Glioblastoma Gene Expression Data from TCGA and GEO

Analyses related to genomic, proteomic, clinical and envirointal interactions in brain tumor

Glioblastoma Gene Expression Data from TCGA and GEO

Postby schen072 » Mon Mar 07, 2016 9:19 pm

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.
Attachments
Subjects Demographics.txt
This File Only contains Subject Demgraphics
(9.47 KiB) Downloaded 532 times
Full Dataset with Demographics and Gene Expression.txt
Full dataset
(46.8 KiB) Downloaded 568 times
Gene Expression Data.txt
Gene Expression data relating to Above file
(42.15 KiB) Downloaded 554 times
Last edited by schen072 on Thu Jun 30, 2016 1:41 pm, edited 1 time in total.
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Re: Glioblastoma Gene Expression Data from TCGA and GEO

Postby schen072 » Tue Mar 08, 2016 6:50 am

The Gene expression data were normalized and a set of genes are selected based on the correlation statistics between gene expression and disease.
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Re: Glioblastoma Gene Expression Data from TCGA and GEO

Postby lsand039 » Thu Jun 30, 2016 10:13 am

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?
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Re: Glioblastoma Gene Expression Data from TCGA and GEO

Postby schen072 » Thu Jun 30, 2016 1:41 pm

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.
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Re: Glioblastoma Gene Expression Data from TCGA and GEO

Postby lsand039 » Fri Jul 01, 2016 1:41 pm

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.
Attachments
GDS1816_full.soft.tar.gz
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