What data is available in Tcga?
TCGA contains molecular data from multiple types of analysis:
- DNA sequencing. Whole genome sequences.
- RNA sequencing. miRNA sequences (calculated expression per miRNA and isoform)
- Copy number. Arrays (raw, unnormalized, normalized)
- Array-based expression. Gene expression (raw, normalized, calls)
- DNA methylation.
How do I download Tcga RNA Seq data?
- Go to GDC data portal.
- Click ‘Data’
- Select types of cancer and files (RNA-seq in your case)
- Click ‘Download Manifest’ and save the manifest file.
- Install ‘GDC data transfer tool (gdc-client)’.
- Go to the directory containing the manifest file.
How do you estimate gene expression?
In addition to Northern blot tests and SAGE analyses, there are several other techniques for analyzing gene expression. Most of these techniques, including microarray analysis and reverse transcription polymerase chain reaction (RT-PCR), work by measuring mRNA levels.
How many Tcga tumors are there?
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.
How do I access TCGA data?
Popular Answers (1)
- Connect to https://tcga-data.nci.nih.gov/tcga/
- Select the cancer subtype you are interested in (i.e breast invasive carcinoma)
- Select mRNA.
- Now you can see a table where rows are representing different patients.
How do you reference TCGA data?
An example of a proper acknowledgement is: “The results here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.” Citation of original TCGA marker papers producing the data utilized is optional.
What is GDC client?
The GDC provides a standard client-based mechanism supporting high-performance data downloads and submission. The GDC Data Transfer Tool provides an optimized method of transferring data to and from the GDC and enables resumption of interrupted transfers.
How do I access Tcga?
Please go to this page: https://tcga-data.nci.nih.gov/docs/publications/ to access all data associated with TCGA tumor specific publications.
How do you study gene regulation?
Proteins called transcription activator-like effectors, or TALEs, have now been developed into a tool to study enhancer regions in DNA. Scientists can use engineered TALEs to bind any DNA region and then study the resulting changes in an organism’s gene expression.
What is a gene expression pattern?
A gene’s expression pattern can be defined as a series of differential accumulations of its products in subsets of cells as development progresses. RNA in situ hybridization has the potential to reveal both spatial and temporal aspects of gene expression during development.
Does TCGA have normal samples?
Solid tissue normal samples from TCGA patients are typically limited in number but some cancer types may have enough for a robust statistical comparison. It is important to note that their proximity to tumor may introduce signals of tumor microenvironment in its transcriptome profile.
How is rsubread used for RNA Seq in TCGA?
We used the ‘Rsubread’ R package to align and summarize reads at the gene level for 9264 tumor and 741 normal TCGA RNA-Seq samples. The R scripts we provide here can also be used to process samples that did not come from TCGA.
Where can I Find my RNA Seq file?
All the RNA-Seq and clinical data files that we have processed are available from Gene Expression Omnibus (accession numbers: GSE62820 and GSE62944).
How to analyze data from TCGA database?
1. Fold change Since the values from UCSC are already log 2 transformed, for a gene x, of tumor y, Log 2 fold change can be calculated as (log 2 transformed gene expression value of tumor sample) – (log 2 transformed gene expression value of matched normal sample). 2.
How to calculate differential expression gene list from TCGA?
Z-score (if comparing tumor vs. normal) = [ (value gene X in tumor Y) – (mean gene X in normal)] / (standard deviation of gene X in normal) Query 1: Have I understood these methods correct? How else we can calculate differential from TCGA datasets? Query 2.