I am interested in identifying molecules, genes, epigenetic marks or cells from the microenvironment that are responsible for a dormant phenotype in cancer. What bioinformatic tools and approaches would you suggest for identifying the proteins/molecules/cells most implicated in this phenotype?
I know it is a broad question, and as such, bioinformatics tools could help narrow down the options without alot of time, reagents and money to identify the most likely to study in-vitro/in-vivo.
Thank you for your response.
EDIT:
For clarification:
- I understand that the phenotype is dormant, and that is exactly what I am investigating - what is responsible for this?
- I want to understand what proteins or other cellular molecules, as well as what microenvironmental cells are involved in triggering this shift to dormancy
- As you can understand, there are many different molecules and cells to look at, and as such, I was inquiring as to assessing the best path forward using bioinformatics to analyse laboratory data as to which cells/molecules are most strongly implicated or to provide an analysis from existing databases to narrow down molecules/cells
- As a beginner to bioinformatics, I was wondering what approaches, what software, what analyses can be used to best refine my approach to understanding tumour dormancy
Examples of this would be Principle Component Analysis, or Gene Network Analysis
Thanks!
I hope I have provided a clearer question now
Please can you explain what you mean by a cancer dormant phenotype?
Because phenotype is something expressed, something you can see with the microscope or measure it in the lab. Its there and is self evident.
May be you are refering to dormant cancer genotype?
Hi, this is a general question, please explain a bit more in details....
You can probably start with the
The Cancer Genome Atlas - Cancer Genome - TCGA
https://cancergenome.nih.gov/
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