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Re: Master Table of GEO Brain Tumor Datasets

PostPosted: Mon Mar 11, 2019 8:21 pm
by bernardoj
I've been working with Zhenghua to prepare the datasets and we've managed to merge a few of the datasets. We've run into an issue where we don't have enough memory to merge the Case Control datasets and the Astrocytoma datasets. We're going to need a more powerful computer.

Cleaned and merged datasets for brain tumor

PostPosted: Thu Aug 15, 2019 3:03 pm
by zgong001
The attachment is the cleaned and merged dataset based on the above posted. For each of Glioblastoma and Astrocytoma, it has two cleaned and merged datasets. One was cleaned and merged by gene, and another was cleaned and merged by subject.

Re: Master Table of GEO Brain Tumor Datasets

PostPosted: Thu Sep 26, 2019 8:02 am
by bernardoj
Here is the Glioblastoma and Astroyctoma Case Control Datasets seperated and merged by gene and subject.
I couldn't directly upload the zip files but here is the google drive link to it.
https://drive.google.com/open?id=1UbVDX ... HhN0TglfiF

Re: Master Table of GEO Brain Tumor Datasets

PostPosted: Thu Oct 03, 2019 1:24 pm
by Olu1
I try to make sense of the original glioblastoma data before merging by reviewing them in NCBI database, and i found out that some datasets grouped witth GRADE do not have any grade information. Also, some grouped with SURVIVAL do not have any survival info. Treatment group is okay.

The following were grouped as GRADE: GSE9885, GSE84010, GSE73038, GSE53228, GSE42670, GSE36426, GSE31545, GSE25632, GSE10878. But GSE9885, GSE73038 and GSE42670 do not have any grade info, even though the are tumor samples. Instead GSE9885 has survival info, although not extracted. It will be good to merged it with survival group instead.

The following also were grouped as SURVIVAL: GSE84010, GSE7696, GSE42670, GSE31545 but GSE42670 and GSE31545 do not have any survival info. I suggest the should be removed from the group.

Re: Master Table of GEO Brain Tumor Datasets

PostPosted: Tue Feb 18, 2020 11:15 am
by Olu1
Hello everyone.

I merged astrocytoma and glioblastoma (case-control and grade) data set.
Please see attached file, and review for comments and corrections.

Thanks.

Re: Master Table of GEO Brain Tumor Datasets

PostPosted: Mon Apr 06, 2020 12:46 pm
by bernardoj
Here is the list of all the datasets with how many genes and subjects as well as their study focus.

Re: Master Table of GEO Brain Tumor Datasets

PostPosted: Tue May 26, 2020 12:36 pm
by bernardoj
Here are some datasets I found looking through the recent GEO datasets

Re: Master Table of GEO Brain Tumor Datasets

PostPosted: Mon Jul 06, 2020 5:45 pm
by RLWIII
Updated Table to Include

GSE 2223
GSE 4536
GSE 4290

Re: Master Table of GEO Brain Tumor Datasets

PostPosted: Mon Jul 20, 2020 8:24 am
by zgong001
Updated Master Table.
Added datasets from what Bernado found. http://smlg.fiu.edu/phpbb/viewtopic.php?f=84&t=145&p=1866#p1852

Added datasets from paper: Reverse Engineering of Modified Genes by Bayesian Network Analysis Defines Molecular Determinants Critical to the Development of Glioblastoma.

Added datasets from paper: Genome-wide expression profling of glioblastoma using a large combined cohort.

Re: Master Table of GEO Brain Tumor Datasets

PostPosted: Mon Jul 20, 2020 2:00 pm
by RLWIII
Zhenghua,

Thank you so much for doing this. I was about to do the top portion of it it today. I really appreciate you taking the time to work on this.

Best Wishes,
-Roy