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 zgong001 » Tue Jul 28, 2020 8:20 am

Updated Master Table.
Added number of Diseased and number of control.
Attachments
Brain Tumor Datasets updated on Jul-27-2020.xlsx
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Re: Master Table of GEO Brain Tumor Datasets

Postby RLWIII » Tue Jul 28, 2020 12:06 pm

Thanks for doing this Zhenghua. I'm looking at it now.

Best,
-Roy
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Re: Master Table of GEO Brain Tumor Datasets

Postby RLWIII » Tue Jul 28, 2020 12:14 pm

It looks like overall, we were able to obtain 2447 diseased samples and 10 new controls from Bernardo's GEO list. From Tang et al, there were 4,218 diseased sample and 720 control samples obtained .
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Re: Master Table of GEO Brain Tumor Datasets

Postby zgong001 » Thu Aug 13, 2020 2:15 pm

The attachment is the updated Master table.

From Paper: Genome-wide expression profiling of glioblastoma using a large combined cohort. We took out the following datasets (which include both gender and age information and are highlighted in yellow in Master Table).

The first number in () is number of gene and the second number in () is the number of sample.
GSE35864.csv: (42990, 72)
GSE36245.csv: (36889, 46)
GSE5281.csv: (42990, 161)
GSE43378.csv: (42990, 50)
GSE19728.csv: (42990, 21)
GSE21354.csv: (42990, 18)
GSE13041.csv: (74263, 267)
GSE48350.csv: (42990, 253)
GSE44971.csv: (42990, 58)
GSE73038.csv: (42990, 182)
GSE24244.csv: (42990, 8)
GSE34824.csv: (32992, 27)
GSE15824.csv: (42990, 45)
GSE32374.csv: (42990, 21)
GSE21935.csv: (42990, 42)
GSE53890.csv: (42990, 41)
GSE13564.csv: (42990, 44)
GSE7696.csv: (42990, 84)
GSE49822.csv: (42990, 22)
GSE62802.csv: (42990, 20)
GSE43289.csv: (42990, 40)

The number of common gene in GSE5281, GSE7696, GSE13564, GSE15824, GSE19728, GSE21354, GSE21935, GSE24244, GSE32374, GSE35864, GSE36245, GSE43289, GSE43378, GSE44971, GSE48350, GSE49822, GSE53890, GSE62802, GSE73038 is 21659. After merge with GSE34824, the number of common gene is 17496. Then after merge with GSE13041, the number of common gene is 233.
Attachments
Brain Tumor Datasets updated on Aug-12-2020.xlsx
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Re: Master Table of GEO Brain Tumor Datasets

Postby RLWIII » Tue Aug 18, 2020 1:15 pm

Thank you Zhenghua for updating this table.

Clinical Variables from master table containing both age and gender summary.

Survival: 2 Total: GSE7696, GSE43378

Control/ Disease 4 total: GSE5281, GSE21935, GSE35864, GSE19728,

Grade 5 total: GSE43378, GSE43289, GSE15824, GSE19728, GSE21354

Notes: GSE19728 has grade and normal.
GSE48350 may contain grade
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Re: Master Table of GEO Brain Tumor Datasets

Postby zgong001 » Wed Sep 02, 2020 3:43 pm

The attachments are merged continuous and discrete datasets.
Attachments
Merged-discret.csv
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Merged-continue.csv
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Re: Master Table of GEO Brain Tumor Datasets

Postby zgong001 » Mon Sep 21, 2020 9:19 am

The attachments are the updated tables.
Male - 1, Female - 0, there are 720 males and 504 females, others are unknow.
Normal - 0, Disease - 1, there are 1127 disease and 128 normal
Attachments
Merged-continue-updated.csv
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Merged-discret-updated.csv
(42.03 MiB) Downloaded 79 times
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Re: Master Table of GEO Brain Tumor Datasets

Postby vsteb002 » Sun Oct 11, 2020 3:59 pm

Hi Zhenghua!

Thank you for the dataset!

Some of the genes has the following names

1-Mar
2-Mar
1-Mar
11-Mar
2-Mar
3-Mar
4-Mar
5-Mar
6-Mar
7-Mar
8-Mar
9-Mar

Are those correct gene names, or they got accidentally converted to the date format in excel?
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Re: Master Table of GEO Brain Tumor Datasets

Postby rtanv003 » Tue Nov 24, 2020 12:30 am

zgong001 wrote:The attachments are the updated tables.
Male - 1, Female - 0, there are 720 males and 504 females, others are unknow.
Normal - 0, Disease - 1, there are 1127 disease and 128 normal


This caused some of the genes to convert into dates because this updating has been done by excel. This also resulted in two genes to have same names, which are MARC1(1-Mar) and MARCH1(1-Mar).
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updated master table

Postby zgong001 » Mon Nov 30, 2020 8:48 am

The following is updated master table.
Attachments
Brain Tumor Datasets updated on Nov-18-2020.xlsx
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