Master Table of GEO Brain Tumor Datasets

GEO Brain Tumor Microarray and RNA-seq Data Cleaning

Re: Master Table of GEO Brain Tumor Datasets

Postby bernardoj » Mon Mar 11, 2019 8:21 pm

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.
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Cleaned and merged datasets for brain tumor

Postby zgong001 » Thu Aug 15, 2019 3:03 pm

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.
Attachments
Merged Data.zip
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Re: Master Table of GEO Brain Tumor Datasets

Postby bernardoj » Thu Sep 26, 2019 8:02 am

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
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Re: Master Table of GEO Brain Tumor Datasets

Postby Olu1 » Thu Oct 03, 2019 1:24 pm

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.
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Re: Master Table of GEO Brain Tumor Datasets

Postby Olu1 » Tue Feb 18, 2020 11:15 am

Hello everyone.

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

Thanks.
Attachments
Astro&Glio.csv
Astrocytoma and Glioblastoma merged data
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Re: Master Table of GEO Brain Tumor Datasets

Postby bernardoj » Mon Apr 06, 2020 12:46 pm

Here is the list of all the datasets with how many genes and subjects as well as their study focus.
Attachments
Gene Sets.xlsx
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Re: Master Table of GEO Brain Tumor Datasets

Postby bernardoj » Tue May 26, 2020 12:36 pm

Here are some datasets I found looking through the recent GEO datasets
Attachments
Recent Gene Datasets.xlsx
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Re: Master Table of GEO Brain Tumor Datasets

Postby RLWIII » Mon Jul 06, 2020 5:45 pm

Updated Table to Include

GSE 2223
GSE 4536
GSE 4290
Attachments
0706RW.xlsx
Datesets appear to lack age, gender. These are mentioned in the paper. Two missing gene number.
(143.02 KiB) Downloaded 77 times
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Re: Master Table of GEO Brain Tumor Datasets

Postby zgong001 » Mon Jul 20, 2020 8:24 am

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.
Attachments
Brain Tumor Datasets updated on Jul-16-2020.xlsx
(152.99 KiB) Downloaded 78 times
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Re: Master Table of GEO Brain Tumor Datasets

Postby RLWIII » Mon Jul 20, 2020 2:00 pm

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
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