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发表于 2016-11-28 09:29:45 | 显示全部楼层 |阅读模式
原帖:https://www.biostars.org/p/15890/  
Does anyone know of a good source of human genes that act as a tumor suppressor or oncogene? The source can be a database or data mining approach that queries a more general database.
Some possible features of a 'good' source:
  • More than just a list of 'cancer genes'. One abstract with the name of the gene and the word cancer in it does not make it a convincing cancer gene. But a more sophisticated text-mining based approach would be acceptable
  • The gene will be annotated as a tumor suppressor or oncogene with additional information on how this classification is justified
  • Other relevant annotation such as whether the gene is involved in DNA repair, apoptosis, etc.
  • Up to date. A spreadsheet from 10 years ago is less useful than a routinely updated source.
  • Free and open source. Although if you know of commercial options please suggest them.
Here are some of the things I have found so far:
  • The Wikipedia entries above list categories of oncogenes .. but not all RTKs for example will necessarily act as an oncogene
  • The Gene Ontology used to have a term 'Tumor Suppressor' but this has been superseded by the term 'regulation of cell cycle'. A gene involved in regulation of the cell cycle may generally have the potential to function as a tumor suppressor but it would be nice to know which had been demonstrated to do so and how. A combination of GO terms and evidence codes might be acceptable if someone wishes to elaborate on this approach
  • UniProtKB has a keyword 'Proto-oncogene' associated with 560 genes and a keyword 'Tumor Suppressor' associated with 631 genes.
  • A compilation of cancer gene lists from the 'Bushman Lab'
  • The Sanger cancer gene census
  • A more empirical approach might involve using patterns of somatic mutation across many cancers to identify likely tumor suppressors and oncogenes. Where tumor suppressors are expected to be characterized by loss-of-function mutations (copy number deletions, nonsense, or missense mutations spread across multiple sites in the gene) and oncogenes would be characterized by recurrent mutation sites (amplifications, mutation hotspots, gene fusions involving a particular gene partner, etc.). COSMIC is already working along these lines but if there are others, please post.
  • A variety of older websites that list tumor suppressors: TSGDB, Tumor Gene Database, and TAG
Useful suggestions gathered from below (refer there for more details):
Sources you could mine to develop your own lists:
Organizations that are annotating druggable/actionable genes:
Some relevant posts:




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