SSM Affected Cases in Cohort from DNA mutation of TCGA data portal
Hi All,
I am a little confused about how to understand the mutation information from mutation data of the TCGA data portal.
Take SMARCB1 as an example,
127 cases have SMARCB1 mutation 10202 is totally TCGA cohort samples.
Who can explain what's 705 and 751 in the figure?
Thanks.
ssm
tcga
mutation
smarcb1
• 2,363 views
•
link
updated
by
Zhenyu Zhang
•
written
by
Shicheng Guo
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Appropriate genome reference for converting TCGA VCF files to MAF
written by melissachua90 •I have a directory of MAF files obtained from TCGA and I want to convert it to VCF format. Data source: https://portal.gdc.cancer.gov/repository?facetTab=files&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%5B%22TCGA-KIRP%22%5D%7D%2C%22op%22%3A%22in%22%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.access%22%2C%22value%22%3A%5B%22open%22%5D%7D%7D%2C%7B%22content%22%3A%7B%22field%22%3A%22files.data_category%22%2C%22value%22%3A%5B%22Simple%20Nucleotide%20Variation%22%5D%7D%2C%22op%22%3A%22in%22%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.data_format%22%2C%22value%22%3A%5B%22maf%22%5D%7D%7D%5D%7D&searchTableTab=cases Reference: GRCh38.d1.vd1 Reference …
-
How to download Gene expression data and associate clinical data from TCGA
written by Jakpa •Hello, I am new to TCGA database. I have been using GEO database to get data for my analysis. Now , I am mandated to …
-
HT-seq CPTAC,RNA-seq
written by Rob •Hi friends I am trying to download HT-seq CPTAC RNA-seq for kidney and there is no HT-seq in the workflow section. Instead there is star-count. …
-
Matched tumor/normal RNASeq expression counts in TCGA
written by arielI would like to download matched tumor/normal expression data from TCGA. I would also sample data like age, sex, race, etc. I looked at the …
-
Meaning letters in TCGA sample barcode field
written by sumitguptabt •I have mapped the UUIDs to TCGA barcode using TCGAutils, however, I got some unexplained barcode such as UUID (Associated Barcode) 3d50d8ca-cabd-4129-80b9-ff1e84c190e5 (CPT0051690007) 54b12749-b94c-4284-a44b-ee890084141b (CPT0069370006) …
-
TCGAbiolink does not download all the data requested
written by guillepalou4 •Hi everyone, I am using TCGAbiolinks and trying to download all RNA-seq data from a specific tumor as an example (TCGA-THYM). I am able to …
-
Pan-cancer dataset of GENIE control data download and sharing
written by Shicheng GuoHi All, The [GDC has released genomic data for 44,756 cancer cases spanning 294 disease types from AACR][1] Project GENIE. Who knows how to download …
-
Why do BRAF mutations appear more in skin cutaneous melanoma?
written by rafi.zon •When looking at the [tissue expression][1] of the BRAF protein it seems that BRAF is regularly expressed in almost all of the tissues. Yes, there …
-
Help convert GDC exploration url to API download?
written by simplitia •Hi all, I have the search query from GDC https://portal.gdc.cancer.gov/exploration?cases_size=10000&facetTab=mutations&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.available_variation_data%22%2C%22value%22%3A%5B%22ssm%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22TCGA%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%5B%22TCGA-COAD%22%2C%22TCGA-READ%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22ssms.ssm_id%22%2C%22value%22%3A%5B%224fb37566-16d1-5697-9732-27c359828bc7%22%2C%22edd1ae2c-3ca9-52bd-a124-b09ed304fcc2%22%5D%7D%7D%5D%7D&format=tsv Is there a way to manipulate this perhaps through their api so that it points …
-
How to get the simple somatic mutation vcf file from GDC data portal?
written by VasuHi, I wanted to download WXS somatic mutation file (VCF format) from GDC data portal [vcf file in gdc portal][1]. With the vcf file I …