. The website CBioPortal (http://www.cbioportal.org)is an exceptionally useful program for visualizing thecancer genes and genomes of tumors from thousandsof patients with different kinds of cancer that havebeen analyzed by whole genome sequencing and insome cases, by RNA-Seq.Go the the CBioPortal site and click All underSelect Cancer Study and in Enter Gene Set typePTEN, then hit Submit. On the page that is returnedyou will see how the coding region of the PTEN geneis altered in tumors investigated in the various studies.Hitting the tab Mutations will let you see the detailsof these mutations relative to the PTEN protein, whilethe tab Expression lets you see how the gene’s expression (in terms of cDNA reads) is altered in individual tumor samples.a. Is PTEN an oncogene or a tumor suppressor gene?What kinds of evidence lead you to this conclusion?b. What kinds of cancer are most likely to involvealterations of PTEN?c. How would you identify patients whose tumorcells are particularly likely to have a somatic mutation in the PTEN gene that is outside of the codingregion but nonetheless contributes to cancer byaffecting the gene’s regulation?Now return to the CBioPortal home page. Again, selectAll under Select Cancer Study, but this time type ERBB2under Enter Gene Set and then hit Submit.d. Is ERBB2 an oncogene or a tumor-suppressorgene? What kinds of evidence lead you to thisconclusion?e. Are any kinds of listed mutations in the ERBB2gene almost certainly passenger mutations asopposed to driver mutations? What does it meanto be a passenger mutation?f. If you were looking for regulatory mutations in theERBB2 gene that are not in the coding sequencebut that contribute to cancer, what attributes wouldyou look for under the Expression tag?g. In comparing your results with the PTEN andERBB2 genes, how informative are missensemutations in these genes with respect to possiblecontributions of such mutations to cancerphenotypes?
. The website CBioPortal (http://www.cbioportal.org)
is an exceptionally useful program for visualizing the
cancer genes and genomes of tumors from thousands
of patients with different kinds of cancer that have
been analyzed by whole genome sequencing and in
some cases, by RNA-Seq.
Go the the CBioPortal site and click All under
Select Cancer Study and in Enter Gene Set type
PTEN, then hit Submit. On the page that is returned
you will see how the coding region of the PTEN gene
is altered in tumors investigated in the various studies.
Hitting the tab Mutations will let you see the details
of these mutations relative to the PTEN protein, while
the tab Expression lets you see how the gene’s expression (in terms of cDNA reads) is altered in individual tumor samples.
a. Is PTEN an oncogene or a tumor suppressor gene?
What kinds of evidence lead you to this conclusion?
b. What kinds of cancer are most likely to involve
alterations of PTEN?
c. How would you identify patients whose tumor
cells are particularly likely to have a somatic mutation in the PTEN gene that is outside of the coding
region but nonetheless contributes to cancer by
affecting the gene’s regulation?
Now return to the CBioPortal home page. Again, select
All under Select Cancer Study, but this time type ERBB2
under Enter Gene Set and then hit Submit.
d. Is ERBB2 an oncogene or a tumor-suppressor
gene? What kinds of evidence lead you to this
conclusion?
e. Are any kinds of listed mutations in the ERBB2
gene almost certainly passenger mutations as
opposed to driver mutations? What does it mean
to be a passenger mutation?
f. If you were looking for regulatory mutations in the
ERBB2 gene that are not in the coding sequence
but that contribute to cancer, what attributes would
you look for under the Expression tag?
g. In comparing your results with the PTEN and
ERBB2 genes, how informative are missense
mutations in these genes with respect to possible
contributions of such mutations to cancer
Step by step
Solved in 2 steps
