What is cBioPortal?
What is cBioPortal?
The cBioPortal is an exploratory analysis tool for exploring large-scale cancer genomic data sets that hosts data from large consortium efforts, like TCGA and TARGET, as well as publications from individual labs.
What is cBioPortal for Cancer Genomics?
The cBio Cancer Genomics Portal (http://cbioportal.org) is an open-access resource for interactive exploration of multidimensional cancer genomics data sets, currently providing access to data from more than 5,000 tumor samples from 20 cancer studies.
What is Gistic score?
gistic) is the Gistic Scores File output from the GenePattern GISTIC module. It is a tab-delimited text file that defines a feature track displaying the q-value for regions of amplification or deletion found using GISTIC (Beroukhim et al., 2007).
How do I download RNA Seq data from cBioPortal?
Step 1) Go to cBioPortal’s home page: http://www.cbioportal.org Step 2) Click on the “Download Data” tab. Step 3) Under “Select Cancer Study” drop-down select “tcga” (the first option). Step 5) Under “Select Genomic Profiles” choose “mRNA expression (RNA Seq V2 RSEM)” .
What is UCSC Xena?
UCSC Xena (http://xena.ucsc.edu (link is external)) is a web-based, visual exploration tool for all modes of multi-omic data and associated annotations. Xena has several seminal cancer datasets pre-loaded and ready for visualization including TCGA, ICGC, GTEx and more.
What is Tcga database?
The Cancer Genome Atlas (TCGA), a landmark cancer genomics program, molecularly characterized over 20,000 primary cancer and matched normal samples spanning 33 cancer types.
What is somatic copy number alterations?
Copy number alterations (CNAs) are somatic changes to chromosome structure that result in gain or loss in copies of sections of DNA, and are prevalent in many types of cancer (2). Mutation of certain genes has a broad impact across a variety of cancers.
What is OncoPrint?
OncoPrint is a way to visualize multiple genomic alteration events by heatmap. Besides the default style which is provided by cBioPortal, there are additional barplots at both sides of the heatmap which show numbers of different alterations for each sample and for each gene.
What is Tcga classification?
What is Tcga in DNA?
The Cancer Genome Atlas (TCGA), a project supported by the National Cancer Institute (NCI) and National Human Genome Research Institute (NHGRI), hosts tremendous amount of multi-omics data and allows systematic study of the genetic or epigenetic basis of cancer [8].
What is a chromosome arm?
Each chromosome has a constriction point called the centromere, which divides the chromosome into two sections, or “arms.” The short arm of the chromosome is labeled the “p arm.” The long arm of the chromosome is labeled the “q arm.” The location of the centromere on each chromosome gives the chromosome its …
What data is available in the cbioportal?
Note that for many studies, only somatic mutation data and limited clinical data are available. For TCGA studies, the other data types are also available. Germline mutations are supported by cBioPortal, but are, with a few exceptions, not available in the public instance.
How is the significance level of co-occurrence and mutual exclusivity calculated?
The significance level of co-occurrence and mutual exclusivity, calculated by the statistical method Mutual Exclusivity Modules (MEMo), is found under the Mutual Exclusivity tab. When gene queries are performed across all studies, the Portal returns a graphical summary of alterations, as well as OncoPrints for every individual study.
What is the cbioportal for cancer genomics?
In the latest edition, we spotlight the cBioPortal for Cancer Genomics, a tool developed at Memorial Sloan Kettering Cancer Center’s Computational Biology Center (cBio).
