<p>I am trying to build a database of different cancer genes i.e lung cancer, throat cancer etc. Searched through NCBI website by searching for nucleotide sequences, but I am unable to find appropriate results. Any help in this regard is much appreciated</p>

CC BY-SA 4.0
2019-04-19T15:23:59.497Z
[COSMIC](https://cancer.sanger.ac.uk/cosmic) has a set of mutations and the [Cancer Gene Census](https://cancer.sanger.ac.uk/census) already curates cancer-related genes. What is the purpose behind your venture?
Ram RS
CC BY-SA 4.0
2019-04-19T15:31:39.340Z
@RamRS To perform clustering
Prabhuraj Metipatil
CC BY-SA 4.0
2019-04-19T15:36:07.290Z
Why not just cluster based on existing annotations? You could get information from the CGC, use the HGNC symbols or other identifiers to download additional data using biomaRt and then perform all sorts of analysis on that. Why build a new database?
Ram RS
CC BY-SA 4.0
2019-04-19T15:44:11.530Z
@RamRS i have taken up this as part of my PhD , wherein I will be clustering cancer gene data treating them as pure categorical data and ultimately try to identify similar patterns across clusters if they exist
Prabhuraj Metipatil
CC BY-SA 4.0
2019-04-19T15:57:29.150Z
What will you be clustering (the term `data` is too generic and vague) and what sort of patterns will you be looking for? If this is part of your PhD, you definitely would have looked into literature on such protocols and the sorts of data available at the gene level on various cancer types. Can you give us any more detail on it?
Ram RS
CC BY-SA 4.0
2019-04-19T16:09:33.847Z
@RamRS gene expression to be specific
Prabhuraj Metipatil
CC BY-SA 4.0
2019-04-19T16:34:24.893Z
And will you be clustering gene expression data from a public resource such as TCGA? I ask because if it's based on public datasets, this would not be a novel endeavor at all. In fact, there exist explorer tools that let you run correlations between various omics dimensions on the fly.
Ram RS
<gene><sequence-analysis><cancer>
Building cancer gene database
# Building cancer gene database

(Asked by: username_0 on 2019-04-19)

I am trying to build a database of different cancer genes i.e lung cancer, throat cancer etc. Searched through NCBI website by searching for nucleotide sequences, but I am unable to find appropriate results. Any help in this regard is much appreciated

**Tags:** gene, sequence-analysis, cancer
> **Comments:**
> **username_1**: [COSMIC](https://cancer.sanger.ac.uk/cosmic) has a set of mutations and the [Cancer Gene Census](https://cancer.sanger.ac.uk/census) already curates cancer-related genes. What is the purpose behind your venture?  
> **username_0**: @RamRS To perform clustering  
> **username_1**: Why not just cluster based on existing annotations? You could get information from the CGC, use the HGNC symbols or other identifiers to download additional data using biomaRt and then perform all sorts of analysis on that. Why build a new database?  
> **username_0**: @RamRS i have taken up this as part of my PhD , wherein I will be clustering cancer gene data treating them as pure categorical data and ultimately try to identify similar patterns across clusters if they exist  
> **username_1**: What will you be clustering (the term `data` is too generic and vague) and what sort of patterns will you be looking for? If this is part of your PhD, you definitely would have looked into literature on such protocols and the sorts of data available at the gene level on various cancer types. Can you give us any more detail on it?  
> **username_0**: @RamRS gene expression to be specific  
> **username_1**: And will you be clustering gene expression data from a public resource such as TCGA? I ask because if it's based on public datasets, this would not be a novel endeavor at all. In fact, there exist explorer tools that let you run correlations between various omics dimensions on the fly.  

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## 0 answers

