Question: How TCGA generanker works ?
1
gravatar for Nicolas Rosewick
5.4 years ago by
Belgium, Brussels
Nicolas Rosewick8.1k wrote:

Hi,

I found this usefull website http://cbio.mskcc.org/tcga-generanker/index.jsp based on mutliple cancer gene list. I searched, but I cannot find any information on how this tcga-generanker is made ? and which statistics it used to compute the score ? And also it says Gene Ranker: TCGA GBM 6000. Is it only for GBM (Glioblastoma Multiforme) .

tcga • 2.1k views
ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by Nicolas Rosewick8.1k
2
gravatar for Giovanni M Dall'Olio
5.4 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:
and which statistics it used to compute the score ?

If you look at their TCGA generator sources page, you can see that their list of candidate genes comes from a collection of lists of from other sources. Each list has a specific weight, and from the way it looks, it seems that they attributed scores based on the confidence they had on each list. Then, each gene is ranked with the sum of of the scores of all the lists to which it belongs

Is it only for GBM (Glioblastoma Multiforme) .?

The database contains genes specific to other tissues (e.g. COL11A1 which is specific to Lung cancer), so it seems the database is not only for GBM.

ADD COMMENTlink written 5.4 years ago by Giovanni M Dall'Olio26k
1

Ok I understand better. It gives a score for each list. And if a gene is found in several of these lists, the score is the sum of the list score's where the gene is found. Thanks

ADD REPLYlink written 5.4 years ago by Nicolas Rosewick8.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1896 users visited in the last hour