I have a Protein, which could have some role in Cancer progression. How can I check , whether my protein is oncogenic or not.
You would need to pursue this study along two lines. As a primary evidence, you will need to see if your protein is being expressed by cancer cell lines in sufficient amounts.Then you will need to either over express or down regulate by RNA silencing your protein of interest in those cancer cell lines.Do some functional assays for the cancerous properties.These set of experiments should give you initial evidence.
You would need to pursue this study along two lines. As a primary evidence, you will need to see if your protein is being expressed by cancer cell lines in sufficient amounts.Then you will need to either over express or down regulate by RNA silencing your protein of interest in those cancer cell lines.Do some functional assays for the cancerous properties.These set of experiments should give you initial evidence.
You can also to check some database, to find expression level of this gene on cancer cell lines or tissues...if no correlation, you should consider to forget it, don't waste the time.
First of all you should check the datbases: OMIM (http://www.ncbi.nlm.nih.gov/omim), uniprot (uniprot.org) here you will get some basic information about your gene/protein.
Oncoprotein databseses: http://www.sanger.ac.uk/genetics/CGP/Census/ Here is a list of diffenrent cancer genes.
http://www.sanger.ac.uk/genetics/CGP/cosmic/ here you can chech whether your gene has a mutation in cancer or not, and how often.
If find nothing about the gene's function in the literatures, you may chek the gene's map in the genome to see if it's location is frequently deleted (as a TSG) or amplified (as a oncogene). This kind of information is always helpful
First of all you will need to see if your protein is being expressed by any one cancer cell lines and do some functional assays for the cancerous properties.These experiments should be give you some idea.
That's a full fledged project :) Anyway, I agree with the above posts - the best place to start, perhaps, is to look at different databases such as Oncomine and see if here is any correlation with tumour progression/stage/survival, etc with the expression of your protein. You could also look at the effects of overexpression or silencing, as suggested above, on the phenotype. i.e cell survival/death. This should give you some indication of whether it is involved in cancer progression. This all, of course, will only give you preliminary results and will merely indicate or suggest its involvement in cancer. If the results are positive, you could follow different chains of protocols and approaches to determine the answer, but like I said, it could be a full project in itself. All the best.
One suggestion. Establishment of force expression system of your gene of interest, such as retrovirus or lentivirus or plasmid expression system. Better not to forget to involve the antibiotic marker to select the high expression cell (e.g. ires-marker). After the introduction to the fibroblasts, select the high expression cells by the antibiotic selection. Then, implants the selected cell to the SCID or the nude mice. You can see the enhanced cell growth if your gene of interest is really contributes to the oncogenesis. It is the simple method, but good starting point to evaluate the tumorigenesis. The data base work is fine, but this type of result would give you some insight.
Use RNAi for depletion and examine the effects. Use lentiviral vectors and examine the effects of expression of the protein.
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