I am currently working on finding the relation between specific genes such Tpl2 and colon cancer using RNA seq data from TCGA. Can anyone help me with the best way to do query the database to get the right info?
I am also finding it difficult to perform a complex query (by including factors such as age, gender, tumour stage) on GEO Daatasets/Profiles even applying the rules from the FAQs. Can anyone help?
For obtaining data from GEO, using GEOquery in R. For TCGA data, use TCGAbiolinks (also R), and / or search the data contained at UCSC Xena Browser and / or cBioPortal.
In some cases, you will have to obtain data manually from the source, i.e., the GEO record or the Genomic Data Commons, for GEO and TCGA data, respectively.
please help me to response this question: Give two examples of the transcriptome databases of cancer. And, compare and contrast between the two databases in terms of 1) methods of construction (transcriptomics technologies) 2) organisms 3) additional data provided in the databases apart from transcriptome data (such as genomics data, proteomics data, clinical data, etc.)
