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Glioblastoma Gene Expression Data from TCGA and GEO

PostPosted: Mon Mar 07, 2016 9:19 pm
by schen072
Below attached file are the data from TCGA and GEO filtered by
Disease of Interest: Glioblastoma
Variables of Interest Age, Gender, Genes Expressed, Tumor Status
Genes Expressed in Tumor free and with Tumor Patients.

Re: Glioblastoma Gene Expression Data from TCGA and GEO

PostPosted: Tue Mar 08, 2016 6:50 am
by schen072
The Gene expression data were normalized and a set of genes are selected based on the correlation statistics between gene expression and disease.

Re: Glioblastoma Gene Expression Data from TCGA and GEO

PostPosted: Thu Jun 30, 2016 10:13 am
by lsand039
I have a few questions regarding the GEO samples in the Full Dataset with Demographics and Gene expression file. Which GEO data sets did you use? I've tried to find out by searching the sample ID name/ patient barcode (GSM#####) in the GEO Accession viewer, but the ages and the genders don't match up to the sample IDs. It looks like the data were taken from the file GDS1816, based off the order the sample ID names/ patient barcodes, but the rest of the information doesn't match up. Were the ages descretized? Were the gene expression values normalized? If so, how?

Re: Glioblastoma Gene Expression Data from TCGA and GEO

PostPosted: Thu Jun 30, 2016 1:41 pm
by schen072
lsand039 wrote:I have a few questions regarding the GEO samples in the Full Dataset with Demographics and Gene expression file. Which GEO data sets did you use? I've tried to find out by searching the sample ID name/ patient barcode (GSM#####) in the GEO Accession viewer, but the ages and the genders don't match up to the sample IDs. It looks like the data were taken from the file GDS1816, based off the order the sample ID names/ patient barcodes, but the rest of the information doesn't match up. Were the ages descretized? Were the gene expression values normalized? If so, how?



You can check the file now. I have submitted the Non discretized data for your reference.

Re: Glioblastoma Gene Expression Data from TCGA and GEO

PostPosted: Fri Jul 01, 2016 1:41 pm
by lsand039
Did you use data set GDS1816? I can't seem to find the gene expression values for A2BP1, ACSBG1, ACTR3B, ADAM18, and AARS in the original file I found of GDS1816.