Sorting tools??: Oncogenes/tumor suppressor genes - (Aug/14/2013 )
I have a set of several hundred genes. I would like to select (putative) oncogenes or tumor suppressor genes from them. Is there any software available which can select and sort them? Thanks in advance.
If you obtain the list of genes from NCBI database, you cannot simply sort the list to find oncogenes or TSGs since there is no such annotation attached to NCBI genes. There are databases built by researchers listing oncogenes or TSGs. You can google to find out. This paper also provides useful information http://www.biostars.org/p/15890/
I suggest you first try to see which of you genes are from curated list of oncogenes (aka Cancer Gene Census), see http://cancer.sanger.ac.uk/cancergenome/projects/census/. For tumor suppressor genes see http://bioinfo.mc.vanderbilt.edu/TSGene/. If you need some gene name conversions try this web service http://david.abcc.ncifcrf.gov/.
Many so called oncogenes or tumor suppressor genes are not clear cut, and in a different tumor they may have the opposite role.