TCGA data in Glioblastoma and Lower grade Brain Cancer

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

TCGA data in Glioblastoma and Lower grade Brain Cancer

Postby cwyoo » Fri Apr 10, 2015 5:52 am

Please goto https://tcga-data.nci.nih.gov/tcga/tcgaHome2.jsp and download gene expression data for Glioblastoma and Lower Grade Brain Cancer. Post the original data, discritized data, and analysis results of banjo and ARACNE.
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Re: TCGA data in Glioblastoma and Lower grade Brain Cancer

Postby Kaumudi » Thu Mar 01, 2018 12:29 pm

Here are more links
Data Analysis
" The data and analysis results can be explored through
1. the Broad Institute FireBrowse portal (http://firebrowse.org/?cohort=GBMLGG),
2. the cBioPortal for Cancer Genomics (http://www.cbioportal.org/study.do?canc ... m_tcga_pub),
3. in a Tumor Map (http://tumormap.ucsc.edu/?p=ynewton.gliomas-paper),
4. the TCGA transcript fusion portal (http://www.tumorfusions.org),
5. TCGA Batch Effects (http://bioinformatics.mdanderson.org/tcgambatch/),
6. Regulome Explorer (http://explorer.cancerregulome.org/),
7. Next-Generation Clustered Heat Maps (http://bioinformatics.mdanderson.org/TCGA/NGCHMPortal/).
8. See also Supplemental Information and the TCGA publication page (https://tcga-data.nci.nih.gov/docs/publ ... ggbm_2015/).

that take you to glioblastoma and lower grade glioma data that was used in the following paper:

Cell. Author manuscript; available in PMC 2017 Jan 28.
Published in final edited form as:
Cell. 2016 Jan 28; 164(3): 550–563.
doi: 10.1016/j.cell.2015.12.028
PMCID: PMC4754110
NIHMSID: NIHMS746836
Molecular profiling reveals biologically discrete subsets and pathways of progression in diffuse glioma
Michele Ceccarelli,1,2,23 Floris P. Barthel,3,4,23 Tathiane M. Malta,5,23 Thais S. Sabedot,5,23 Sofie R. Salama,6 Bradley A. Murray,7 Olena Morozova,6 Yulia Newton,6 Amie Radenbaugh,6 Stefano M. Pagnotta,2,8 Samreen Anjum,1 Jiguang Wang,9 Ganiraju Manyam,4 Pietro Zoppoli,9 Shiyung Ling,4 Arjun A. Rao,6 Mia Grifford,6 Andrew D. Cherniack,7 Hailei Zhang,7 Laila Poisson,10 Carlos Gilberto Carlotti, Junior,5 Daniela Pretti da Cunha Tirapelli,5 Arvind Rao,4 Tom Mikkelsen,10 Ching C. Lau,11,12 W.K. Alfred Yung,4 Raul Rabadan,9 Jason Huse,13 Daniel J. Brat,14 Norman L. Lehman,15 Jill S. Barnholtz-Sloan,16 Siyuan Zheng,3 Kenneth Hess,3 Ganesh Rao,3 Matthew Meyerson,7,17 Rameen Beroukhim,7,17,18 Lee Cooper,14 Rehan Akbani,3 Margaret Wrensch,19 David Haussler,6 Kenneth D. Aldape,20 Peter W. Laird,21 David H. Gutmann,22 TCGA Research Network, Houtan Noushmehr,5,24,* Antonio Iavarone,9,24,* and Roel G.W. Verhaak3,24,*
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Re: TCGA data in Glioblastoma and Lower grade Brain Cancer

Postby Kaumudi » Sat Mar 03, 2018 5:17 pm

Excel sheet with gene expression values of 20330 genes for 667 patients with lower grade glioma (LGG) or glioblastoma. This is the LGGGBM cohort from Cell. 2016 Jan 28; 164(3): 550–563. detailed below. This data was downloaded from TCGa (the link to the site given below) as a text file, then converted to a .csv file and immediately transposed (through Perl commands in the terminal) so that the data could fit into Excel (20330 columns would not fit, but 20330 rows fit without a problem).
Attachments
LGT.xlsx
(72.07 MiB) Downloaded 506 times
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Re: TCGA data in Glioblastoma and Lower grade Brain Cancer

Postby cwyoo » Wed Sep 26, 2018 2:38 pm

Here is the dataset that I downloaded from Genomic Data Commons (GDC) at NIH via TCGA. This includes the clinical data as well.
Attachments
gdc_download_20180925_192141.767917.tar.gz
677 subject cases (511 LGG, 166 GBM)
(880.46 MiB) Downloaded 351 times
NIH-GDC-portal-LGG-GBM.jpg
Description
NIH-GDC-portal-LGG-GBM.jpg (151.97 KiB) Viewed 5053 times
clinical.cart.2018-09-25.tar.gz
Clinical Data
(49.93 KiB) Downloaded 339 times
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