this GEO dataset with levels in non cancerous samples. I dont know which ones are the control (non cancer) samples, if any

ADD REPLYlink written 4.8 years ago by hAjmal40

Can you mention the GEO ID?

ADD REPLYlink written 4.8 years ago by Deepak Tanwar4.1k

The acession number is GEO GDS4296

ADD REPLYlink written 4.8 years ago by hAjmal40

The cancer panel doesn't have controls with it. You can only look at differences between cell types.

ADD REPLYlink written 4.8 years ago by Devon Ryan98k

Thanks. I have moved to another dataset "GSE62944"

ADD REPLYlink written 4.8 years ago by hAjmal40
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2316 users visited in the last hour