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2025-01-21 Update From: SLTechnology News&Howtos shulou NAV: SLTechnology News&Howtos > Internet Technology >
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This article introduces you how to understand the database, the content is very detailed, interested friends can refer to it, I hope it can help you.
COSMIC is one of the largest databases of cancer-associated somatic mutation loci available at:
https://cancer.sanger.ac.uk/cosmic/
The latest version is v85, updated on May 8, 2018.
The entire website consists of the following 4 projects
1. COSMIC
Cancer-related somatic loci are the core of the site, which contains somatic mutation data from different research institutions and databases, and provides convenient browsing, retrieval, and downloading functions.
2. Cell Lines Project
In-depth study of cell line samples commonly used in cancer research to analyze mutation information. There will be less variation data covered in the overall project than in COSMIC. The project website is as follows:
https://cancer.sanger.ac.uk/cell_lines
3. COSMIC-3D
Through interactive web pages, the changes in protein domains caused by gene mutations are displayed. The project website is as follows
https://cancer.sanger.ac.uk/cosmic3d/
Enter a specific gene name or protein name in the search box to view specific records. officer
The DEMO data are as follows
4. Cancer Gene Census
In cancer research, finding relevant mutated genes is one of the most central goals. A list of cancer-associated mutant genes was compiled by investigating various cancers, and this list is called Cancer Gene Census (CGC). The project website is as follows
https://cancer.sanger.ac.uk/census
In the CGC species, all cancer-related genes are grouped into two categories
Tier1
For these genes, there is ample evidence that mutations in these genes lead to further cancer.
Tier2
For this part of the gene, it can only be said that a large number of mutations in this gene have been detected in cancer, but there is no sufficient evidence that this gene mutation has an impact on cancer development.
After logging in, you can download the complete list of CGC
COSMIC not only provides the download function of raw data, but also organizes many important data sets for our reference and download.
1. Downloads
Download data from Cosmic database. There are several types of data available for download.
Classification Information
COSMIC Complete Mutation Data(Targeted Screens)
COSMIC Matation Data(Genome Screens)
COSMIC Mutation Data
Structural Genomic Rearrangements
Complete Fusion Export
All Mutations in Census Genes
Non coding variants
Copy Number Variants
Gene Expression
Methylation
Cancer Gene Census
COSMIC Sample Features
COSMIC HGNC
COSMIC Resistance Mutations
ASCAT Ploidy and Purity Estimates
VCF Files
Download on demand. Download requires login, and some of the data is only available to users of universities and nonprofits.
2. Gene Curation
From the Cancer Gene Census gene list, select genes without known database for display
3. Gene Fusion Curation
List of fusion genes
4. Genome Screens
All data sets were sorted and presented in two parts: large-scale genome-wide data and data from ICGC, TCGA and PCGP.
5. Drug Resistance
It is important for clinical treatment to study the mutation of drug target gene. Cosmic collects and collates mutations associated with drug target genes.
6. Mutational Signatures
In cancer, mutation sites are very numerous. The researchers put forward the concept of Mutational Signatures. The feature set of mutations was divided into 96 mutation types. First, according to the type of base mutation, there were 6 basic types: C>A, C>G, C>T, T>A, T>C, T>G. Then, there were 4 possible cases of A,T,C,G for each base at the mutation site under consideration. There were 6X4X4 = 96 mutation types in total.
These 96 mutation types occur at different frequencies in different cancers, and when combined, they can be used as a fixed mutation pattern to characterize a type of cancer.
Cosmic identified 30 Mutational Signatures based on 10952 exons and 1048 genome-wide data. An example of Signature1 is as follows
A range of tools are also available on the website.
1. Cancer Browser
It is more intuitive to view related types of cancer through different tissues.
2. Genome Broswer
Genome Browser
3. CONAN
copy nunber analysis, a tool for querying copy number variation.
4. GA4GH Beacon Query
An API tool that can quickly query the COSMIC database for a mutation. Returns data in JSON format,
The links to the above queries are as follows
https://cancer.sanger.ac.uk/api/ga4gh/beacon? allele=A&chrom=7&dataset=cosmic&format=json&pos=140753336&ref=38
The returned content is as follows
{ "response" : { "exists" : "true" }, "query" : { "allele" : "A", "ref" : "GRCh48", "pos" : "140753336", "dataset" : "cosmic", "chrom" : "7" }, "beacon_id" : "COSMIC Beacon", "version" : "85"}
The default coordinates in the COSMIC database are based on the hg38 version of the genome. You can select CRCH37 in the Genome Version on the home page and switch to the hg19 version.
About how to understand the database to share here, I hope the above content can be of some help to everyone, you can learn more knowledge. If you think the article is good, you can share it so that more people can see it.
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