Question: Is it possible to get seq data for cancers via database?
1
gravatar for gooshiroy
3.8 years ago by
gooshiroy20
United States
gooshiroy20 wrote:

I am looking for resources to download actual sequence data in terms of nucleotide arrays for certain cancer mutations. Are there any databases available to do so by filtering specific cancers and genes? I am looking for something akin to the regular vanilla NCBI website. However, the gene sequences of interest at the NCBI are not of cancer genes. For example, I can only get a regular vimentin protein sequence, not a mutated gene sequence from a specific brain glioblastoma case or a prostate cancer case, etc. 

 

EDIT: I am an undergraduate student and I cannot access UCSC's Cancer Genomics Hub. 

cancer sequence gene • 1.2k views
ADD COMMENTlink modified 3.8 years ago by Cyriac Kandoth5.3k • written 3.8 years ago by gooshiroy20
1
gravatar for Cyriac Kandoth
3.8 years ago by
Cyriac Kandoth5.3k
Memorial Sloan Kettering, New York, USA
Cyriac Kandoth5.3k wrote:

Ensembl's Variant Effect Predictor (VEP) has a plugin that generates a FASTA file containing mutated mRNA sequence. It will only do this for one mutation at a time. If this is what you want, you can find what you need here and here.

If you provide more info on the experiment you're trying to perform or the specific biological questions you're trying to answer, I can expand this answer to be more helpful.

ADD COMMENTlink written 3.8 years ago by Cyriac Kandoth5.3k
0
gravatar for Benn
3.8 years ago by
Benn7.7k
Netherlands
Benn7.7k wrote:

Did you check The Cancer Genome Atlas? There is a lot of data available in their resources.

http://cancergenome.nih.gov/

ADD COMMENTlink written 3.8 years ago by Benn7.7k

They say that do not have lower level seq data. Higher order data needs to be acquired via dbGap

ADD REPLYlink written 3.8 years ago by gooshiroy20
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