What is the significance of this file in COSMIC database? · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

What is the significance of this file in COSMIC database?

I was going through the COSMIC database and came across a particular file in the downloads page. This file was named Fasta file (genes) and its description was "CDS sequence for all the genes in COSMIC". Now I understand that these are the fasta sequences of all the genes listed in the COSMIC database. But my question is are these gene sequences extracted from cancer patients? Or are they reference sequences of the genes?

snp genome next-gen

• 1,613 views • link

written 7.9 years ago by Gene_MMP8

1 answer

They are references of genes they used to call mutations. The were no interests to show references cancer patients , because that will mean a de novo assembly from exom/panel sequencing . . .

• 1 views • link

written 7.9 years ago by Titus

Log in to answer this question.

More posts like this

COSMIC Actionability data files format (mutation ID)
written 3.1 years ago by bt_cepo •

Hi all! I was trying to retrieve information from [COSMIC's Actionability project][1]: > The aim of COSMIC Mutation Actionability in Precision Oncology product > (Actionability) …
SBS Mutational Signatures aetiology
written 3.2 years ago by Z_Wael •

Hello, I am working with some mutational signatures "cosmic SBS v3.3", until now I used this cosmic page to search the signature proposed aetiology https://cancer.sanger.ac.uk/signatures/sbs/ …
TCGA driver mutation data
written 5.8 years ago by aksam •

I would like to download driver mutation data for TCGA patients ( in particular lung cancer but ideally 'pan cancer'. For example I would like …
Default strand of mutations
written 6.8 years ago by Gene_MMP8

I have downloaded 10000 SNVs from the COSMIC database. These are all cancer-causing variants. Each of these mutations has strand information attached to them. The …
PCA-based clustering gene expression data
written 7.1 years ago by Gene_MMP8

I have the gene expression data and mortality labels for a group of patients. I have performed differential gene expression analysis and found the top …
Flanking sequences around cancer variants
written 7.9 years ago by Gene_MMP8

I want to analyze the flanking sequences around cancer variants. I have already downloaded cancer variants from COSMIC database. Now I am planning to extract …
Implementation of the COSMIC database for somatic variant annotation and filtering pipeline for WES…
written 8.1 years ago by svlachavas

Dear Community, I would like to ask a question concerning the putative implementation of the COSMIC database, in a developed somatic filtering and annotation pipeline, …
COSMIC to Ensembl mapping
written 8.2 years ago by Gene_MMP8

I have downloaded the COSMIC mutation file based on GRCH38. I have the cosmic mutation ids for each mutation (eg, COSM521,COSM520 etc). If I copy …
convert DNA FASTA to protein FASTA format (faa)
written 9.3 years ago by nkuo •

Evening. I have de novo assembled whole genome DNA sequences and an embl annotation file that contains CDS regions for multiple genes. I am wondering …
Cancer gene list enrichment
written 11.8 years ago by Saad Khan

Suppose I have an RNA-seq experiment in which I have 5000 deferentially expressed genes. In which around 120 are cancer causing genes or genes that …